Rosetta command line option descriptions.

(This is an automatically generated file, do not edit!) Generated: 2018-05-12

• in

  -in <Boolean>

  in option group
  

  -fconfig <FileVector>

  A list of flag configurations to look for. These can be in either your working directory or $HOME/.rosetta/flags directory. Ex: -fconfig common design
  Default: ['"common"']
  

  -no_fconfig <Boolean>

  Do not load the [common] config file if present.
  Default: false
  

  -Ntermini <String>

  Put full N termini on pose
  Default: "ALL"
  

  -Ctermini <String>

  Put full C termini on pose
  Default: "ALL"
  

  -use_truncated_termini <Boolean>

  Will not add extra OXT/Hs at termini if not in input structure
  Default: false
  

  -ignore_unrecognized_res <Boolean>

  Do not abort if unknown residues are found in PDB file; instead, ignore them. Note this implies -in:ignore_waters
  Default: false
  

  -ignore_waters <Boolean>

  Ignore HOH residues found in PDB file. Note: HOH residues, and waters in general, are incompatible with the default solvation model (LK).
  Default: true
  

  -guarantee_no_DNA <Boolean>

  Do not rename A/C/G to DA/DC/DG even if missing their 2' hydroxyl; expert knowledge says this structure has no DNA.
  Default: false
  

  -add_orbitals <Boolean>

  Will add orbitals to residues only. Does not include orbitals to ligands. Done through params file reading.
  Default: false
  

  -show_all_fixes <Boolean>

  Show all residue & atom name fixes
  Default: false
  

  -include_sugars <Boolean>

  Sets whether or not carbohydrate residues will beloaded into Rosetta. The default value is false.
  Default: false
  

  -include_lipids <Boolean>

  Sets whether or not lipid residues will beloaded into Rosetta. The default value is false.
  Default: false
  

  -include_surfaces <Boolean>

  Sets whether or not mineral surface residues will beloaded into Rosetta. The default value is false.
  Default: false
  

  -read_only_ATOM_entries <Boolean>

  Sets whether to ignore everything except ATOM entries.
  Default: false
  

  -auto_detect_glycan_connections <Boolean>

  Sets whether to search for non-protein connections using PDB coordinates and generate LINK records.
  Default: false
  

  -max_bond_length <Real>

  Sets maximum O-C distance for glycan connection search. Default is 1.65 Angstroms.
  Default: 1.65
  

  -min_bond_length <Real>

  Sets minimum O-C distance for glycan connection search. Default is 1.15 Angstroms.
  Default: 1.15
  

  -glycan_virtual_offset <Real>

  Apply a very small offset to the glycan virtual positions to avoid collinearity in the angle minimization.
  Default: 0
  

  -membrane <Boolean>

  Initialize pose as a membrane protein using specified membrane parameters. Default is false
  Default: false
  

  -remember_unrecognized_res <Boolean>

  Ignore unrecognized residues, but remember them in PDBInfo.
  Default: false
  

  -remember_unrecognized_water <Boolean>

  Remember waters along with other unrecognized residues.
  Default: false
  

  -preserve_crystinfo <Boolean>

  Preserve information important for crystal refinement (B factors +CRYST1 line)
  Default: false
  

  -detect_oops <Boolean>

  Detect oligooxopiperazines (oops) and add required constraints
  Default: false
  

  -detect_disulf <Boolean>

  Forcably enable or disable disulfide detection. When unspecified, rosetta conservatively detects disulfides in full atom input based on SG distance, but will not form centroid disulfides. Setting '-detect_disulf true' will force aggressive disulfide detection in centroid poses based on CB distance. Setting '-detect_disulf false' disables all detection, even in full atom poses. Note that disabling disulfides causes severe clashes for native disulfides.
  

  -detect_disulf_tolerance <Real>

  disulf tolerance
  Default: 0.5
  

  -constraints_from_link_records <Boolean>

  Turn link records into atom pair and angle constraints
  Default: false
  

  -auto_setup_metals <Boolean>

  Automatically adds covalent linkages to bound metal ions, as well as atom pair constraints and angle constraints to hold ions in place, on PDB import. Also, sets the atom_pair_constraint and angle_constraint weights in the default score function to 1.0. False by default.
  Default: false
  

  -prevent_auto_setup_metal_bb_variants <Boolean>

  When automatically setting up metals, in cases where there is a bond detected between a metal and a backbone heavyatom (e.g. a backbone carbonyl oxygen), by default Rosetta will set up bonded variant types for the current residue and for all orther residue types with an equivalent backbone heavyatom, to permit mutations. Setting this flag to true prevents this. False by default.
  Default: false
  

  -metals_detection_LJ_multiplier <Real>

  When -auto_setup_metals is used, overlap between metal atoms and metal-binding atoms is used as the criterion by which covalent bonds are detected. The Lennard-Jones radii of the atoms can be multiplied by a constant factor in order to detect longer bonds to metal ions. Default 1.0.
  Default: 1.0
  

  -metals_distance_constraint_multiplier <Real>

  Distances between metals and metal-binding atoms are constrained using harmonic potentials, scaled by this multiplier. Default 1.0. Set to 0.0 to skip adding distance constraints.
  Default: 1.0
  

  -metals_angle_constraint_multiplier <Real>

  Angles between metals, metal-binding atoms, and metal-binding atom parents are constrained using circular harmonic potentials, scaled by this multiplier. Default 1.0. Set to 0.0 to skip adding angle constraints.
  Default: 1.0
  

  -name3_property_codes <StringVector>

  File that describes name3-property correspondence to fix up atom assignments
  Default: utility::vector1<std::string>(1,"code_properties.codes")
  

  -alternate_3_letter_codes <StringVector>

  Specify the filename(s) of (a) *.codes files that includes a list of alternative 3-letter codes. The default directory is database/input_output/3-letter_codes/ but any path can be provided. Duplicate codes in successive files will overwrite previous ones.
  

  -maintain_links <Boolean>

  Maintains link records in the PDB when using auto_detect_glycans
  Default: false
  

  -fix_disulf <File>

  Specify disulfide connectivity via a file. Disulfides are specified as two whitespace-separated residue indices per line. This option replaces the old '-run:fix_disulf' option.
  

  -missing_density_to_jump <Boolean>

  If missing density is found in input pdbs, replace with a jump
  Default: false
  

  -target_residues <IntegerVector>

  which residue numbers to pass for getDistConstraints
  

  -replonly_residues <IntegerVector>

  residue numbers regarded as repulsive-only residues
  

  -replonly_loops <Boolean>

  all loops will be regarded as repulsive-only
  Default: false
  

  -use_database <Boolean>

  Read in structures from database. Specify database via -inout:dbms:database_name and wanted structures with -in:file:tags or select_structures_from_database
  

  -select_structures_from_database <StringVector>

  specify an SQL query to determine which structures get read in from a database specified with -inout:dbms:database_name. SELECT query must return structures.tag
  

• in:dbms

  -dbms <Boolean>

  dbms option group
  

  -struct_ids <StringVector>

  List of struct_ids (hex representation) to be used by the database job inputter
  

• in:path

  -path <PathVector>

  Paths to search for input files (checked after type-specific paths)
  Default: "."
  

  -fragments <PathVector>

  Fragment file input search paths
  

  -pdb <PathVector>

  PDB file input search paths
  

  -database <PathVector>

  Database file input search paths. If the database is not found the ROSETTA3_DB environment variable is tried.
  

  -database_cache_dir <Path>

  Which directory to use when caching processed database files.
  

• in:file

  -file <Boolean>

  Input file option group
  

  -s <FileVector>

  Name(s) of single PDB file(s) to process
  Default: []
  

  -t <FileVector>

  Name(s) of second PDB file(s) to process (pairs with -s)
  

  -l <FileVector>

  File(s) containing list(s) of PDB files to process
  

  -job_definition_file <File>

  File used by JD3 in which multiple jobs with different inputs can be specified
  

  -list <FileVector>

  File(s) containing list(s) of PDB files. PDBs on the same line become one pose
  

  -screening_list <FileVector>

  Files containing lists of PDB files. all permutations of the files in the list become poses
  

  -screening_job_file <File>

  A JSON file containing groups of ligands and proteins to screen
  

  -shuffle_screening_jobs <Boolean>

  Randomize the order of jbos input through -in:file:screening_job_file
  Default: false
  

  -native <File>

  Native PDB filename
  

  -torsion_bin_probs <File>

  File describing probabilities over torsion bins A,B,E,G,O
  Default: "empty"
  

  -PCS_frag_cst <File>

  File that containts PCS constraints for use in fragment picking
  

  -talos_phi_psi <File>

  File that provides Phi-Psi angles in Talos+ format
  

  -talos_cs <File>

  File that provides chemical shifts in Talos format
  

  -ambig_talos_cs_A <File>

  File that provides 1st set of ambigious chemical shift options in Talos format
  

  -ambig_talos_cs_B <File>

  File that provides 2nd set of ambigious chemical shift options in Talos format
  

  -native_exclude_res <IntegerVector>

  Residue numbers to be excluded from RMS calculation
  

  -no_detect_pseudobonds <Boolean>

  By default, Rosetta automatically detects pseudobonds on file import. If this is set to true, this auto-detection is disabled. False by default.
  Default: false
  

  -tags <StringVector>

  Tag(s) of structures to be used from silent-file
  

  -user_tags <StringVector>

  user_tag(s) of structures to be used from silent-file
  

  -tagfile <File>

  File with list of tags tou be used from silent-file. (an -in:file:l for silent file tags.)
  Default: "TAGS"
  

  -frag_files <FileVector>

  Fragment input file names
  Default: []
  

  -remap_pdb_atom_names_for <StringVector>

  When reading PDBs, use geometry to rename atoms for the residues with the given three letter codes.
  

  -extra_res <FileVector>

  .params file(s) for new residue types (e.g. ligands)
  Default: []
  

  -extra_res_fa <FileVector>

  .params file(s) for new fullatom residue types (e.g. ligands)
  Default: []
  

  -extra_res_mol <FileVector>

  .mol file(s) for new fullatom residue types (e.g. ligands)
  Default: []
  

  -extra_res_mmCIF <FileVector>

  .mmCIF file(s) for component dictionary for residue types (e.g. ligands)
  Default: []
  

  -load_PDB_components <Boolean>

  Use the PDB ligand definitions to load all standard residue descriptions.
  Default: true
  

  -PDB_components_file <StringVector>

  The CIF file from which to load the PDB component definitions. (An example can be found at http://www.wwpdb.org/data/ccd
  Default: ['"chemical/pdb_components/components.Nov01_2017.A_to_C.cif"', '"chemical/pdb_components/components.Nov01_2017.D_to_Z.cif"']
  

  -check_all_PDB_components <Boolean>

  Check all PDB components even if they have a name3 that overlaps with a Rosetta type.
  Default: false
  

  -extra_res_database <String>

  the name of a database containing fullatom residue types (e.g. ligands)
  

  -extra_res_pq_schema <String>

  the name of a postgreSQL schema in the database containing fullatom residue types (e.g. ligands)
  Default: ""
  

  -extra_res_database_mode <String>

  The type of database driver to use for -in:file:extra_res_database.
  Default: "sqlite3"
  

  -extra_res_database_resname_list <File>

  Path to a list of residue names to be read in from the residue database. The list should have one residue name per line
  

  -extra_res_cen <FileVector>

  .params file(s) for new centroid residue types (e.g. ligands)
  Default: []
  

  -extra_res_path <PathVector>

  directories with .params files. Only files containing 'param' will be chosen
  Default: []
  

  -extra_rot_lib_path <PathVector>

  directories with NCAA rotamer files.
  Default: []
  

  -override_rot_lib_path <PathVector>

  if rotamer libraries are found in this directory, prioritize them and not others
  Default: []
  

  -extra_res_batch_path <PathVector>

  directories generated by src/python/apps/public/batch_molfile_to_params.py. Only files containing 'param' will be chosen
  Default: []
  

  -extra_patch_fa <FileVector>

  patch files for full atom variants not specified in the database
  Default: []
  

  -extra_patch_cen <FileVector>

  patch files for centroid atom variants not specified in the database
  Default: []
  

  -frag3 <String>

  No description
  

  -frag9 <String>

  No description
  

  -fragA <String>

  No description
  

  -fragB <String>

  No description
  

  -surface_vectors <String>

  Input file containing three sets of xyz coordinates which define the plane and periodicity of the solid surface
  

  -xyz <String>

  Input coordinates in a raw XYZ format (three columns)
  

  -keep_input_scores <Boolean>

  Keep/Don't keep scores from input file in Pose.
  Default: true
  

  -lazy_silent <Boolean>

  Activate LazySilentFileJobInputter
  Default: false
  

  -silent <FileVector>

  silent input filename(s)
  Default: []
  

  -force_silent_bitflip_on_read <Boolean>

  Force bit-flipping when reading binary silent files. This is useful if the files are produced on a little-endian system and read on a big-endian system.
  Default: false
  

  -atom_tree_diff <FileVector>

  atom_tree_diff input filename(s)
  

  -zip <String>

  zipped input file, used for BOINC database
  

  -boinc_wu_zip <FileVector>

  zipped input file with files for a specific BOINC workunit
  

  -fullatom <Boolean>

  Enable full-atom input of PDB or centroid structures
  Default: false
  

  -centroid_input <Boolean>

  why input in the name twice ? in:file:centroid_input Enable centroid inputs of PDBs
  Default: false
  

  -centroid <Boolean>

  Enable centroid inputs of PDBs
  Default: false
  

  -assign_gasteiger_atom_types <Boolean>

  Automatically assign GasteigerAtomTypes to all residues in the ResidueTypeSet
  Default: false
  

  -treat_residues_in_these_chains_as_separate_chemical_entities <String>

  Create a chemical jump for each residue in these chains (String of 1-letter chain IDs)
  Default: " "
  

  -residue_type_set <String>

  ResidueTypeSet for input files
  Default: "fa_standard"
  

  -pca <File>

  compute PCA projections
  Default: ""
  

  -silent_energy_cut <Real>

  energy cut for silent-files
  Default: 1.0
  

  -silent_list <FileVector>

  Silent input filename list(s) - like -l is to -s
  

  -silent_renumber <Boolean>

  renumber decoys in not_universal_main or not
  Default: false
  

  -silent_struct_type <String>

  Type of SilentStruct object to use in silent-file input
  Default: "protein"
  

  -silent_read_through_errors <Boolean>

  will ignore decoys with errors and continue reading
  Default: false
  

  -silent_score_prefix <String>

  Prefix that is appended to all scores read in from a silent-file
  Default: ""
  

  -silent_select_random <Integer>

  Select a random subset of this number of decoys from every silent-file read
  Default: 0
  

  -silent_select_range_start <Integer>

  Select a ranged subset of decoys from every silent-file read. Start at this decoy.
  Default: -1
  

  -silent_select_range_mul <Integer>

  Select a blocksize multiplier. This param pasically multiplies -silent_select_range_start. E.g. when set to, say, 5, -silent_select_range_start 0,1,2,3,4 will result in decoys being read starting from 0,5,10,15,20
  Default: 1
  

  -silent_select_range_len <Integer>

  Select a ranged subset of decoys from every silent-file read. Start at this decoy.
  Default: 1
  

  -skip_failed_simulations <Boolean>

  Ignore failed simulations (prefixed by W_) during silent file input. Existing behavior is preserved by default.
  Default: false
  

  -silent_scores_wanted <StringVector>

  Only put these silent-scores into the Pose.
  

  -fasta <FileVector>

  Fasta-formatted sequence file
  Default: []
  

  -pssm <FileVector>

  NCBI BLAST formatted position-specific scoring matrix
  

  -seq <StringVector>

  List of input files for constructing sequences
  

  -checkpoint <File>

  Sequence profile (flat text file format) prepared by NCBI BLAST
  

  -binary_chk <File>

  Sequence profile (binary file format) prepared by NCBI BLAST
  

  -alignment <FileVector>

  Input file for sequence alignment
  

  -alignment2 <FileVector>

  Input file for second sequence alignment
  

  -rama2b_map <File>

  Ramachandran file used by rama2b
  Default: "scoring/score_functions/rama/Rama08.dat"
  

  -psipred_ss2 <File>

  psipred_ss2 secondary structure definition file
  Default: "tt"
  

  -dssp <File>

  dssp secondary structure definition file
  Default: "tt"
  

  -fail_on_bad_hbond <Boolean>

  exit if a hydrogen bonding error is detected
  Default: true
  

  -movemap <File>

  No description
  Default: "default.movemap"
  

  -repair_sidechains <Boolean>

  Attempt a repack/minmize to repair sidechain problems, such as proline geometry and His tautomerization
  Default: false
  

  -no_binary_dunlib <Boolean>

  Do not attempt to read from or write to a binary file for the Dunbrack library
  

  -extended_pose <Integer>

  number of extended poses to process in not_universal_main
  Default: 1
  

  -template_pdb <FileVector>

  Name of input template PDB files for comparative modeling
  

  -template_silent <File>

  input templates for comparative modeling – tag needs to fit alignment id
  

  -rdc <FileVector>

  Experimental NMR Residual Dipolar Coupling File — one file per alignment medium
  

  -csa <FileVector>

  Experimental NMR Chemical Shift Anisotropy File
  

  -dc <FileVector>

  Experimental NMR Dipolar Coupling File
  

  -burial <FileVector>

  WESA-formatted burial prediction
  

  -hrf_ms_labeling <File>

  Experimental Mass Spec HRF labeling data
  

  -vall <FileVector>

  Fragment database file, e.g vall.dat.2006-05-05
  Default: "/sampling/filtered.vall.dat.2006-05-05"
  

  -rescore <Boolean>

  Governs whether input poses are rescored or not in not_universal_main, defaults to false.
  Default: false
  

  -spanfile <String>

  Membrane spanning file
  

  -lipofile <String>

  Membrane exposure file
  

  -HDX <String>

  HDX (Hydrogen exchange data file
  

  -d2h_sa_reweight <Real>

  d2h_sa reweight
  Default: 1.00
  

  -sucker_params <File>

  Parameter file containing SplineEnergy parameters
  Default: "scoring/spline_energy_functions/sucker.params"
  

  -fold_tree <File>

  User defined fold tree to be imposed on the pose after reading from disk
  

  -obey_ENDMDL <Boolean>

  Stop reading a PDB after ENDMDL card; effectively read only first model in multimodel NMR PDBs
  Default: false
  

  -new_chain_order <Boolean>

  ensures chain from different MODEL records have differnet mini chains
  Default: false
  

  -ddg_predictions_file <File>

  File that contains mutational ddG information. Used by ddG task operation/filter.
  Default: ""
  

  -input_res <ResidueChainVector>

  Residues already present in starting file
  Default: []
  

  -minimize_res <IntegerVector>

  Residues to minimize
  Default: []
  

  -md_schfile <String>

  File name containing MD schedule
  

  -native_contacts <File>

  native contacts pair list for fnat/fnon-nat calculation in Docking
  

• in:rdf

  -rdf <Boolean>

  rdf option group
  

  -sep_bb_ss <Boolean>

  separate RDFs by SS for backbone atypes
  Default: true
  

• inout

  -inout <Boolean>

  Ouput option group
  

  -fold_tree_io <Boolean>

  Ignore 'CHECKPOINT' file and the overwrite the PDB file(s)
  

  -skip_connect_info <Boolean>

  If true, skips writing CONECT information in PDB files. False by default (writes CONECT records).
  Default: false
  

  -write_all_connect_info <Boolean>

  By default, CONECT information is written for all noncanonicals and HETATMs, except waters. If this flag is set to true, it will be written for ALL residues, subject to the distance cutoff (-inout:connect_info_cufoff) and overridden by -inout:skip_connect_info.
  Default: false
  

  -connect_info_cutoff <Real>

  The atom separation cutoff above which bonded atoms have explicit CONECT records written so that programs like PyMOL know the atomic connectivity. Default 0.0 Angstroms (write all records).
  Default: 0.0
  

  -output_alternate_atomids <Boolean>

  Use the alternate atom IDS as stored in the params files when available
  Default: false
  

• inout:dbms

  -dbms <Boolean>

  database option group
  

  -mode <String>

  Which backend to use by default for database access. Note, usage of 'mysql' requires building with 'extras=mysql' and usage of 'postgres' requires building with 'extras=postgres'
  Default: "sqlite3"
  

  -database_name <String>

  name of the database. For sqlite3 databases this is a path in the file system usually with the '.db3' extension.
  

  -pq_schema <String>

  For posgres databases, specify the default schema with the database. For PostgreSQL database, schemas are like namespaces.
  Default: ""
  

  -host <String>

  default hostname of database server
  

  -user <String>

  default username for database server access
  

  -password <String>

  default password for database server access
  

  -port <Integer>

  default port for database server access
  

  -readonly <Boolean>

  open sqlite3 database in read-only mode by default
  Default: false
  

  -separate_db_per_mpi_process <Boolean>

  In MPI mode, open a separate sqlite3 database for each process with extension _<mpi_rank> and write partitioned schema to that database.
  Default: false
  

  -database_partition <Integer>

  Open a sepearte sqlite3 database with the extension _<partition> and write a partitioned schema to that database.
  Default: -1
  

  -use_compact_residue_schema <Boolean>

  Store all the atoms for a residue in a binary silent file style blob. Sacrifices analyzability for scalability. If you don't know if you want this you probably don't.
  Default: false
  

  -retry_failed_reads <Boolean>

  If a database read fails for an unknown reason, try again several times before giving up
  Default: false
  

  -path <Path>

  Directory the database should be read from or exported to.
  Default: "."
  

• out

  -out <Boolean>

  Ouput option group
  

  -overwrite <Boolean>

  Ignore 'CHECKPOINT' file and the overwrite PDB and silent file(s)
  

  -nstruct <Integer>

  Number of times to process each input PDB
  Default: 1
  

  -shuffle_nstruct <Integer>

  total number of decoys to produce
  Default: 1
  

  -prefix <String>

  Prefix for output structure names, like old -series code
  Default: ""
  

  -suffix <String>

  Suffix for output structure names
  Default: ""
  

  -mover_controlled_output_name <Boolean>

  allows the mover to control the output name
  Default: false
  

  -no_nstruct_label <Boolean>

  Do not tag the first output structure with 0001
  Default: false
  

  -pdb_gz <Boolean>

  Compress (gzip) output pdbs
  Default: false
  

  -pdb <Boolean>

  Output PDBs
  Default: false
  

  -silent_gz <Boolean>

  Use gzipped compressed output (silent run level)
  Default: false
  

  -membrane_pdb <Boolean>

  Write out the membrane in the PDB - on/off.
  

  -membrane_pdb_thickness <Real>

  Thickness of the written membrane in the PDB file. Using this flag, turns on -out:membrane_pdb automatically. If flag is not given, it uses the default (30) or the one from the -mp:thickness flag.
  

  -mmCIF <Boolean>

  output mmCIF files (broadly, as opposed to PDB files)
  Default: false
  

  -mmCIF_gz <Boolean>

  if outputting mmCIF files, gzip them
  Default: false
  

  -use_database <Boolean>

  Write out structures to database. Specify database via -inout:dbms:database_name and wanted structures with -in:file:tags
  

  -database_protocol_id <Integer>

  Manually specify a protocol ID for database output. MPI-distributed jobs are the only time when you will want to use this. It is a temporary workaround to a limitation of the MPI distributor
  

  -database_filter <StringVector>

  Filter to use with database output. Arguments for filter follow filter name
  

  -resume_batch <IntegerVector>

  Specify 1 or more batch ids to finish an incomplete protocol. Only works with the DatabaseJobOutputter. The new jobs will be generated under a new protocol and batch ID
  

  -nooutput <Boolean>

  Surpress outputfiles
  Default: false
  

  -output <Boolean>

  Force outputfiles
  Default: false
  

  -scorecut <Real>

  Only output lowest energy fraction of structures - default 1.0, i.e. output all
  Default: 1.0
  

  -show_accessed_options <Boolean>

  In the end of the run show options that has been accessed.
  Default: false
  

  -show_unused_options <Boolean>

  In the end of the run show options that were set by the user but never accessed. (Will automatically happen for JD2 protocols.)
  Default: false
  

  -sf <File>

  filename for score output
  Default: "score.fsc"
  

  -mute <StringVector>

  Mute specified Tracer channels; specify 'all' to mute all channels.
  

  -unmute <StringVector>

  UnMute specified Tracer channels; specify 'all' to unmute all channels.
  

  -level <Integer>

  Level of Tracer output, any level above will be muted. Availible levels: 0 - fatal, 100 - error, 200 - warning, 300 - info, 400 - debug, 500 - trace. For additional info please see: src/basic/Tracer.hh and doc page 'Tracer, tool for debug IO'. Default output level is 'info': 300
  Default: 300
  

  -levels <StringVector>

  Specified hierarchical mute levels for individual channels in following format: -levels all:300 core.pose:500. Numeric values could be substituted with mute level names like: debug, info, error etc. Please note that all:<num> is synonymous to -level:<num>
  

  -no_color <Boolean>

  Suppress use of tracer color codes, which can appear as '^[[0m' in log files
  Default: false
  

  -chname <Boolean>

  Add Tracer chanel names to output
  Default: true
  

  -chtimestamp <Boolean>

  Add timestamp to tracer channel name
  Default: false
  

  -dry_run <Boolean>

  If set ComparingTracer will not generate any asserts, and save all Tracer output to a file
  Default: false
  

  -mpi_tracer_to_file <String>

  MPI ONLY: Redirect all tracer output to this file with '<mpi_rank>' appened as a suffix
  Default: "tracer.out"
  

  -std_IO_exit_error_code <Integer>

  Specify error code that will be used to exit if std::IO error detected. This is useful if you want to detect situations like: Rosetta output was redirected to a file but the disk got full, etc. Default value is 0 which means that error detection code is turned off.
  Default: 0
  

  -user_tag <String>

  add this tag to structure tags: e.g., a process id
  Default: ""
  

  -output_tag <String>

  Prefix output files with this tag, if code checks for it
  Default: ""
  

  -save_times <Boolean>

  Save modeling time for each model in seconds
  Default: false
  

• out:file

  -file <Boolean>

  Output file option group
  

  -o <String>

  Name of output file
  

  -design_contrast <File>

  output list comparing design sequence to native sequence
  Default: "redesign"
  

  -residue_type_set <String>

  ResidueTypeSet for output files
  Default: "fa_standard"
  

  -atom_tree_diff <String>

  Use atom_tree_diff file output, use filename after this flag
  Default: "default.out"
  

  -atom_tree_diff_bb <Integer>

  For atom_tree_diff output, how many digits of precision to use for backbone dihedrals
  Default: 6
  

  -atom_tree_diff_sc <Integer>

  For atom_tree_diff output, how many digits of precision to use for sidechain dihedrals
  Default: 4
  

  -atom_tree_diff_bl <Integer>

  For atom_tree_diff output, how many digits of precision to use for bond lengths
  Default: 2
  

  -alignment <String>

  Output file for sequence alignment
  Default: "out.align"
  

  -score_only <String>

  Only output scores, no silent files or pdb files
  Default: "default.sc"
  

  -scorefile <String>

  Write a scorefile to the provided filename
  Default: "default.sc"
  

  -scorefile_format <String>

  Scorefile format: text, json
  Default: "text"
  

  -silent <String>

  Use silent file output, use filename after this flag
  Default: "default.out"
  

  -silent_struct_type <String>

  Type of SilentStruct object to use in silent-file output
  Default: "protein"
  

  -silent_print_all_score_headers <Boolean>

  Print a SCORE header for every SilentStruct in a silent-file
  Default: false
  

  -raw <Boolean>

  Use silent-type file output
  Default: false
  

  -weight_silent_scores <Boolean>

  Weight scores in silent-file output.
  Default: true
  

  -silent_preserve_H <Boolean>

  Preserve hydrogrens in PDB silent-file format.
  Default: false
  

  -fullatom <Boolean>

  Enable full-atom output of PDB or centroid structures
  Default: false
  

  -suppress_zero_occ_pdb_output <Boolean>

  Suppress output of atoms with zero (or negative) occupancy
  Default: false
  

  -output_virtual <Boolean>

  Output virtual atoms in output of PDB
  Default: false
  

  -output_virtual_zero_occ <Boolean>

  Set occupancy to 0.0 for virtual atoms in output of PDB
  Default: false
  

  -no_chainend_ter <Boolean>

  If true, TER records are not written at the ends of chains in PDB files – only at the end of all of the ATOM records (the legacy Rosetta behaviour). False by default (which results in TER records at the ends of every chain).
  Default: false
  

  -no_output_cen <Boolean>

  Omit outputting centroids
  Default: false
  

  -output_orbitals <Boolean>

  Output all orbitals into PDB.
  Default: false
  

  -renumber_pdb <Boolean>

  Use Rosetta residue numbering and arbitrary chain labels in pdb output.
  Default: false
  

  -pdb_parents <Boolean>

  If the pose contains a comment named template, print this as a REMARK in the pdb file
  Default: false
  

  -per_chain_renumbering <Boolean>

  When used in conjunction with renumber_pdb, restarts residue numbering at each chain.
  Default: false
  

  -output_secondary_structure <Boolean>

  output HELIX and SHEET records to StructFileRep / PDB
  Default: false
  

  -do_not_autoassign_SS <Boolean>

  Depends on -out:file:output_secondary_structure. If outputting SS, if this flag is true, it will NOT generate the secondary structure automatically; it will instead assume the secstruct string in the pose is correct
  Default: false
  

  -output_torsions <Boolean>

  Output phi, psi, and omega torsions in the PDB output if the pose is ideal.
  Default: false
  

  -use_occurrence_data <Boolean>

  if option is true reads probabilty matrix from pssm file.
  Default: false
  

  -pdb_comments <Boolean>

  If the pose contains any comment print it as a COMMENT in the pdb file.
  Default: false
  

  -force_nonideal_structure <Boolean>

  Force ResidueConformationFeatures to treat the structure as nonideal. If you know all your structures are non-ideal this decreases pose output time
  Default: true
  

  -write_pdb_link_records <Boolean>

  Sets whether or not the LINK records in PDB files are written. The default value is false.
  Default: true
  

  -use_pdb_format_HETNAM_records <Boolean>

  Sets whether or not the HETNAM records in PDB files are written in the standard PDB format with a single record per 3-letter code. The default value is false, which means that the file will use the Rosetta format, which provides a unique HETNAM record for each residue.
  Default: false
  

  -write_pdb_parametric_info <Boolean>

  If true, parametric poses have their parameter info included in the REMARK lines of the output PDB file. True by default.
  Default: true
  

  -write_glycan_pdb_codes <Boolean>

  If true glycans will be written based on the pdb codes rather than the rosetta names
  Default: false
  

  -output_pose_energies_table <Boolean>

  Output the pose energies table. This can be overridden
  Default: true
  

  -output_pose_cache_data <Boolean>

  Output the pose cache.
  Default: true
  

  -output_pose_fold_tree <Boolean>

  Output the foldtree of the pose. Will go in rosetta_additional column for cif files.
  Default: false
  

  -cif_extra_data_separate_file <Boolean>

  When outputting mmCIF, write extra data and energies to separate files (JOBNAME.extradata and JOBNAME.eneriges)
  Default: false
  

  -dont_rewrite_dunbrack_database <Boolean>

  Disables the default behavior of rewriting the Dunrack library in binary format if a binary version is not found
  

  -frag_prefix <String>

  Prefix for fragment output
  Default: "default.frags"
  

  -no_extra_sdf_data <Boolean>

  Do not add extra round-tripping data to SDF file output
  Default: false
  

  -no_scores_in_pdb <Boolean>

  Deprated option. See -output_pose_energies_table and -output_pose_cache_data
  

• out:path

  -all <Path>

  Default file output path
  Default: "."
  

  -path <Path>

  Default file output path
  Default: "."
  

  -pdb <Path>

  PDB file output path
  

  -db <Path>

  Database file output path if using FeatureReporters or database output
  Default: "."
  

  -score <Path>

  Score file output path
  

  -scratch <Path>

  use this path as scratch drive
  Default: ['"/scratch/USERS/"']
  

  -mpi_rank_dir <Boolean>

  Put silent-output files in individual directory as determined by mpi-rank
  Default: false
  

  -mmCIF <Path>

  if outputting mmCIF, mmCIF file output path
  

• run

  -run <Boolean>

  Run option group
  

  -batches <FileVector>

  batch_flag_files
  Default: ""
  

  -no_prof_info_in_silentout <Boolean>

  no time-columns appears in score/silent - files
  Default: false
  

  -archive <Boolean>

  run MPIArchiveJobDistributor
  Default: false
  

  -n_replica <Integer>

  run MPIMultiCommJobDistributor with n_replica processes per job
  Default: 1
  

  -shuffle <Boolean>

  Shuffle job order
  Default: false
  

  -msd_job_dist <Boolean>

  Use MSD Job Distributor
  Default: false
  

  -msd_randomize <Boolean>

  Randomize order of input poses for MSD
  Default: false
  

  -n_cycles <Integer>

  Option to control miscellaneous cycles within protocols. This has no core meaning - it is meant to reduce option-bloat by having every protocol define separate cycles options. Check your protocol's documentation to see if it is used.
  Range: 1-
  Default: 1
  

  -repeat <Integer>

  Repeat mover N times
  Range: 0-
  Default: 1
  

  -max_min_iter <Integer>

  Maximum number of iterations of dfpmin
  Default: 200
  

  -maxruntime <Integer>

  Maximum runtime in seconds. JobDistributor will signal end if time is exceeded no matter how many jobs were finished.
  Default: -1
  

  -maxruntime_bufferfactor <Real>

  If set, the JobDistributor will attempt to stop if there doesn't appear to be enough time for maxruntime_bufferfactor jobs before maxruntime occurs.
  Default: 0
  

  -write_failures <Boolean>

  write failed structures to output
  Default: false
  

  -benchmark <Boolean>

  Run in benchmark mode
  

  -test_cycles <Boolean>

  When running tests, use reduced cycles. Cycles must be defined in the code itself
  Default: false
  

  -memory_test_cycles <Boolean>

  use together with test_cycles to keep number of copies of anything as high as in production mode
  Default: false
  

  -dry_run <Boolean>

  Run through structures/tasks/etc skipping the actual calculation step for testing of I/O and/or setup
  Default: false
  

  -debug <Boolean>

  Run in debug mode
  

  -profile <Boolean>

  Run in profile mode
  Default: false
  

  -max_retry_job <Integer>

  If a job fails with FAIL_RETRY retry this many times at most
  Default: 10
  

  -version <Boolean>

  write out detailed version info, if it was available at compile time
  Default: false
  

  -nodelay <Boolean>

  Do not delay launch of minirosetta
  

  -delay <Integer>

  Wait N seconds before doing anything at all. Useful for cluster job staggering.
  Default: 0
  

  -random_delay <Integer>

  Wait a random amount of 0..N seconds before doing anything at all. Useful for cluster job staggering.
  Default: 0
  

  -timer <Boolean>

  write out time per decoy in minutes in scorefile
  

  -chain <String>

  -chain <chain_id>
  Default: "-"
  

  -score_only <Boolean>

  calculate the score only and exit
  Default: false
  

  -decoystats <Boolean>

  calculate values of a series of additional structural properties, including counting unsatisfied buried Hbond donors and acceptors, SASApack, etc. Additional output associated with this flag is written both to stdout and to output PDB files
  

  -output_hbond_info <Boolean>

  print hydrogen bond info in the stats section of written out PDB files
  

  -wide_nblist_extension <Real>

  Amount to extend the wide neighbor list
  Default: 2.0
  

  -constant_seed <Boolean>

  Use a constant seed (1111111 unless specified)
  

  -jran <Integer>

  Specify seed (requires -constant_seed)
  Default: 1111111
  

  -use_time_as_seed <Boolean>

  Use time as random number seed instead of default rng seed device.
  

  -rng_seed_device <String>

  Obtain random number seed from specified device.
  Default: "/dev/urandom"
  

  -seed_offset <Integer>

  This value will be added to the random number seed. Useful when using time as seed and submitting many jobs to clusters. Using the condor job id will force jobs that are started in the same second to still have different initial seeds
  Default: 0
  

  -rng <String>

  Random number generation algorithm: Currently only mt19937 is a accepted here
  Default: "mt19937"
  

  -rebuild_disulf <Boolean>

  Attempt to build correct disulfide geometry when converting from a centroid pose to a full atom pose. Disulfides must be previously annotated, either by enabling -detect_disulf or by specifying a file to -fix_disulf.
  Default: false
  

  -preserve_header <Boolean>

  Maintain header info from input PDB when writing output PDBs
  

  -suppress_checkpoints <Boolean>

  Override & switch off checkpoints.
  

  -checkpoint <Boolean>

  Turn checkpointing on
  

  -delete_checkpoints <Boolean>

  delete the checkpoints after use
  Default: true
  

  -checkpoint_interval <Integer>

  Checkpoint time interval in seconds
  Range: 10-
  Default: 600
  

  -protocol <String>

  Which protocol to run, for Rosetta wrapper
  Default: "abrelax"
  

  -remove_ss_length_screen <Boolean>

  Sets the use_ss_length_screen flag in the Fragment Mover to false
  

  -min_type <String>

  type of minimizer to use
  Default: "lbfgs_armijo_nonmonotone"
  

  -min_tolerance <Real>

  minimizer tolerance
  Default: 0.000001
  

  -nblist_autoupdate <Boolean>

  Turn on neighborlist auto-updates for all minimizations
  Default: false
  

  -nblist_autoupdate_narrow <Real>

  With nblist autoupdate: the reach in Angstroms for the narrow neighbor list
  Default: 0.5
  

  -nblist_autoupdate_wide <Real>

  With nblist autoupdate: the reach in Angstroms for the wide neighbor list
  Default: 2.0
  

  -skip_set_reasonable_fold_tree <Boolean>

  Do not run set_reasonable_fold_tree when creating a pose from a pdb. Useful for unreasonable PDBs where the user sets a fold tree explicitly.
  Default: false
  

  -randomize_missing_coords <Boolean>

  Insert random coordinates for missing density atoms ( occupancy is zero ) and for any atoms with negative occupancy, randomizing coords is done by default
  Default: false
  

  -ignore_zero_occupancy <Boolean>

  discard coords information for missing density atoms ( occupancy is zero ) defined in input structures. Default is to keep those coordinates because this is a consistent problem for end users
  Default: true
  

  -cycles_outer <Integer>

  number of outer cycles
  Range: 1-
  Default: 1
  

  -cycles_inner <Integer>

  number of inner cycles
  Range: 1-
  Default: 1
  

  -repack_rate <Integer>

  repack after every [value] cycles during certain protocols
  Range: 1-
  Default: 10
  

  -reinitialize_mover_for_each_job <Boolean>

  job distributor will generate fresh copy of its mover before each apply (once per job)
  Default: false
  

  -reinitialize_mover_for_new_input <Boolean>

  job distributor will generate fresh copy of its mover whenever the pose being passed to the mover is going to change (e.g., next PDB in -l)
  Default: false
  

  -multiple_processes_writing_to_one_directory <Boolean>

  activates .in_progress files used to communicate between independent processes that a job is underway. UNSAFE but may be convenient.
  Default: false
  

  -jobdist_miscfile_ext <String>

  extension for JobOutputter file() function (miscellaneous file output).
  Default: ".data"
  

  -no_scorefile <Boolean>

  do not output scorefiles
  Default: false
  

  -other_pose_to_scorefile <Boolean>

  write other_pose (JobOutputter) to a scorefile; path by other_pose_scorefile; be warned you can get garbage if scorefunctions for poses do not match. Overridden by no_scorefile
  Default: false
  

  -other_pose_scorefile <File>

  Path to other_pose (JobOutputter) scorefiles. Default is same scorefile as regular result poses. The default will cause problems if your output poses were scored on different scorefunctions.
  Default: ""
  

  -intermediate_scorefiles <Boolean>

  write intermediate evaluations to disk (depends on your protocol if and how often this happens
  Default: false
  

  -intermediate_structures <Boolean>

  write structures together with intermediate evaluations
  Default: false
  

  -idealize_before_protocol <Boolean>

  run idealize first, before running whatever.
  

  -interactive <Boolean>

  Signal Rosetta is to be run as a library in an interactive application. In particular, favor throwing exceptions on bad inputs rather than exiting.
  Default: false
  

  -condor <Boolean>

  if condor say yes – proc_id counting starts at 0
  Default: false
  

  -nproc <Integer>

  number of process... needed if proc_id is specified
  Default: 0
  

  -proc_id <Integer>

  give process number... Jobdistributor will only work on proc_id mod nproc part of work
  Default: 0
  

  -exit_if_missing_heavy_atoms <Boolean>

  quit if heavy atoms missing in pdb
  Default: false
  

  -show_simulation_in_pymol <Real>

  Attach PyMOL observer to pose at the beginning of the simulation. Waits until at least every [argument] seconds before sending pose if something has changed, default 5. A value of 0 indicates to not skip any packets from sending! Don't forget to run the PyMOLPyRosettaServer.py script within PyMOL!
  Default: 5.0
  

  -update_pymol_on_energy_changes_only <Boolean>

  Only Update the simulation in on energy change. Useful if pymol observer is segfaulting on length changes.
  Default: false
  

  -update_pymol_on_conformation_changes_only <Boolean>

  Only update the simulation in pymol on conformation change.
  Default: false
  

  -keep_pymol_simulation_history <Boolean>

  Keep history when using show_simulation_in_pymol flag?
  Default: false
  

• run:PyMOLMover

  -PyMOLMover <Boolean>

  PyMOLMover option group
  

  -address <String>

  TCP port address to use when initializing PyMOLMover
  Default: ""
  

  -port <Integer>

  TCP port to use when initializing PyMOLMover
  Default: 0
  

  -max_packet_size <Integer>

  Max size of packet to send to PyMOL. Default value is dependable from address: for 127.0.0.1 it will be set to 7678 and any other addresses to 1500.
  Default: 0
  

• parser

  -parser <Boolean>

  parser option group
  

  -protocol <String>

  The protocol you will be running. (Input XML File
  

  -script_vars <StringVector>

  Variable substitutions for xml parser, in the form of name=value
  

  -view <Boolean>

  Use the viewer?
  

  -info <StringVector>

  Have the rosetta_scripts application print out the available XML-accessible options for a given mover, filter, task operation, or residue selector, and then exit.
  

  -output_schema <String>

  Have the rosetta_scripts application write out its XML Schema to the given file and then exit.
  

  -validate_and_exit <Boolean>

  After XML Schema validation completes, exit
  

  -patchdock <String>

  Patchdock output file name.
  

  -patchdock_random_entry <IntegerVector>

  Pick a random patchdock entry between two entry numbers. inclusive
  

  -inclusion_recursion_limit <Integer>

  How many recursions to perform when parsing an XML file with inclusions
  Default: 8
  

• jd3

  -jd3 <Boolean>

  jd3 option group
  

  -mpi_work_partition_job_distributor <Boolean>

  determine if we should use the WorkPartition job distributor
  Default: false
  

  -job_definition_schema <File>

  If provided on the command line, the job distributor will write the XML Schema for the applciation's job definition file out to disk and then exit
  

  -mpi_fast_nonblocking_output <Boolean>

  By default the master node blocks while a slave node outputs to avoid two slaves writing to a score file or silent file at the same time setting this to true disables that feature
  Default: false
  

  -n_archive_nodes <Integer>

  The number of nodes that should perform archival roles only. This flag is only used by the MPIWorkPoolJobDistributor
  Default: 0
  

  -do_not_archive_on_node0 <Boolean>

  Should the master node in the MPIWorkPoolJobDistributor archive any JobResults on it? Only relevant for MPI builds when using -n_archive_nodes
  Default: false
  

  -mpi_fraction_outputters <Real>

  Fraction of the MPI nodes that node0 is allowed to use to output job results; non-archive nodes that output will also perform regular work in addition to their output work. This flag should range from 0 to 1. Note that node0 never outputs, so even if this is set to 0, one node will be deputized as an output node.
  Default: 0.01
  

  -nthreads <Integer>

  For the multithreaded job distributor, how many threads should be run at the same time
  

  -archive_on_disk <String>

  Sometimes job results use a ton of memory. This option tells Rosetta to store job results on disk instead of in memory. The string you pass here should be the name of a (preferably empty) directoy where we can put all of our temporary files. You can delete this directory and everything in it when Rosetta is done running.
  Default: "null"
  

  -compress_job_results <Boolean>

  Sometimes job results use a ton of memory. This option tells Rosetta to compress all job results so they use less memory.
  Default: true
  

  -resource_definition_files <FileVector>

  Specify all the resources to available for the jobs running.
  

  -resource_definition_schema <File>

  If provided on the command line, the job distributor will write the XML Schema for the applciation's resource definition file out to disk and then exit
  

• jd2

  -jd2 <Boolean>

  jd2 option group
  

  -pose_input_stream <Boolean>

  Use PoseInputStream classes for Pose input
  Default: false
  

  -lazy_silent_file_reader <Boolean>

  use lazy silent file reader in job distributor, read in a structure only when you need to
  Default: false
  

  -mpi_nowait_for_remaining_jobs <Boolean>

  exit immediately (not graceful – not complete) if the last job has been sent out
  Default: false
  

  -mpi_timeout_factor <Real>

  timeout is X times average job-completion time - set to 0 to switch off
  Default: 0
  

  -mpi_work_partition_job_distributor <Boolean>

  determine if we should use the WorkPartition job distributor
  Default: false
  

  -mpi_file_buf_job_distributor <Boolean>

  determine if we should use the MPIFileBufJobDistributor (warning: silent output only)
  Default: true
  

  -mpi_filebuf_jobdistributor <Boolean>

  same as mpi_file_buf_job_distributor but with more intuitive spacing... determine if we should use the MPIFileBufJobDistributor (warning: silent output only)
  Default: true
  

  -mpi_fast_nonblocking_output <Boolean>

  By default the master node blocks while a slave node outputs to avoid two slaves writing to a score file or silent file at the same time setting this to true disables that feature
  Default: false
  

  -dd_parser <Boolean>

  determine whether to use the dock_design_parser
  Default: false
  

  -ntrials <Integer>

  number of attempts at creating an output file for each nstruct. e.g., ntrials 3 and nstruct 10 would mean that each of 10 trajectories would attempt to write an output file 3 times and if unsuccessful would fail.
  Default: 1
  

  -generic_job_name <String>

  job name when using GenericJobInputter (i.e. abinitio)
  Default: "S"
  

  -no_output <Boolean>

  use NoOutputJobOutputter; do not store the pose after a run (no silent or scorefile)
  Default: false
  

  -enzdes_out <Boolean>

  causes an enzdes-style scorefile (with information about catalytic res and some pose metric stuff ) to be written instead of the regular scorefile
  Default: false
  

  -buffer_silent_output <Integer>

  write structures to silent-files in blocks of N structures to
  Default: 1
  

  -buffer_flush_frequency <Real>

  when N structures (buffer_silent_output) are collected dump to file with probability X
  Default: 1.0
  

  -delete_old_poses <Boolean>

  Delete poses after they have been processed. For jobs that process a large number of structures, the memory consumed by old poses is wasteful.
  Default: false
  

  -checkpoint_file <File>

  write/read nstruct-based checkpoint files to the desired filename.
  

  -failed_job_exception <Boolean>

  If JD2 encounters an error during job execution, raise an exception at the end of the run
  Default: true
  

  -max_nstruct_in_memory <Integer>

  If nstruct is set higher than this number, JD2 will keep only this many jobs in memory in the jobs list at any given time (to keep the jobs list from filling up memory). As jobs complete, they will be deleted and the jobs list will be filled out with new jobs. This option is intended for exteremly large runs on systems like the Blue Gene/Q supercomputer. To disable this sort of memory management, set this option to 0.
  Default: 1000000
  

  -sequential_mpi_job_distribution <Boolean>

  If specified, MPI versions of the JobDistributor send jobs to each slave in sequence (slave1, slave2, slave3 etc.). False by default. Note that this should NOT be used for production runs; it is intended only for regression tests in which non-sequential job distribution would result in stochastic variations.
  Default: false
  

  -grid_ensemble <Boolean>

  Do an ensemble search where each input pdb is used for an ensemble based search. Instead of each in file outputting nstruct, we use the input files to generate a total nstruct across the inputs
  Default: false
  

  -seed_ensemble <Boolean>

  Do an ensemble search as in grid_search, but randomly choose the seeds over the inputs. See seed_ensemble_weights to weight the inputs
  Default: false
  

  -seed_ensemble_weights <RealVector>

  Specifiy weights for seeded ensemble. Must match number of inputs. See also: -seed_ensemble_weights_file
  

  -seed_ensemble_weights_file <File>

  A file specifying weights to use for each input structure. Two columns. basename with extension (or relative path or full path), weight
  

• view

  -view <Boolean>

  view option group
  

  -show_virtual_residues <Boolean>

  Show virtual residues?
  Default: true
  

  -single_glycan_color <Boolean>

  Show glycans as a single color instead of default
  Default: true
  

• score

  -score_pose_cutpoint_variants <Boolean>

  Include cutpoint variants in the pose during linear chainbreak
  Default: false
  

  -score <Boolean>

  scorefunction option group
  

  -weights <String>

  Name of weights file (without extension .wts)
  Default: "ref2015"
  

  -set_weights <StringVector>

  Modification to weights via the command line. Applied in ScoreFunctionFactory::create_score_function inside the function apply_user_defined_reweighting_. Format is a list of paired strings: -score::set_weights <score_type1> <setting1> <score_type2> <setting2> ...
  

  -pack_weights <String>

  Name of packing weights file (without extension .wts)
  Default: "ref2015"
  

  -soft_wts <String>

  Name of the 'soft' weights file, for protocols which use it.
  Default: "soft_rep"
  

  -docking_interface_score <Boolean>

  the score is computed as difference between bound and unbound pose
  Default: false
  

  -min_score_score <Real>

  do not consider scores lower than min-score in monte-carlo criterion
  Default: 0.0
  

  -custom_atom_pair <String>

  filename for custom atom pair constraints
  Default: "empty"
  

  -patch <FileVector>

  Name of patch file (without extension)
  Default: ""
  

  -empty <Boolean>

  Make an empty score - i.e. NO scoring
  

  -fa_max_dis <Real>

  How far does the FA pair potential go out to ?
  Default: 6.0
  

  -fa_Hatr <Boolean>

  Turn on Lennard Jones attractive term for hydrogen atoms
  Default: true
  

  -no_smooth_etables <Boolean>

  Revert to old style etables
  

  -no_lk_polar_desolvation <Boolean>

  Disable the polar-desolvation component of the LK solvation model; effectively set dGfree for polar atoms to 0
  

  -lk_polar_without_proline_N <Boolean>

  Force class LK_PolarNonPolarEnergy to treat the N atom of proline as non-polar
  Default: false
  

  -input_etables <String>

  Read etables from files with given prefix
  

  -output_etables <String>

  Write out etables to files with given prefix
  

  -analytic_etable_evaluation <Boolean>

  Instead of interpolating between bins, use an analytic evaluation of the lennard-jones and solvation energies
  Default: true
  

  -put_intra_into_total <Boolean>

  Put intra-residue terms inside hbond, geom_sol_fast, fa_atr. (Contributions will not show up in hbond_intra, fa_atr_intra_xover4.) Off for proteins by default.
  Default: false
  

  -include_intra_res_protein <Boolean>

  Include computation of intra-residue terms for proteins.
  Default: false
  

  -fa_stack_base_base_only <Boolean>

  Only calculate fa_stack for RNA base/base.
  Default: true
  

  -fa_stack_include_rna_protein <Boolean>

  Calculate fa_stack for RNA/protein
  Default: true
  

  -fa_stack_sol_prefactor <Real>

  Strength of sol penalty in fa_stack_sol.
  Default: 0.1
  

  -fa_stack_sol_stack_cutoff <Real>

  distances below this get full sol stack.
  Default: 5.5
  

  -fa_stack_sol_dist_cutoff <Real>

  distances below this get some sol stack.
  Default: 6.5
  

  -fa_stack_lr_prefactor <Real>

  Strength of lr penalty in fa_stack_lr.
  Default: -0.05
  

  -fa_stack_lr_stack_cutoff <Real>

  distances below this get full lr stack.
  Default: 6.5
  

  -fa_stack_lr_dist_cutoff <Real>

  distances below this get some lr stack.
  Default: 7.5
  

  -geom_sol_interres_path_distance_cutoff <Integer>

  Minimum no. bonds between atoms in different residues to calculate geom_sol
  Default: 0
  

  -geom_sol_intrares_path_distance_cutoff <Integer>

  Minimum no. bonds between atoms in same residues to calculate geom_sol
  Default: 6
  

  -rms_target <Real>

  Target of RMS optimization for RMS_Energy EnergyMethod
  Default: 0.0
  

  -ramaneighbors <Boolean>

  Uses neighbor-dependent ramachandran maps
  Default: false
  

  -optH_weights <String>

  Name of weights file (without extension .wts) to use during optH
  

  -optH_patch <String>

  Name of weights file (without extension .wts) to use during optH
  

  -hb_don_strength <StringVector>

  Modification of hbond donor-atom strengths, over-rides any database file settings. Format is -hb_don_strength <atm1>:<wt1> <atm2>:<wt2> ... For example -hb_don_strength hbdon_IND:1.5 hbdon_AHX:0.5
  

  -hb_acc_strength <StringVector>

  Modification of hbond acceptor-atom strengths, over-rides any database file settings. Format is -hb_acc_strength <atm1>:<wt1> <atm2>:<wt2> ... For example -hb_acc_strength hbacc_CXA:1.5 hbdon_HXL:0.5
  

  -hbe_for_dH2O_aGEN_SP3SC_ssother <String>

  HBEvalType for HBEvalTuple(hbdon_H2O, hbacc_GENERIC_SP3SC, seq_sep_other)
  Default: "hbe_dH2OaHXL"
  

  -hbond_params <String>

  Directory name in the database for which hydrogen bond parameters to use.
  Default: "ref2015_params"
  

  -hbond_bb_per_residue_energy <Boolean>

  In score tables, separate out backbone hydrogens bond energies per residue. By default, bb hbonds are included in the total energy, but not per residue energies
  Default: false
  

  -hbond_disable_bbsc_exclusion_rule <Boolean>

  Disable the rule that protein bb/sc hbonds are excluded if the backbone group is already forming a hydrogen bond to a backbone group; with this flag, no hbonds are excluded
  Default: false
  

  -use_hb_env_dep <Boolean>

  Use hydrogen bond environment dependency. Smaller in the surface of the protein.
  Default: true
  

  -water_hybrid_sf <Boolean>

  Use a hybrid scoring function, which includes energy terms hbond_wat and wat_entropy.
  Default: false
  

  -show_etable_contributions <Boolean>

  Shows atom-atom and res-res contributions to Lennard-Jones and solvation energies when scoring.
  Default: false
  

  -symE_units <Integer>

  Number of symmetric Units in design for use with symE scoring
  Default: -1
  

  -symE_bonus <Real>

  Energy bonus per match for use with symE scoring
  Default: 0.0
  

  -symmetric_gly_tables <Boolean>

  If true, the Ramachandran and P_AA_PP tables for glycine will be symmetrized on load. If false (the default), then the statistical tables will be used, which are asymmetric due to the contribution of chiral amino acids.
  Default: false
  

  -NV_lbound <Real>

  Lower Bound for neighbor Vector scoring
  Default: 3.3
  

  -NV_ubound <Real>

  Upper Bound for neighbor Vector scoring
  Default: 11.1
  

  -NV_table <String>

  Location of path to potential lookup table
  Default: "scoring/score_functions/NV/neighbor_vector_score.histogram"
  

  -find_neighbors_3dgrid <Boolean>

  Use a 3D lookup table for doing neighbor calculations. For spherical, well-distributed conformations, O(N) neighbor detection instead of general O(NlgN)
  Default: false
  

  -find_neighbors_stripehash <Boolean>

  should be faster than 3dgrid and use 1/8th the memory
  Default: false
  

  -seqdep_refene_fname <String>

  Filename for table containing sequence-dependent reference energies
  

  -secondary_seqdep_refene_fname <String>

  Additional filename for table containing sequence-dependent reference energies
  

  -exact_occ_pairwise <Boolean>

  When using occ_sol_exact, compute energies subject to pairwise additivity (not recommended - intended for parameterization / evaluation purposes)
  Default: false
  

  -exact_occ_skip_Hbonders <Boolean>

  When using occ_sol_exact, do not count contributions from occluding groups which form Hbonds to the polar group of interest
  Default: true
  

  -exact_occ_pairwise_by_res <Boolean>

  When using occ_sol_exact, compute energies subject to by-residue pairwise additivity (not recommended - intended for parameterization / evaluation purposes)
  Default: false
  

  -exact_occ_split_between_res <Boolean>

  When using occ_sol_exact with the exact_occ_pairwise flag, split the energies between both contributing residues instead of assigning it just to the polar residue (not recommended - intended for parameterization / evaluation purposes)
  Default: false
  

  -exact_occ_self_res_no_occ <Boolean>

  Setting this to false means that the self-residue CAN occlude when using the exact ODO model, leading to potential double-counting with the Dunbrack energy but better results in loop discrimination.
  Default: false
  

  -exact_occ_radius_scaling <Real>

  When using occ_sol_exact, scale the radii of occluding atoms by this factor (intended for parameterization / evaluation purposes)
  Default: 1.0
  

  -ref_offsets <StringVector>

  offset reference energies using 3 character residue types (example: TRP 0.9 HIS 0.3)
  

  -ref_offset <Real>

  offset all reference energies by this amount
  Default: 0.0
  

  -output_residue_energies <Boolean>

  Output the energy for each residue
  Default: false
  

  -fa_custom_pair_distance_file <String>

  Name of custom pair distance energy file
  Default: ""
  

  -disulf_matching_probe <Real>

  Size of probe to use in disulfide matching score
  Default: 2.5
  

  -bonded_params <RealVector>

  Default spring constants for bonded parameters [length,angle,torsion,proton-torsion,improper-torsion]
  

  -bonded_params_dir <String>

  Spring constants for bonded parameters [length,angle,torsion,proton-torsion,improper-torsion]
  Default: "scoring/score_functions/bondlength_bondangle"
  

  -extra_improper_file <String>

  Add extra parameters for improper torsions
  

  -pro_close_planar_constraint <Real>

  stdev of CD,N,CA,prevC trigonal planar constraint in pro_close energy method
  Default: 0.1
  

  -no_pro_close_ring_closure <Boolean>

  The pro_close term holds the proline ring closed, but also has some inter-residue energy associated with the psi value of the preceding residue. If this flag is set to 'true', the term ONLY does the torsional stuff – it doesn't hold the ring closed. For use with cart_bonded or ring_close. False by default.
  Default: false
  

  -ring_close_shadow_constraint <Real>

  Standard deviation of the harmonic potential used to hold shadow atoms atop real atoms in order to hold rings closed with the ring_close scoring term. Analogous to pro_close_planar_constraint option for the pro_close energy term.
  Default: 0.1
  

  -linear_bonded_potential <Boolean>

  use linear (instead of quadratic) bonded potential
  Default: false
  

  -free_side_chain_bonus <Real>

  Amount to reward virtualization of a protein side chain, per free chi
  Default: -0.5
  

  -compute_mg_sol_for_hydrogens <Boolean>

  mg_sol includes penalties for hydrogens near Mg(2+)
  Default: false
  

  -rg_local_span <IntegerVector>

  First,last res in rg_local. For example to calc rg_local from 1-20 would be 1,20
  Default: 0
  

  -unmodifypot <Boolean>

  Do not call modify pot to add extra repulsive interactions between Obb/Obb atom types at distances beneath 3.6 Angstroms
  Default: true
  

  -conc <Real>

  intermolecular concentration to use in intermol term (give in M)
  Default: 1.0
  

  -sidechain_buried <IntegerVector>

  count buried residues (rvernon pilot app)
  Default: -1
  

  -sidechain_exposed <IntegerVector>

  count exposed residues (rvernon pilot app)
  Default: -1
  

  -aa_composition_setup_file <StringVector>

  The filename of one or more setup files for the aa_composition scoring term. (Multiple such files can be listed, separated by a space.) The default location for these files (which have a .comp extension) is /database/scoring/score_functions/aa_composition/.
  

  -aa_repeat_energy_penalty_file <String>

  The filename of a penalty file for the aa_repeat_energy term. The penalty file should be a series of numbers on a single line, representing the penalty for having a repeat of 1, 2, 3, etc. of the same residue. Penalty files are stored in database/scoring/score_functions/aa_repeat_energy/ and should have the suffix .rpt_pen. The default is default_repeat_penalty_table.rpt_pen.
  Default: "default_repeat_penalty_table.rpt_pen"
  

  -aspartimide_penalty_value <Real>

  The penalty for each aspartimide-forming two-residue sequence found, when the aspartimide_penalty score term weight is set to 1.0. Default is 25.0.
  Default: 25.0
  

  -elec_min_dis <Real>

  changes the minimum distance cut-off for hack-elec energy
  Default: 1.6
  

  -elec_max_dis <Real>

  changes the maximum distance cut-off for hack-elec energy
  Default: 5.5
  

  -elec_die <Real>

  changes the dielectric constant for hack-elec energy
  Default: 10.0
  

  -elec_r_option <Boolean>

  changes the dielectric from distance dependent to distance independent
  Default: false
  

  -elec_sigmoidal_die <Boolean>

  changes the dielectric from distance dependent to sigmoidal
  Default: true
  

  -elec_sigmoidal_die_D <Real>

  D parameter for sigmoidal dielectric
  Default: 80.0
  

  -elec_sigmoidal_die_D0 <Real>

  D0 parameter for sigmoidal dielectric
  Default: 6.0
  

  -elec_sigmoidal_die_S <Real>

  S parameter for sigmoidal dielectric
  Default: 0.4
  

  -stack_elec_sigmoidal_die <Boolean>

  override of -elec_sigmoidal_die for stack_elec
  Default: false
  

  -elec_representative_cp <Boolean>

  Use representative atoms for countpair to avoid dipole splits
  Default: true
  

  -elec_representative_cp_flip <Boolean>

  Enable elec_representative_cp, but FLIP the order in the table
  Default: true
  

  -eval_intrares_elec_ST_only <Boolean>

  Intrares elec only for free DOF atoms in Ser/Thr
  Default: false
  

  -smooth_fa_elec <Boolean>

  Smooth the discontinuities in the elec energy function using a sigmoidal term
  Default: true
  

  -grpelec_fade_type <String>

  use standard way (shift/switch function) of Coulomb function for fa_grpelec
  Default: "false"
  

  -grpelec_fade_param1 <Real>

  fading distance for shift/switch
  Default: 1.0
  

  -grpelec_fade_param2 <Real>

  exponent for shift
  Default: 1.0
  

  -elec_group_file <String>

  file where group information is stored
  Default: "/scoring/score_functions/elec_group_def.dat"
  

  -elec_group_extrafile <String>

  file where group information for extra_res is stored
  Default: ""
  

  -grpelec_fade_hbond <Boolean>

  fade grpelec for hbonding group
  Default: false
  

  -grpelec_max_qeps <RealVector>

  Max abs charge for the group types, used when fading hbond [nonpolar/polar/charged]
  Default: ['0', '0.10', '0.25', '0.5']
  

  -grpelec_context_dependent <Boolean>

  whether grpelec depends on context
  Default: false
  

  -grp_cpfxn <Boolean>

  rule for trying cpfxn on group
  Default: true
  

  -grpelec_cpfxn_weight <RealVector>

  cpfxn weight on group(1-4/1-5/>1-5)
  Default: ['0.0', '0.2', '1.0']
  

  -hbnet_bonus_function_ramping <String>

  The hbnet score term's bonus function can scale in different ways as the size of a network grows. The default is quadratic growth, though linear, logarithmic, and square root growth are all allowed.
  Default: "quadratic"
  

  -hbnet_max_network_size <Integer>

  This is the maximum hydrogen bond network size, beyond which the hbnet score term will not give any more bonus. Defaults to 0, which means no limit.
  Default: 0
  

  -elec_context_minstrength <Real>

  strength at min burial
  Default: 0.2
  

  -elec_context_minburial <Real>

  num. cb assigned as min burial
  Default: 7.0
  

  -elec_context_maxburial <Real>

  num. cb assigned as max burial
  Default: 24.0
  

  -use_polarization <Boolean>

  whether multipole electrostatics includes polarization (induced dipoles)
  Default: true
  

  -use_gen_kirkwood <Boolean>

  whether multipole electrostatics includes treatment of reaction field
  Default: true
  

  -protein_dielectric <Real>

  dielectric constant for protein in generalized Kirkwood treatment of reaction field
  Default: 1.0
  

  -water_dielectric <Real>

  dielectric constant for water in generalized Kirkwood treatment of reaction field
  Default: 78.3
  

  -facts_GBpair_cut <Real>

  GBpair interaction distance cutoff (same as elec_max_dis)
  Default: 10.0
  

  -facts_kappa <Real>

  GBpair interaction screening factor
  Default: 12.0
  

  -facts_asp_patch <Integer>

  AtomicSolvationParameter set for nonpolar interaction in FACTS
  Default: 3
  

  -facts_plane_to_self <Boolean>

  Add atoms in same plane to self energy pairs
  Default: true
  

  -facts_saltbridge_correction <Real>

  FACTS Self energy parameter scaling factor for polarH
  Default: 1.0
  

  -facts_dshift <RealVector>

  FACTS pair term denominator distance shift[bb/bbsc/scsc/saltbridge]
  Default: ['0.0', '1.5', '1.5', '1.5']
  

  -facts_die <Real>

  FACTS dielectric constant
  Default: 1.0
  

  -facts_binding_affinity <Boolean>

  Activate FACTS options for binding affinity calculation
  Default: false
  

  -facts_intrascale_by_level <Boolean>

  Apply internal scaling by path_dist to CA? (definition below becomes G/D/E/Z/>Z
  Default: false
  

  -facts_intbb_elec_scale <RealVector>

  FACTS Coulomb scale for intrares bonded pairs: [1-4, 1-5, >1-5]
  Default: ['0.0', '0.2', '0.0']
  

  -facts_intbb_solv_scale <RealVector>

  FACTS GB scale for intrares bb-bb bonded pairs: [1-4, 1-5, >1-5]
  Default: ['0.4', '0.4', '0.0']
  

  -facts_adjbb_elec_scale <RealVector>

  FACTS Coulomb scale for adjacent bb-bb bonded pairs: [1-4, 1-5, 1-6, 2res-coupled, 1res-decoupled]
  Default: ['0.0', '0.2', '1.0', '0.5', '0.5']
  

  -facts_adjbb_solv_scale <RealVector>

  FACTS GB scale for adjacent bb-bb bonded pairs: [1-4, 1-5, 1-6, 2res-coupled, 1res-decoupled]
  Default: ['0.0', '0.2', '1.0', '0.5', '0.5']
  

  -facts_intbs_elec_scale <RealVector>

  FACTS Coulomb scale for intrares bb-sc bonded pairs: [1-4, 1-5, 1-6, >1-6, dumm]
  Default: ['0.2', '0.2', '0.2', '0.2', '0.0']
  

  -facts_intbs_solv_scale <RealVector>

  FACTS GB scale for intrares bb-sc bonded pairs: [1-4, 1-5, 1-6, >1-6, dumm]
  Default: ['1.0', '0.6', '0.6', '0.6', '0.0']
  

  -facts_adjbs_elec_scale <RealVector>

  FACTS Coulomb scale for adjacent bb-sc bonded pairs: [1-4, 1-5, 1-6, 1-7, >1-7]
  Default: ['0.0', '0.2', '0.2', '0.2', '0.2']
  

  -facts_adjbs_solv_scale <RealVector>

  FACTS GB scale for adjacent bb-sc bonded pairs: [1-4, 1-5, 1-6, 1-7, >1-7]
  Default: ['1.0', '0.6', '0.6', '0.6', '0.6']
  

  -facts_intsc_elec_scale <RealVector>

  FACTS Coulomb scale for intrares sc-sc pairs: [1-4, 1-5, >1-5]
  Default: ['0.0', '0.0', '0.0']
  

  -facts_intsc_solv_scale <RealVector>

  FACTS GB scale for intrares sc-sc pairs: [1-4, 1-5, >1-5]
  Default: ['1.0', '0.0', '0.0']
  

  -facts_charge_dir <String>

  directory where residue topology files for FACTS charge are stored
  Default: "scoring/score_functions/facts"
  

  -facts_eff_charge_dir <String>

  directory where residue topology files for FACTS charge are stored
  Default: "scoring/score_functions/facts/eff"
  

  -facts_plane_aa <StringVector>

  AAs to apply plane rule
  

  -facts_eq_type <String>

  FACTS equation type
  Default: "exact"
  

  -ignore_terminal_ss_elements <Integer>

  number of secondary structure elements to be ignored
  Default: 0
  

  -length_dep_srbb <Boolean>

  Enable helix-length-dependent sr backbone hbonds
  Default: false
  

  -ldsrbb_low_scale <Real>

  Helix-length-dependent scaling at minlength.
  Default: 0.5
  

  -ldsrbb_high_scale <Real>

  Helix-length-dependent scaling at maxlength.
  Default: 2.0
  

  -ldsrbb_minlength <Integer>

  Helix-length-dependent scaling minlength.
  Default: 4
  

  -ldsrbb_maxlength <Integer>

  Helix-length-dependent scaling maxlength.
  Default: 17
  

  -max_motif_per_res <Real>

  maximum value for motifs
  Default: 3.0
  

  -max_contacting_ss <Integer>

  maximum number of interconnecting SS
  Default: 4
  

  -motif_ignore_symmmetry <Boolean>

  only counts motifs inside monomer
  Default: true
  

  -motif_residues <IntegerVector>

  which residue numbers to calculate motifs
  

  -netcharge_setup_file <StringVector>

  The filename of one or more setup files for the netcharge scoring term. (Multiple such files can be listed, separated by a space.) The default location for these files (which have a .charge extension) is /database/scoring/score_functions/netcharge/.
  

  -ms_dist_midpoint <Real>

  distance midpoint for distance factor for HRF_MSLabeling score term
  Default: 9.0
  

  -ms_dist_exponent <Real>

  distance exponent for distance factor for HRF_MSLabeling score term
  Default: 0.1
  

  -ms_fit_slope <Real>

  slope for burial measure calc from lnPF for HRF_MSlabeling score term
  Default: 3.827
  

  -ms_fit_intercept <Real>

  intercept for burial measure calc from lnPF for HRF_MSlabeling score term
  Default: 36.202
  

  -ms_fade_outer <Real>

  outer limit for FadeFunc in HRF_MSLabeling score term
  Default: 10.0
  

  -ms_fade_dist <Real>

  fade distance for FadeFunc in HRF_MSLabeling score term
  Default: 5.0
  

  -nmer_ref_energies <String>

  nmer ref energies database filename
  

  -nmer_ref_energies_list <String>

  list of nmer ref energies database filenames
  

  -nmer_pssm <String>

  nmer pssm database filename
  

  -nmer_pssm_list <String>

  list of nmer pssm database filenames
  

  -nmer_pssm_scorecut <Real>

  nmer pssm scorecut gate for ignoring lowscore nmers
  Default: 0.0
  

  -nmer_svm <String>

  nmer svm filename (libsvm)
  

  -nmer_svm_list <String>

  list of nmer svm filenames (libsvm)
  

  -nmer_svm_scorecut <Real>

  nmer svm scorecut gate for ignoring lowscore nmers
  Default: 0.0
  

  -nmer_svm_aa_matrix <String>

  nmer svm sequence encoding matrix filename
  

  -nmer_svm_term_length <Integer>

  how many up/dnstream res to avg and incl in svm sequence encoding
  Default: 3
  

  -nmer_svm_pssm_feat <Boolean>

  add pssm features to svm encoding?
  Default: true
  

  -nmer_ref_seq_length <Integer>

  length of nmers in nmer_ref score
  Default: 9
  

  -just_calc_rmsd <Boolean>

  In rna_score, just calculate rmsd – do not replace score.
  Default: false
  

  -envsmooth_zero_negatives <Boolean>

  use alternative envsmooth table with a floor of 0.0 (envsmooth awards no energy bonus)
  Default: false
  

  -rama_power <Real>

  If rama > 0.0, raise to the nth power. This has been useful for Foldit design. Note that this creates derivative discontinuities, so it should be used with caution! If not specified, the default rama behaviour (no power function) is preserved.
  Default: 1.0
  

  -ideal_sugars <Boolean>

  Triggers loading of only the ideal chair conformations of sugars with 6 member rings.
  Default: false
  

  -hbond_fade <Real>

  fade_factor for hbond geometry softmax
  Default: 2.5
  

  -hbond_new_sp3_acc <Boolean>

  fade_factor for hbond geometry softmax
  Default: false
  

  -alignment_sharpness <Real>

  When computing a harmonic function of RMSD for the alignment score, what should the standard deviation be?
  Default: 1.0
  

  -rna_torsion_potential <String>

  In RNA torsion calculation, directory containing 1D torsional potentials
  Default: "ps_04282011"
  

  -mc_optimize_dG <Boolean>

  Optimize the dG during MonteCarlo. It is not possible to do this within overall scoring, but where possible, do this during MC calls. This option does not globally-use the MonteCarloInterface object, but is protocol-specific. This is due to needing to know the interface it will be used on. dG is measured by the InterfaceAnalyzerMover. Supported Code is currently RosettaAntibodyDesign and RosettaDock
  Default: false
  

  -mc_interface_weight <Real>

  Weight of interface score if using MonteCarloInterface with a particular protocol.
  Default: 1.0
  

  -mc_total_weight <Real>

  Weight of total score if using MonteCarloInterface with a particular protocol
  Default: 0.0
  

  -voids_penalty_energy_containing_cones_cutoff <Integer>

  A parameter for the voids_penalty score term. The minimum number of cones projecting from side-chains in which a voxel must lie in order for that voxel to be considerd to be buried. Defaults to 6 cones.
  Default: 6
  

  -voids_penalty_energy_cone_dotproduct_cutoff <Real>

  A parameter for the voids_penalty score term. The cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector.
  Default: 0.1
  

  -voids_penalty_energy_cone_distance_cutoff <Real>

  A parameter for the voids_penalty score term. The cutoff value for the distance from the cone base at which we are considered no longer to be within the cone. Defaults to 8.0 Angstroms.
  Default: 8.0
  

  -voids_penalty_energy_disabled_except_during_packing <Boolean>

  If true, then the voids_penalty term is only evaluated during packing (and not scoring or minimizing). If false, then it is evaluated during packing and scoring (but not minimizing). True by default. Can be overridden for a particular ScoreFunction on a per-instance basis.
  Default: true
  

  -voids_penalty_energy_voxel_size <Real>

  The size, in Angstroms, of the voxels used in the voxel grid for the voids_penalty energy. Defaults to 0.5 A (a cube with a side of 0.5 Angstroms).
  Default: 0.5
  

  -voids_penalty_energy_voxel_grid_padding <Real>

  A parameter for the voids_penalty energy. This is the enlargement (on all sides) of the bounding box for the pose when setting up the voxel grid. Defaults to 1.0 A padding on all sides.
  Default: 1.0
  

• score:rna

  -rna <Boolean>

  rna option group
  

  -disable_orientation_dependent_rna_ch_o_bonds <Boolean>

  Do not use orientation-dependent potential for RNA carbon hydrogen bonds
  Default: false
  

  -rna_suite_potential <String>

  In RNA calculation, directory containing suite potentials
  Default: "Richardson"
  

  -suiteness_bonus <String>

  In RNA calculation, directory containing suiteness bonus definition
  Default: "Richardson"
  

  -rna_torsion_skip_chainbreak <Boolean>

  Don't score RNA torsions located at the chain_breaks (aside from the ones that will be closed)
  Default: true
  

  -rna_chemical_shift_verbose <Boolean>

  print out chemical shifts; useful for debug
  Default: false
  

  -rna_chemical_shift_larmord <Boolean>

  Use LARMORD to calculate 1H chemical shifts
  Default: false
  

  -rna_chemical_shift_exp_data <String>

  rna_chemical_shift_exp_data
  Default: ""
  

  -rna_chemical_shift_larmord_par <String>

  larmord parameters file
  Default: "larmord_1.0_nocut_parameters.dat"
  

  -rna_chemical_shift_larmord_wt <String>

  larmord expected accuracy file
  Default: "larmord_noweights.txt"
  

  -rna_chemical_shift_larmord_ref <String>

  larmord reference chemical shift file
  Default: "larmord_1.0_reference_shifts.dat"
  

  -rna_chemical_shift_larmord_nei <String>

  larmord neighbor atom shift file
  Default: "larmord_1.0_neighbor_atoms.dat"
  

  -rna_chemical_shift_larmord_cut <Real>

  larmord distance cutoff
  Default: 9999.9
  

  -rna_chemical_shift_larmord_beta <Real>

  larmord beta value (the exponent)
  Default: -3.0
  

  -rna_chemical_shift_H5_prime_mode <String>

  rna_chemical_shift_H5_prime_mode
  Default: ""
  

  -rna_chemical_shift_include_res <IntegerVector>

  rna_chemical_shift_include_res
  

  -DMS_separate_features <Boolean>

  in RNA DMS scoring, calculate N1-bonded, occupancy, and binding-energy-based scores as if they were uncorrelated features and sum scores.
  Default: false
  

  -DMS_careful_base_pair_classifier <Boolean>

  in RNA lo-res DMS scoring, use detailed base pair classification to assess lores score
  Default: false
  

  -rna_chem_map_lores_weight <Real>

  In RNA lo-res chemical mapping scoring, final strength of rna_chem_map_lores term when -data_file is specified.
  Default: 0.0
  

  -use_2prime_OH_potential <Boolean>

  Use torsional potential for RNA 2prime OH.
  Default: true
  

  -use_rna_chi_potential <Boolean>

  Use chi potential for RNA glyocosidic torsion.
  Default: true
  

  -include_neighbor_base_stacks <Boolean>

  In RNA score calculation, include stacks between i,i+1
  Default: false
  

  -FA_low_res_rnp_scoring <Boolean>

  RNA/protein low-res scoring using full atom protein residues
  Default: false
  

  -free_suite_bonus <Real>

  Amount to reward virtualization of a nucleotide suite
  Default: -1.0
  

  -free_sugar_bonus <Real>

  Amount to reward virtualization of a sugar/ribose
  Default: -1.0
  

  -free_2HOprime_bonus <Real>

  Amount to reward virtualization of a 2'-OH
  Default: -0.5
  

  -syn_G_potential_bonus <Real>

  Amount to reward syn chi conformation of guanosine
  Default: 0.0
  

  -rna_bulge_bonus_once_per_loop <Boolean>

  For legacy stepwise term rna_bulge in SWM runs, compute bulge bonus on a per-loop basis, rather than a bonus for each virtual residue.
  Default: true
  

  -pack_phosphate_penalty <Real>

  Amount to penalize instantiation of a 5' or 3' phosphate
  Default: 0.25
  

• score:saxs

  -saxs <Boolean>

  saxs option group
  

  -min_score <Real>

  minimum value of saxs score; the parameter is used to flatten the energy funnel around its minimum
  Default: -5
  

  -custom_ff <String>

  Name of config file providing extra from factors
  Default: ""
  

  -print_i_calc <String>

  File to optionally write scaled computed spectra
  Default: ""
  

  -ref_fa_spectrum <File>

  reads reference full-atom spectrum from a file
  

  -ref_cen_spectrum <File>

  reads reference centroid spectrum from a file
  

  -ref_spectrum <File>

  reads reference spectrum from a file
  

  -ref_pddf <File>

  reads reference pairwise distance distribution function
  

  -d_min <Real>

  minimum value of distance used in PDDF score evaluation (in [A])
  Default: 5.0
  

  -d_max <Real>

  maximum value of distance used in PDDF score evaluation (in [A])
  Default: 100.0
  

  -d_step <Real>

  step of distance used in PDDF score evaluation (in [A])
  Default: 0.1
  

  -q_min <Real>

  minimum value of q used in spectra calculations (in [A^-1])
  Default: 0.01
  

  -q_max <Real>

  maximum value of q used in spectra calculations (in [A^-1])
  Default: 0.25
  

  -q_step <Real>

  step of q used in spectra calculations (in [A^-1])
  Default: 0.01
  

  -fit_pddf_area <Boolean>

  PDDF curve for a scored pose will be normalized to match the area under the reference PDDF curve
  Default: false
  

• score:fiber_diffraction

  -fiber_diffraction <Boolean>

  fiber_diffraction option group
  

  -layer_lines <File>

  reads layer_lines from a file
  

  -a <Real>

  number of subunits per repeat
  Default: 0
  

  -b <Real>

  number of turns per repeat
  Default: 0
  

  -p <Real>

  subunit rise
  Default: 0
  

  -radius <Real>

  helical radius
  Default: 0
  

  -resolution_cutoff_low <Real>

  ignore intensity data below this point
  Default: 0.05
  

  -resolution_cutoff_high <Real>

  ignore intensity data above this point
  Default: 0.5
  

  -max_bessel_order <Integer>

  maximum number of bessel orders used in simulations
  Default: 50
  

  -cn_symmetry <Integer>

  cn symmetry at one z level (along fibrilar axis)
  Default: 0
  

  -b_factor <Real>

  b_factor value
  Default: 20
  

  -b_factor_solv <Real>

  b_factor_solv value
  Default: 400
  

  -b_factor_solv_K <Real>

  b_factor_solv_K value
  Default: 0.4
  

  -grid_reso <Real>

  resolution for density sampling on the grid
  Default: 0.5
  

  -grid_r <Integer>

  number of grid points along r
  Default: 256
  

  -grid_phi <Integer>

  number of grid points along phi
  Default: 128
  

  -grid_z <Integer>

  number of grid points along z
  Default: 256
  

  -qfht_K1 <Real>

  value of K1 for Hankel sampling
  Default: 2.0
  

  -qfht_K2 <Real>

  value of K2 for Hankel sampling
  Default: 2.2
  

  -chi_iterations <Integer>

  number of iterations to calculate chi e.g. number of layer lines
  Default: 0
  

  -rfactor_refinement <Boolean>

  R-factor refinement
  Default: false
  

  -output_fiber_spectra <Boolean>

  Output intensity, reciprocal R, layer line
  Default: false
  

  -gpu_processor <Integer>

  GPU processor number - for systems with more than 1
  Default: 0
  

  -centroid_density_mass <Real>

  density mass of centroid
  Default: 0.0
  

• score:occ_sol_fitted

  -occ_sol_fitted <Boolean>

  occ_sol_fitted option group
  

  -Ntrp_amp_scaling <Real>

  scaling factor for Ntrp atoms's amplitude of the gaussian
  Default: 1.0
  

  -NH2O_amp_scaling <Real>

  scaling factor for NH2O atoms's amplitude of the gaussian
  Default: 1.0
  

  -Nlys_amp_scaling <Real>

  scaling factor for Nlys atoms's amplitude of the gaussian
  Default: 1.0
  

  -Narg_amp_scaling <Real>

  scaling factor for Narg atoms's amplitude of the gaussian
  Default: 1.0
  

  -Nbb_amp_scaling <Real>

  scaling factor for Nbb atoms's amplitude of the gaussian
  Default: 1.0
  

  -Nhis_amp_scaling <Real>

  scaling factor for Nhis atoms's amplitude of the gaussian
  Default: 1.0
  

  -OH_amp_scaling <Real>

  scaling factor for OH atoms's amplitude of the gaussian
  Default: 1.0
  

  -ONH2_amp_scaling <Real>

  scaling factor for ONH2 atoms's amplitude of the gaussian
  Default: 1.0
  

  -OOC_amp_scaling <Real>

  scaling factor for OOC atoms's amplitude of the gaussian
  Default: 1.0
  

  -Oaro_amp_scaling <Real>

  scaling factor for Oaro atoms's amplitude of the gaussian
  Default: 1.0
  

  -Oet2_amp_scaling <Real>

  scaling factor for Oet2 atoms's amplitude of the gaussian
  Default: 1.0
  

  -Oet3_amp_scaling <Real>

  scaling factor for Oet3 atoms's amplitude of the gaussian
  Default: 1.0
  

  -OCbb_amp_scaling <Real>

  scaling factor for OCbb atoms's amplitude of the gaussian
  Default: 1.0
  

  -HOH_amp_scaling <Real>

  scaling factor for HOH atoms's amplitude of the gaussian
  Default: 1.0
  

  -OPha_amp_scaling <Real>

  scaling factor for OPha atoms's amplitude of the gaussian
  Default: 1.0
  

  -OHha_amp_scaling <Real>

  scaling factor for OHha atoms's amplitude of the gaussian
  Default: 1.0
  

  -OC3_amp_scaling <Real>

  scaling factor for OC3 atoms's amplitude of the gaussian
  Default: 1.0
  

  -OSi_amp_scaling <Real>

  scaling factor for OSi atoms's amplitude of the gaussian
  Default: 1.0
  

  -Oice_amp_scaling <Real>

  scaling factor for Oice atoms's amplitude of the gaussian
  Default: 1.0
  

• score:loop_close

  -loop_close <Boolean>

  loop_close option group
  

  -loop_fixed_cost <Real>

  For loop_close term, a fixed cost of instantiating an end of a Gaussian chain; calibrated based on RNA bulge/loop data
  Default: -0.29
  

  -allow_complex_loop_graph <Boolean>

  LoopGraph hack - allow sharing of loops between cycles
  Default: false
  

  -use_6D_potential <Boolean>

  for implicit modeling of RNA loops, use 6D potentials instead of simple 1D Gaussian chain model
  Default: false
  

  -force_6D_potential_file <String>

  use this 6D potential for all loop_close instead of database files (for testing only!)
  Default: ""
  

  -use_cubic_interp <Boolean>

  cubic interpolation for 6D potential, instead of polylinear
  Default: true
  

• packing

  -packing <Boolean>

  Packing option group
  

  -repack_only <Boolean>

  Disable design at all positions
  Default: false
  

  -prevent_repacking <Boolean>

  Disable repacking (or design) at all positions
  Default: false
  

  -cenrot_cutoff <Real>

  Cutoff to generate centroid rotamers
  Default: 0.16
  

  -ignore_ligand_chi <Boolean>

  Disable param file chi-angle based rotamer generation in SingleLigandRotamerLibrary
  Default: false
  

  -quasisymmetry <Boolean>

  Turn on quasisymmetric packing using when using RotamerLinks
  Default: false
  

  -ndruns <Integer>

  Number of fixbb packing iterations. Each time packing occurs, it will pack this many times and return only the best result. Implemented at level of PackRotamersMover.
  Range: 1-
  Default: 1
  

  -soft_rep_design <Boolean>

  Use larger LJ radii for softer potential
  

  -mainchain_h_rebuild_threshold <Real>

  Cutoff for rebuilding mainchain hydrogens during rotamer generation during packing. If the position of the hydrogen is less than the threshold from its ideal position, it is not rebuilt. Default 0.75 A.
  Default: 0.75
  

  -use_electrostatic_repulsion <Boolean>

  Use electrostatic repulsion
  

  -dump_rotamer_sets <Boolean>

  Output NMR-style PDB's with the rotamer sets used during packing
  

  -dunbrack_prob_buried <Real>

  fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'buried' residues
  Range: 0-1
  Default: 0.98
  

  -dunbrack_prob_nonburied <Real>

  fraction of possible dunbrack rotamers to include in each single residue rotamer set, for 'nonburied' residues
  Range: 0-1
  Default: 0.95
  

  -no_optH <Boolean>

  Do not optimize hydrogen placement at the time of a PDB load
  Default: true
  

  -optH_MCA <Boolean>

  If running optH, use the Multi-Cool Annealer (more consistent, but slower)
  Default: false
  

  -pack_missing_sidechains <Boolean>

  Run packer to fix residues with missing sidechain density at PDB load
  Default: true
  

  -preserve_c_beta <Boolean>

  Preserve c-beta positions during rotamer construction
  

  -flip_HNQ <Boolean>

  Consider flipping HIS, ASN, and GLN during hydrogen placement optimization (must turn off -no_optimizeH)
  

  -fix_his_tautomer <IntegerVector>

  seqpos numbers of his residus whose tautomer should be fixed during repacking
  Default: []
  

  -print_pymol_selection <Boolean>

  include pymol-style selections when printing a PackerTask
  Default: false
  

  -extrachi_cutoff <Integer>

  number of neighbors a residue must have before extra rotamers are used. default: 18
  Default: 18
  

  -resfile <FileVector>

  resfile filename(s). Most protocols use only the first and will ignore the rest; it does not track against -s or -l automatically.
  Default: ['"resfile"']
  

  -sc_branch_rotamers <Boolean>

  construct rotamers for conjugated side chains. Warning: results in deformation of the conjugation bond length and angles, so should be followed by some correction
  Default: ['false']
  

  -outeriterations_scaling <Real>

  Multiplier for number of outer iterations
  Default: 1.0
  

  -inneriterations_scaling <Real>

  Multiplier for number of inner iterations
  Default: 1.0
  

  -adducts <StringVector>

  Gives list of adduct names to generate for residue definitions. Each adduct name may be followed by an optional integer, which gives a maximum number of adducts of that type which will be generated.
  

  -use_input_sc <Boolean>

  Use rotamers from input structure in packing By default, input sidechain coords are NOT included in rotamer set but are discarded before the initial pack; with this flag, the the input rotamers will NOT be discarded. Note that once the starting rotamers are replaced by any mechanism, they are no longer included in the rotamer set (rotamers included by coordinates)
  

  -unboundrot <FileVector>

  Read 'native' rotamers from supplied PDB(s). Unlike -use_input_sc, these rotamers will not be lost during repacks. This option requires specific support from the protocol; it is NOT built in to PackerTask.initialize_from_command_line()
  

  -max_rotbump_energy <Real>

  discard rotamers with poor interactions with the background using the specified cutoff. Values must be in the range of 0 to 5.0.
  Default: 5.0
  

  -lazy_ig <Boolean>

  Force the packer to always allocate pair energy storage but procrastinate energy caclulation until each RPE is needed; each RPE is computed at most once. Memory use is quadratic in rotamers per residue. The InteractionGraphFactory will prefer the linear-memory interaction graph to the Lazy Interaction graph, so specifying both linmem_ig and lazy_ig results in the use of the linear-memory interaction graph. The Surface-series IGs (surface weight in scorefunction is nonzero) also overrides this IG.
  Default: false
  

  -double_lazy_ig <Boolean>

  Force the packer to always procrastinate allocation AND energy caclulation until each RPE is needed; each RPE is computed at most once. The InteractionGraphFactory will prefer the linear-memory interaction graph to the DoubleLazy Interaction graph, so specifying both linmem_ig and lazy_ig results in the use of the linear-memory interaction graph. The Surface-series IGs (surface weight in scorefunction is nonzero) also overrides this IG.
  Default: false
  

  -linmem_ig <Integer>

  Force the packer to use the linear memory interaction graph; each RPE may be computed more than once, but recently-computed RPEs are reused. The integer parameter specifies the number of recent rotamers to store RPEs for. 10 is the recommended size. Memory use scales linearly with the number of rotamers at about 200 bytes per rotamer per recent rotamers to store RPEs for (~4 KB per rotamer by default)
  Default: 10
  

  -multi_cool_annealer <Integer>

  Alternate annealer for packing. Runs multiple quence cycles in a first cooling stage, and tracks the N best network states it observes. It then runs low-temperature rotamer substitutions with repeated quenching starting from each of these N best network states. 10 is recommended.
  

  -minpack_temp_schedule <RealVector>

  Alternate annealing schedule for min_pack.
  

  -minpack_inner_iteration_scale <Integer>

  The number of inner iterations per rotamer to run at each temperature in min pack.
  

  -minpack_disable_bumpcheck <Boolean>

  Disable bump check in min pack (i.e. include rotamers that collide with the background.
  

• packing:ex1

  -ex1 <Boolean>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex1 rotamers
  

• packing:ex2

  -ex2 <Boolean>

  use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex2 rotamers
  

• packing:ex3

  -ex3 <Boolean>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi3 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex3 rotamers
  

• packing:ex4

  -ex4 <Boolean>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi4 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

  -operate <Boolean>

  apply special operations (see RotamerOperation class) on ex4 rotamers
  

• packing:ex1aro

  -ex1aro <Boolean>

  use extra chi1 sub-rotamers for aromatic residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:ex2aro

  -ex2aro <Boolean>

  use extra chi1 sub-rotamers for aromatic residues that pass the extrachi_cutoff
  

  -level <Integer>

  use extra chi2 sub-rotamers for all residues that pass the extrachi_cutoff The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:ex1aro_exposed

  -ex1aro_exposed <Boolean>

  use extra chi1 sub-rotamers for all aromatic residues
  

  -level <Integer>

  use extra chi1 sub-rotamers for all aromatic residues The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:ex2aro_exposed

  -ex2aro_exposed <Boolean>

  use extra chi2 sub-rotamers for all aromatic residues
  

  -level <Integer>

  use extra chi2 sub-rotamers for all aromatic residues The integers that follow the ex flags specify the pattern for chi dihedral angle sampling There are currently 8 options; they all include the original chi dihedral angle. NO_EXTRA_CHI_SAMPLES 0 original dihedral only; same as using no flag at all EX_ONE_STDDEV 1 Default +/- one standard deviation (sd); 3 samples EX_ONE_HALF_STEP_STDDEV 2 +/- 0.5 sd; 3 samples EX_TWO_FULL_STEP_STDDEVS 3 +/- 1 & 2 sd; 5 samples EX_TWO_HALF_STEP_STDDEVS 4 +/- 0.5 & 1 sd; 5 samples EX_FOUR_HALF_STEP_STDDEVS 5 +/- 0.5, 1, 1.5 & 2 sd; 9 samples EX_THREE_THIRD_STEP_STDDEVS 6 +/- 0.33, 0.67, 1 sd; 7 samples EX_SIX_QUARTER_STEP_STDDEVS 7 +/- 0.25, 0.5, 0.75, 1, 1.25 & 1.5 sd; 13 samples
  Default: 1
  

• packing:exdna

  -exdna <Boolean>

  use extra dna rotamers
  

  -level <Integer>

  extra dna rotamer sample level – rotbuilder converts from 0-7 to number
  Default: 1
  

• archive

  -archive <Boolean>

  archive option group
  

  -reread_all_structures <Boolean>

  ignore pool file... reread from batches
  Default: false
  

  -completion_notify_frequency <Integer>

  tell Archive every X completed decoys
  Default: 100
  

• carbohydrates

  -carbohydrates <Boolean>

  carbohydrates option group
  

  -glycam_pdb_format <Boolean>

  Indicates that the input PDB files were generated by GLYCAM and thus join any HO- or RO- "residues" to the following one since Rosetta is smart enough to patch reducing ends. The default value is false.
  Default: false
  

  -linkage_conformer_data_file <String>

  Specify the file where glycosidic linkage conformer torsion angle statistical data is stored. The default directory is database/chemical/carbohydrates/linkage_conformers/but any path can be provided. The default filename is default.table
  Default: "default.table"
  

• carbohydrates:glycan_relax

  -glycan_relax <Boolean>

  glycan_relax option group
  

  -glycan_relax_test <Boolean>

  Indicates to go into testing mode for Glycan Relax. Will try all torsions in a given PDB in a linear fashion
  Default: false
  

  -glycan_relax_rounds <Integer>

  Number of rounds to use for Glycan Relax. Total rounds is this # times number of glycan residues in movemap
  Default: 25
  

  -min_rings <Boolean>

  Minimize Carbohydrate Rings during minimization? Otherwise, we keep them at their input values (which is recommended).
  Default: false
  

  -pack_glycans <Boolean>

  Pack Glycan OH groups during Glycan Relax. Currently time consuming
  Default: false
  

  -final_min_glycans <Boolean>

  Do a final minimization of glycans after glycan relax protocol?
  Default: true
  

  -glycan_relax_movie <Boolean>

  Make a movie of accepts and trials (send to pymol)
  Default: false
  

  -glycan_relax_kt <Real>

  KT for GlycanRelaxMover
  Default: 2.0
  

  -glycan_relax_refine <Boolean>

  Set the protocol to not start from a random conformation, and instead refine the structure.
  Default: false
  

  -cartmin <Boolean>

  Use Cartesian-space minimization instead of dihedral
  Default: false
  

  -tree_based_min_pack <Boolean>

  Use a random-tree based method to minimize and pack instead of minimizing and packing all of them during the randommover selection. This makes the speed of the algorithm mostly-linear with the addition of more glycans, and wastes less time packing and minimizing
  Default: true
  

  -population_based_conformer_sampling <Boolean>

  Use the populations of the conformers as probabilities during our linkage conformer sampling. This makes it harder to overcome energy barriers with more-rare conformers
  Default: false
  

  -conformer_sampling_sd <Real>

  Number of SDs to sample within during conformer sampling.
  Default: 2.0
  

  -uniform_sd_sampling <Boolean>

  Set whether if we are sampling uniform within the set number of standard deviations or by uniform within the SD.
  Default: true
  

• carbohydrates:clash_check

  -clash_check <Boolean>

  clash_check option group
  

  -glycan_branches <StringVector>

  Required. Vector of glycan branches. Rosetta Residue numbering or PDB like RosettaScripts
  

  -check_chains <StringVector>

  Required. A list of chains to compute chain-based clashes. If not given, will only compute glycan-glycan clashes!
  

  -soft_clash <Real>

  When we calculate atom-atom distances using VDW, clash if distance < (atomI_vdw + atomJ_vdw)*(1 - soft_clash)
  Default: 0.33
  

  -cb_clash_distance <Real>

  NOT CURRENTLY USED. Distance for CB distance clash check. Residue is clashing if at least 1 atom is less than this distance
  

  -ignore_hydrogens <Boolean>

  Should we calculate only heavy-heavy atom clashes?
  Default: false
  

  -ignore_full_res_output <Boolean>

  Should we output each glycan residue clash information in scorefile? Ignoring will make scorefile a bit smaller.
  Default: false
  

  -output_per_glycan_data <Boolean>

  Should we output per glycan branch data? Easy to compute later on if full res output is on.
  Default: false
  

• rings

  -rings <Boolean>

  rings option group
  

  -lock_rings <Boolean>

  Sets whether or not alternative ring conformations will be sampled by the protocol, (e.g, ring flips or puckering). Only low-energy conformers will be sampled, if known. Otherwise, all ideal ring conformers will be sampled. The default value is false.
  Default: false
  

  -idealize_rings <Boolean>

  Sets whether or not the ring conformations of input poses are idealized (set to the lowest-energy ring conformer, according to the toplogy file for that residue). The default is false: the input ring conformations will be used.
  Default: false
  

  -sample_high_energy_conformers <Boolean>

  Sets whether or not even ring conformations that are energy energy maxima will be sampled by the protocol. The default value is false; however, if the low energy ring conformers are not listed in the topology files, all ideal ring conformers will be sampled anyway.
  Default: false
  

• chemical

  -chemical <Boolean>

  chemical option group
  

  -exclude_patches <StringVector>

  Names of the residue-type-set patches which should not be applied; if you know which patches you do not need for a particular run, this flag can reduce your memory use
  

  -include_patches <StringVector>

  Names of the residue-type-set patches which should be applied even if excluded/commented out in patches.txt; useful for testing non-default patches
  

  -add_atom_type_set_parameters <StringVector>

  Additional AtomTypeSet extra-parameter files that should be read; format is a sequence of paired strings: <atom-type-set-tag1> <filename1> <atom-type-set-tag2> <filename2> ...
  

  -set_atom_properties <StringVector>

  Modify atom properties (the ones in <atom-set>/atom_properties.txt) from the command line. Happens at time of AtomTypeSet creation inside ChemicalManager.cc. Format is: -chemical:set_atom_properties <atom-set1>:<atom_name1>:<param1>:<setting1> <atom-set2>:<atom2>:<param2>:<setting2> ... For example: '-chemical:set_atom_properties fa_standard:OOC:LK_DGFREE:-5 fa_standard:ONH2:LJ_RADIUS:0.5'
  

  -patch_selectors <StringVector>

  allow patch files that have CMDLINE_SELECTOR tags can be switched on with this option
  Default: []
  

  -override_rsd_type_limit <Boolean>

  over-ride cap on number of residue types.
  Default: false
  

  -clone_atom_types <StringVector>

  Optionally clone atom types; copies all properties, which can then be diverged via -set_atom_properties. -clone_atom_types format should be:: -clone_atom_types <set1>:<atomname1>:<cloned-atomname1> <set2>:<atomname2>:<cloned-atomname2> ...; for example: '-chemical:clone_atom_types fa_standard:OOC:OOC2'
  

  -reassign_atom_types <StringVector>

  Switch the atomtype assignments for atoms in specified residue types. Useful along with -clone_atom_types. -reassign_atom_types format should be:: -reassign_atom_types <rsd-type-set1-name>:<rsd-type1-name>:<atom-type1-name>:<new-atom-type1-name> <rsd-type-set2-name>:<rsd-type2-name>:<atom-type2-name>:<new-atom-type2-name> ...; for example: '-chemical:reassign_atom_types fa_standard:ARG:NE:NtpR'
  

  -reassign_icoor <StringVector>

  Update icoor parameters for specified atom types. -reassign_icoor format should be:: -reassign_icoor <rsd-type-set1-name>:<rsd-type1-name>:<atom1-name>:<the-six-icoor-params-as-a-comma-separated-list> <rsd-type-set2-name>:<rsd-type2-name>:<atom2-name>:<icoorparams2> ...; for example: -chemical:reassign_icoor fa_standard:ADE:UPPER:-180,60,1.6,O3',C3',C4'
  

  -set_atomic_charge <StringVector>

  Modify atomic charge from the command line. Happens at time of params file reading, so changes will propagate to patched versions of the residue type. Format is: -chemical:set_atomic_charge <rsd-type-set1-name>:<rsd-type1-name>:<atom1-name>:<new-charge> <rsd-type-set2-name>:<rsd-type2-name>:<atom2-name>:<new-charge> ... For example: '-chemical:set_atomic_charge fa_standard:ARG:NE:-1'
  

  -set_patch_atomic_charge <StringVector>

  Modify patch atomic charge from the command line. Happens at time of patch file reading, so changes will propagate to patched versions of the residue type. Uses a simplified version of the residue selector so will probably not work for patches with complex selector logic. format should be:: -chemical:set_patch_atomic_charge <rsd-type-set1-name>:<rsd-type1-name>:<patch-name>:<atom1-name>:<new-charge> ... For example: '-chemical:set_atomic_charge fa_standard:PRO:NtermProteinFull:1H:-1'
  

  -enlarge_H_lj <Boolean>

  Use larger LJ_WDEPTH for Hs to avoid RNA clashes
  Default: false
  

  -no_hbonds_to_ether_oxygens <Boolean>

  no H-bonds to nucleic acid ether oxygens O3', O4', O5' – deprecated
  Default: false
  

  -unset_acceptor_ether_oxygens <Boolean>

  nucleic acid ether oxygens O3', O4', O5' are not counted as acceptors
  Default: false
  

• constraints

  -constraints <Boolean>

  constraints option group
  

  -exit_on_bad_read <Boolean>

  exit if error is encountered reading constraints
  Default: true
  

  -cst_file <StringVector>

  constraints filename(s) (for proteins, applied in centroid mode; when multiple files are given a random one will be picked).
  

  -cst_weight <Real>

  No description
  Default: 1.0
  

  -max_cst_dist <Real>

  No description
  Default: 12.0
  

  -cst_fa_file <StringVector>

  constraints filename(s) for fullatom. When multiple files are given a random one will be picked.
  

  -cst_fa_weight <Real>

  No description
  Default: 1.0
  

  -normalize_mixture_func <Boolean>

  No description
  Default: false
  

  -penalize_mixture_func <Boolean>

  No description
  Default: true
  

  -forest_file <File>

  file with constraintforest
  Default: ""
  

  -compute_total_dist_cst <Boolean>

  only relevant for debug: atom_pair_constraints during abinito depends on seq_sep, this computes also the score without regarding seq_sep
  Default: false
  

  -cull_with_native <Integer>

  if option is set all constraints that violate the native structure with more than X are thrown out!
  Default: 1
  

  -dump_cst_set <File>

  dump the cstset_ to file
  Default: ""
  

  -evaluate_max_seq_sep <IntegerVector>

  evaluate constraints to this seq-sep [vector]
  Default: 0
  

  -named <Boolean>

  enable named constraints to avoid problems with changing residue-types e.g., cutpoint-variants
  Default: false
  

  -no_cst_in_relax <Boolean>

  remove constraints for relax
  Default: false
  

  -no_linearize_bounded <Boolean>

  dont switch to linearized in BOUNDED func
  Default: false
  

  -pocket_constraint_weight <Real>

  Weight of the Pocket Constraint
  Default: 0
  

  -pocket_zero_derivatives <Boolean>

  Return zero for PocketConstaint derivatives
  Default: false
  

  -viol <Boolean>

  show violations
  Default: false
  

  -viol_level <Integer>

  how much detail for violation output
  Default: 1
  

  -viol_type <String>

  work only on these types of constraints
  Default: ""
  

  -sog_cst_param <Real>

  weight parameter for SOGFunc constraints
  Default: 0.0
  

  -sog_upper_bound <Real>

  Upper cutoff for SOGFunc constraints
  Default: 10.0
  

  -epr_distance <Boolean>

  use epr distance potential
  Default: false
  

  -combine <Integer>

  combine constraints randomly into OR connected groups (Ambiguous). N->1
  Default: 1
  

  -combine_exclude_region <File>

  core-defintion file do not combine constraints that are core-core
  

  -skip_redundant <Boolean>

  skip redundant constraints
  Default: false
  

  -skip_redundant_width <Integer>

  radius of influence for redundant constraints
  Default: 2
  

  -force_pdb_info_mapping <BooleanVector>

  force PDB info mapping for residues in cst file, using " " as default chain.
  Default: []
  

• corrections

  -corrections <Boolean>

  corrections option group
  

  -beta <Boolean>

  Use the most-recent (curr Nov 15) beta score function
  Default: false
  

  -beta_cart <Boolean>

  Use the most-recent (curr Nov 15) beta score function for nonideal optimization
  Default: false
  

  -beta_nov16 <Boolean>

  Use the November 2015 beta score function
  Default: false
  

  -beta_nov16_cart <Boolean>

  Use the November 2015 beta score function for nonideal optimization
  Default: false
  

  -beta_july15 <Boolean>

  Use the July 2015 beta score function
  Default: false
  

  -beta_july15_cart <Boolean>

  Use the July 2015 beta score function for nonideal optimization
  Default: false
  

  -beta_patch <Boolean>

  Apply the extra patch to most-recent (curr Nov 15) beta_score_function.
  Default: false
  

  -newdna <Boolean>

  Apply some dna-specific mods to chemical/scoring (for testing)
  Default: false
  

  -restore_talaris_behavior <Boolean>

  Use talaris score function and residue_type_set
  Default: false
  

  -correct <Boolean>

  turn on default corrections:See src/core/init/score_function_corrections.cc. Note that this is a flag for the older score12 scorefunction, which should NOT be used with talaris2013, talaris2014, ref2015, or the beta scorefunctions.
  Default: false
  

  -hbond_sp2_correction <Boolean>

  turn on the hbond Sp2 correction with a single flag use with sp2_correction.wts. Note, these weight sets are chosen automatically by default. -score::hb_sp2_chipen -hb_sp2_BAH180_rise 0.75 -hb_sp2_outer_width 0.357 -hb_fade_energy -hbond_measure_sp3acc_BAH_from_hvy -lj_hbond_hdis 1.75 -lj_hbond_OH_donor_dis 2.6 -hbond_params sp2_elec_params -expand_st_chi2sampling -smooth_fa_elec -elec_min_dis 1.6 -elec_r_option false -chemical::set_atom_properties fa_standard:ONH2:LK_DGFREE:-5.85 fa_standard:NH2O:LK_DGFREE:-7.8 fa_standard:Narg:LK_DGFREE:-10.0 fa_standard:OH:LK_DGFREE:-6.70
  

  -facts_default <Boolean>

  turn on default options for FACTS use with scorefacts.wts. Incompatible with hbond_sp2_correction option. -correct -lj_hbond_hdis 2.3 -lj_hbond_OH_donor_dis 3.4 -use_bicubic_interpolation -hbond_params sp2_elec_params -hb_sp2_chipen -hbond_measure_sp3acc_BAH_from_hby -facts_GBpair_cut 10.0 -facts_min_dis 1.5 -facts_dshift 1.4 -facts_die 1.0 -facts_kappa 12.0 -facts_asp_patch 3 -facts_intrares_scale 0.4 -facts_elec_sh_exponent 1.8
  Default: false
  

• corrections:score

  -score <Boolean>

  score option group
  

  -bbdep_omega <Boolean>

  Enable phi-psi dependent omega
  Default: true
  

  -bbdep_bond_params <Boolean>

  Enable phi-psi dependent bondlengths and bondangles
  

  -bbdep_bond_devs <Boolean>

  Enable phi-psi dependent deviations for bondlengths and bondangles
  

  -fa_dun_canonicals_use_voronoi <Boolean>

  If true, then canonical amino acids use Voronoi-style detection of neareset rotamer wells during fa_dun scoring instead of hard-coded rotamer well definitions. False by default (i.e. hard-coded definitions are used by defaults).
  Default: false
  

  -fa_dun_noncanonicals_use_voronoi <Boolean>

  If true, then noncanonical amino acids and other polymer building blocks use Voronoi-style detection of neareset rotamer wells during fa_dun scoring instead of hard-coded rotamer well definitions. True by default (i.e. Voronoi-style detection is used by default). Setting this to false creates problems with many noncanonicals that have rotamer wells that aren't simple gauche+/gauche-/anti wells.
  Default: true
  

  -fa_dun_correct_rotamer_well_order <Boolean>

  If true, the rotamer well order for rotamer files is corrected automatically to the Rosetta convention of lowest to highest in the range [0,360). False by default.
  Default: false
  

  -no_his_his_pairE <Boolean>

  Set pair term for His-His to zero
  

  -no_his_DE_pairE <Boolean>

  Set pair term for His-Glu and His-Asp to zero
  

  -p_aa_pp <String>

  Name of scoring/score_functions/P_AA_pp/P_AA_PP potential file (search in the local directory first, then look in the database)
  Default: "scoring/score_functions/P_AA_pp/P_AA_pp"
  

  -p_aa_pp_nogridshift <Boolean>

  the format of p_aa_pp changed from using i*10+5 (5, 15, etc) to i*10 (0,10,etc.) as grid points
  

  -rama_not_squared <Boolean>

  Rama potential calculated as input for both rama and rama2b. By default, the potential is square for (ram a+entropy) > 1.0
  

  -rama_map <File>

  Ramachandran file used by rama
  Default: "scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4"
  

  -rama_pp_map <File>

  Ramachandran dir used by rama_prepro
  Default: "scoring/score_functions/rama/fd"
  

  -rama_map_average_L_flat <File>

  Ramachandran map that's the average of all canonical L amino acids, flattened to give equal probability to the allowed region. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/avg_L_rama.dat"
  

  -rama_map_sym_average_L_flat <File>

  Ramachandran map that's the average of all canonical L amino acids, flattened to give equal probability to the allowed region, and symmetrized. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/sym_all_rama.dat"
  

  -rama_map_sym_gly_flat <File>

  Ramachandran map for glycine, flattened to give equal probability to the allowed region and symmetrized. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/sym_G_rama.dat"
  

  -rama_map_sym_pro_flat <File>

  Ramachandran map for proline, flattened to give equal probability to the allowed region and symmetrized. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/sym_P_rama.dat"
  

  -rama_map_average_L_flat_stringent <File>

  Ramachandran map that's the average of all canonical L amino acids, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/avg_L_rama_str.dat"
  

  -rama_map_sym_average_L_flat_stringent <File>

  Ramachandran map that's the average of all canonical L amino acids, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency, and symmetrized. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/sym_all_rama_str.dat"
  

  -rama_map_sym_gly_flat_stringent <File>

  Ramachandran map for glycine, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency, and symmetrized. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/sym_G_rama_str.dat"
  

  -rama_map_sym_pro_flat_stringent <File>

  Ramachandran map for proline, flattened to give equal probability to the allowed region, with the allowed region selected with high stringency, and symmetrized. Lazily loaded; for sampling only.
  Default: "scoring/score_functions/rama/flat/sym_P_rama_str.dat"
  

  -rama_prepro_steep <Boolean>

  Use steep rama_prepro library
  Default: false
  

  -rama_prepro_nobidentate <Boolean>

  Use rama_prepro library derived by excluding bidentate Hbonding loop residues
  Default: false
  

  -cenrot <Boolean>

  Use the Centroid Rotamer Model.
  Default: false
  

  -dun10 <Boolean>

  Use the 2010 Dunbrack library instead of either the the 2002 library.
  Default: true
  

  -dun10_dir <String>

  Name of dun10 dir
  Default: "rotamer/ExtendedOpt1-5"
  

  -dun02_file <String>

  Name of dun02 input file
  Default: "rotamer/bbdep02.May.sortlib"
  

  -ch_o_bond_potential <String>

  Name of ch_o_bond potential file (search in the local directory first, then look in the database)
  Default: "scoring/score_functions/carbon_hbond/ch_o_bond_potential.dat"
  

  -lj_hbond_hdis <Real>

  Lennard Jones sigma value for hatms, classically it's been at 1.95 but the average A-H distance for hydrogen bonding is 1.75 from crystal structures. (momeara)
  Default: 1.75
  

  -lj_hbond_OH_donor_dis <Real>

  Lennard Jones sigma value for O in OH donor groups. Classically it has been 3.0 but the average distances from crystal structurs is 2.6 (momeara)
  Default: 2.6
  

  -score12prime <Boolean>

  Restore to score funciton parameters to score12 parameters and have getScoreFuntion return with score12prime.wts. The score12prime.wts differs from standard.wts + score12.wts_patch, in that the reference energies have been optimized with optE for sequence profile recovery
  Default: false
  

  -hbond_energy_shift <Real>

  The shift upwards (through addition) of the well depth for the hydrogen bond polynomials; this shift is applied before the weights are applied.
  Default: 0.0
  

  -hb_sp2_BAH180_rise <Real>

  The rise from -0.5 for the BAH=180 value for the additive chi/BAH sp2 potential
  Default: 0.75
  

  -hb_sp2_outer_width <Real>

  The width between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). Use 0.357 in conjunction with the hb_energy_fade flag.
  Default: 0.357
  

  -hb_sp2_chipen <Boolean>

  Experimental term for hydrogen bonds to sp2 acceptors: penalizes out-of-plane geometry by 67%
  Default: true
  

  -hbond_measure_sp3acc_BAH_from_hvy <Boolean>

  If true, then the BAH angle for sp3 (aka hydroxyl) acceptors is measured donor-hydrogen–acceptor-heavyatom–heavyatom-base instead of donor-hydrogen–accptor-heavyatom–hydroxyl-hydrogen
  Default: true
  

  -hb_fade_energy <Boolean>

  Rather than having a strict cutoff of hbond definition at 0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function.
  Default: true
  

  -hb_exclude_ether_oxygens <Boolean>

  no H-bonds to nucleic acid ether oxygens O3', O4', O5'
  Default: false
  

  -hb_cen_soft <Boolean>

  Use softer version of cen_hb term
  Default: false
  

  -use_bicubic_interpolation <Boolean>

  Instead of using bilinear interpolation to evaluate the Ramachandran, P_AA_pp and Dunbrack potentials, use bicubic interpolation. Avoids pile-ups at the grid boundaries where discontinuities in the derivatives frustrate the minimizer
  Default: true
  

  -dun_normsd <Boolean>

  Use height-normalized guassian distributions to model p(chi|phi,psi) instead of height-unnormalized gaussians
  Default: false
  

  -dun_entropy_correction <Boolean>

  Add Shannon entropy correction to rotamer energy: E = -logP + S
  Default: false
  

• corrections:chemical

  -chemical <Boolean>

  chemical option group
  

  -icoor_05_2009 <Boolean>

  New set of idealized coordinates for full atom, 05-2009
  

  -parse_charge <Boolean>

  Use PARSE charge set.
  

  -expand_st_chi2sampling <Boolean>

  Ugly temporary hack. Expand the chi2 sampling for serine and threonine in the fa_standard residue type set so that samples are taken every 20 degrees (instead of every 60 degrees. This will soon be changed in the SER and THR params files themselves. This flag can be used with any residue type set (including the pre-s fa_standard version, and with the fa_standard_05.2009_icoor version) but is unncessary for the talaris2013 version (currently named fa_standard) as the expanded SER and THR sampling is already encoded in .params files for these two residues
  Default: false
  

• corrections

  -shapovalov_lib_fixes_enable <Boolean>

  Apply new code by Maxim Shapovalov from Dunbrack Lab such as for reading/using dun, rama, prop libraries in new format and options for applying different bug fixes. False value will employ old libraries and old code.
  Default: true
  

• corrections:shapovalov_lib

  -shapovalov_lib <Boolean>

  shapovalov_lib option group
  

  -shap_dun10_enable <Boolean>

  Enable new Shapovalov's dun10 fix if the umbrella option is on, shapovalov_lib_fixes
  Default: true
  

  -shap_dun10_smooth_level <String>

  Smoothing level either numeric or word keyword, possible values are 1 or lowest_smooth, 2 or lower_smooth, 3 or low_smooth, 4 or average_smooth, 5 or higher_smooth, 6 or highest_smooth.
  Default: "1"
  

  -shap_dun10_dir <String>

  Name of the new format dun10 dir
  Default: "rotamer/shapovalov/StpDwn_5-5-5"
  

  -shap_dun10_use_minus_log_P_ignore_P <Boolean>

  Use minus log P from text libraries only and ignore any P.
  Default: false
  

  -shap_rama_enable <Boolean>

  Enable new Shapovalov's Rama fix if the umbrella option is on, shapovalov_lib_fixes
  Default: true
  

  -shap_rama_smooth_level <String>

  Smoothing level either numeric or word keyword, possible values are 1 or lowest_smooth, 2 or lower_smooth, 3 or higher_smooth, 4 or highest_smooth.
  Default: "4"
  

  -shap_rama_map <File>

  New Ramachandran file in the new format used by rama
  Default: "scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb"
  

  -shap_rama_nogridshift <Boolean>

  With correct flag there is a bug. Rama09_noEH_kernel25_it08.dat is used where prob values are reported exactly at the 10-deg grid while Rama_smooth_dyn.dat_ss_6.4 has values reported in the middle of bins. There is no need for 5-deg shift for newer Rama maps with values reported at the grid.
  Default: true
  

  -shap_p_aa_pp_enable <Boolean>

  Enable new Shapovalov's propensity map fix if the umbrella option is on, shapovalov_lib_fixes
  Default: true
  

  -shap_p_aa_pp_smooth_level <String>

  Smoothing level either numeric or word keyword, possible values are 1 or low_smooth, 2 or high_smooth.
  Default: "1"
  

  -shap_p_aa_pp <String>

  Name of the new Shapovalov's P_AA_PP potential file (search in the local directory first, then look in the database)
  Default: "scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa50/a20.prop"
  

• corrections:water

  -water <Boolean>

  water option group
  

  -exclude_exposed <Boolean>

  exclude point water rotamers with <= 16 CBs within 10 A
  Default: true
  

  -water_bump_check <Boolean>

  exclude water rotamers that dont pass energy bump check
  Default: false
  

  -lkb_overlap_distance <Real>

  intersection distance when solvating with lkball sites
  Default: 1.25
  

  -lkb_cluster_radius <Real>

  radius for clustering overlapping lkball sites
  Default: 0.35
  

  -wat_rot_params <String>

  for statistical-based placement of potential water positions
  Default: "sampling/waterrots/water.rots"
  

  -record_dwell <Boolean>

  record dwell time for all PWAT rotamers in FixbbPwatSimAnnealer
  Default: true
  

  -print_dwell <Boolean>

  create file with final raw PWAT dwell times from FixbbPwatSimAnnealer
  Default: false
  

  -dwell_name <String>

  file name for PWAT rotamer occupancies
  Default: "dwell.log"
  

  -pack_temp <Real>

  fixed annealing temperature
  Default: 0.3
  

  -spike_anneal <Boolean>

  anneal with temp spikes after each outeriteration
  Default: true
  

  -spike_steps_scale <Real>

  scale for n_totalrot 100 K temp spikes samples during annealing
  Default: 1.0
  

  -spike_cycles <Integer>

  number of rounds of temperature spiking for PWAT sampling
  Default: 50
  

  -innerit <Integer>

  number of fixed temp annealing steps
  Default: 250000
  

  -dwell_cutoff <Real>

  dwell time cutoff value for PWAT rotamers kept after normalizing by number of MC steps
  Default: 0.1200
  

  -cluster_radius <Real>

  radius from dwell-weighted centroid for growing PWAT rotamer clusters
  Default: 1.0
  

  -cluster_cutoff <Real>

  remove cluster if cumulative dwell time is not met
  Default: 0.4000
  

  -cluster_prefix <String>

  prefix for rotset cutoff and centroid outputs
  Default: ""
  

  -watlim_scale <Real>

  scale factor for waters kept if using limit_water: scale factor * # molten residues
  Default: 1.0
  

  -print_clusters <Boolean>

  option to turn on PWAT clustering
  Default: false
  

  -pointwater_params <String>

  PWAT: directory name for pointwater potential databases
  Default: "norm_trunc6"
  

  -ordered_pt_wat_penalty <Real>

  PWAT: Penalty for adding an ordered point water. Implemented through pointwater scoreterm.
  Default: 2.15037006642983
  

  -pointwat_wat_bonus <Real>

  PWAT: water-water bonus for nearby PWAT residues
  Default: 0.810638995223315
  

  -pointwat_wat_bonus_width <Real>

  PWAT: factor determining width of water-water bonus exponential function
  Default: 29.3807301999186
  

  -ordered_wat_penalty <Real>

  HOH: Penalty for adding an ordered water; implemented through ref scoreterm
  Default: 1.7
  

  -hbdon_H2O <Real>

  hydrogen bond donor strength for HOH residues
  Default: 1.15
  

  -hbacc_H2O <Real>

  hydrogen bond acceptor strength for HOH residues
  Default: 1.15
  

  -wat_rot_sampling <Real>

  Stepsize (in degrees) of rotatable waters
  Default: 30.0
  

  -wat_axis_sampling <Boolean>

  align O-H1 vector with nearby backbone O and sample about O-O axes
  Default: true
  

  -axis_rot_sampling <Real>

  Stepsize (in degrees) of rotatable waters when wat_axis_sampling is used
  Default: 15.0
  

  -include_vrt <Boolean>

  allow for water virtualization
  Default: true
  

• evaluation

  -evaluation <Boolean>

  evaluation option group
  

  -rmsd_target <FileVector>

  [vector] determine rmsd against this/these structure(s)
  

  -rmsd_column <StringVector>

  [vector] use xxx as column name: rms_xxx
  

  -rmsd_select <FileVector>

  [vector] a bunch of loop files which makes rmsds with tags: rms_XXX, where XXX is basename of file
  

  -align_rmsd_target <FileVector>

  [vector] determine rmsd against this/these structure(s) using simple sequence alignment
  

  -structural_similarity <FileVector>

  [vector] measure average similarity against these structures (option specifies a silent-file)
  

  -contact_map <Boolean>

  Calculate contact map similarity using the given native
  

  -jscore_evaluator <StringVector>

  Calculate scores using the given score function weights files and, residue type set names (e.g score12 fa_standard score3 centroid)
  

  -align_rmsd_column <StringVector>

  [vector] use xxx as column name for align_rmsd_target: rms_xxx
  

  -align_rmsd_fns <FileVector>

  [vector] of sequence alignments used for align_rmsd files
  

  -align_rmsd_format <String>

  format for sequence alignment between structures used in evaluation
  Default: "grishin"
  

  -rms_type <String>

  RNP if you want both protein and RNA RMSD, blank for protein
  Default: ""
  

  -predicted_burial_fn <String>

  file for burial predictions
  Default: ""
  

  -pool <File>

  find closest matching structure in this pool and report tag and rmsd
  

  -rmsd <FileVector>

  [vector/pairs] tripletts: rmsd_target (or NATIVE / IRMS) col_name selection_file (or FULL)
  

  -chirmsd <FileVector>

  [vector/tripletts]: rmsd_target (or NATIVE / IRMS ) col_name selection_file ( or FULL)
  

  -gdtmm <Boolean>

  for each rmsd evaluator also a gdtmm evaluator is created
  Default: false
  

  -gdttm <Boolean>

  for each rmsd evaluator also a gdttm evaluator is created
  Default: false
  

  -score_with_rmsd <Boolean>

  score the pose on the same subset of atoms as in the rmsd poses
  

  -constraints <FileVector>

  [vector] evaluate against these constraint sets
  

  -constraints_column <FileVector>

  [vector] use xxx as column name: cst_xxx
  

  -combined_constraints <FileVector>

  [vector] use xxx as cst-file but combine constraints before applying
  

  -combined_constraints_column <FileVector>

  [vector] use xxx as cst-file but combine constraints before applying
  

  -combine_statistics <Integer>

  repeat constraint evaluation X times to get statistics of constraint combination
  Default: 10
  

  -chemical_shifts <StringVector>

  compute chemical shift score with SPARTA+ use tuples: talos_file [cs]_column_name (ATTENTION uses filesystem)
  

  -sparta_dir <String>

  [optional] point to an external resource for the sparta directory (instead of minirosetta_database)
  Default: "SPARTA+"
  

  -cam_shifts <StringVector>

  compute chemical shift score with Camshift talos_file [cs]_column_name (ATTENTION uses filesystem)
  

  -pales <StringVector>

  compute Residual Dipolar Couplings using the PALES program (ATTENTION uses filesystem)
  

  -extra_score <FileVector>

  [vector] provide .wts files to generate extra columns
  

  -extra_score_patch <FileVector>

  [vector] provide .patch files, set NOPATCH for columns that are not patched
  

  -extra_score_column <StringVector>

  [vector] use xxx as column name: score_xxx
  

  -extra_score_select <FileVector>

  [vector] /rigid/ files for selection, use SELECT_ALL as placeholder
  

  -rdc_target <FileVector>

  [vector] as rmsd_target/column provide PDB wih missing density to compute RDC score on selected residues
  

  -symmetric_rmsd <Boolean>

  calculate the rmsd symmetrically by checking all chain orderings
  

  -rdc_column <StringVector>

  [vector] column names for rdc_select
  

  -rdc <StringVector>

  [vector] rdc-files and column names for RDC calculation
  

  -built_in_rdc <String>

  evaluate rdc from -in:file:rdc with standard score function and store under column xxx
  

  -jump_nr <Boolean>

  adds the JumpNrEvaluator for the nrjumps column
  Default: false
  

  -score_exclude_res <IntegerVector>

  Calculates a select_score column based on all residues not excluded by the command line vector
  

  -score_sscore_short_helix <Integer>

  defines the maximum length of a helix that is not scored if it terminates a loop
  Default: 5
  

  -score_sscore_maxloop <Integer>

  defines the maximum length of a loop that is still considered for the sscore - score
  Default: 3
  

  -window_size <Integer>

  Window size for local RMSD calculations in windowed_rmsd app
  Default: 5
  

  -I_sc <String>

  score function name used to calculate I_sc
  Default: "score12"
  

  -Irms <Boolean>

  will compute the docking interface rmsd
  Default: false
  

  -Ca_Irms <Boolean>

  will compute the docking Ca-atom interface rmsd
  Default: false
  

  -Fnat <Boolean>

  will compute the docking recovered fraction of native contacts
  Default: false
  

  -Lrmsd <Boolean>

  will compute the docking ligand rmsd
  Default: false
  

  -Fnonnat <Boolean>

  will compute the fraction of non-native contacts for docking
  Default: false
  

  -DockMetrics <Boolean>

  will compute all docking metrics (I_sc/Irms/Fnat/Lrmsd for now) for replica docking
  Default: false
  

• filters

  -filters <Boolean>

  filters option group
  

  -disable_all_filters <Boolean>

  turn off all centroid filters: RG, CO, and Sheet
  Default: false
  

  -disable_rg_filter <Boolean>

  turn off RG filter
  Default: false
  

  -disable_co_filter <Boolean>

  turn off contact order filter
  Default: false
  

  -disable_sheet_filter <Boolean>

  turn off sheet filter
  Default: false
  

  -set_pddf_filter <Real>

  Turns on PDDF filter with a given score cutoff
  Default: 5.0
  

  -set_saxs_filter <Real>

  Turns on SAXS energy filter with a given score cutoff
  Default: -3
  

• gpu

  -gpu <Boolean>

  Enable/Disable GPU support
  Default: true
  

  -device <Integer>

  GPU device to use
  Default: 1
  

  -threads <Integer>

  Max GPU threads to use
  Default: 2048
  

• jumps

  -jumps <Boolean>

  jumps option group
  

  -evaluate <Boolean>

  evaluate N-CA-C gemoetry for all jumps in the fold-tree
  Default: false
  

  -extra_frags_for_ss <File>

  use ss-def from this fragset
  Default: ""
  

  -fix_chainbreak <Boolean>

  minimize to fix ccd in re-runs
  Default: false
  

  -fix_jumps <File>

  read jump_file
  Default: ""
  

  -jump_lib <File>

  read jump_library_file for automatic jumps
  Default: ""
  

  -loop_definition_from_file <File>

  use ss-def from this file
  Default: ""
  

  -no_chainbreak_in_relax <Boolean>

  dont penalize chainbreak in relax
  Default: false
  

  -pairing_file <File>

  file with pairings
  Default: ""
  

  -random_sheets <IntegerVector>

  random sheet topology–> replaces -sheet1 -sheet2 ... select randomly up to N sheets with up to -sheet_i pairgins for sheet i
  Default: 1
  

  -residue_pair_jump_file <File>

  a file to define residue pair jump
  Default: ""
  

  -sheets <IntegerVector>

  sheet topology–> replaces -sheet1 -sheet2 ... -sheetN
  Default: 1
  

  -topology_file <File>

  read a file with topology info ( PairingStats )
  Default: ""
  

  -bb_moves <Boolean>

  Apply bb_moves ( wobble, small, shear) during stage3 and stage 4.
  Default: false
  

  -no_wobble <Boolean>

  Don t apply the useless wobble during stage3 and stage 4.
  Default: false
  

  -no_shear <Boolean>

  Don t apply the useless shear during stage3 and stage 4.
  Default: false
  

  -no_sample_ss_jumps <Boolean>

  sample jump-frags during folding
  Default: false
  

  -invrate_jump_move <Integer>

  give 5 here to have 5 torsion moves for each jump move
  Default: 10
  

  -chainbreak_weight_stage1 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -chainbreak_weight_stage2 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -chainbreak_weight_stage3 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -chainbreak_weight_stage4 <Real>

  the weight on chainbreaks
  Default: 1.0
  

  -ramp_chainbreaks <Boolean>

  ramp up the chainbreak weight stage1-0, stage2 0.25, stage3 alternating 0.5..2.5, stage4 2.5..4
  Default: true
  

  -increase_chainbreak <Real>

  multiply ramped chainbreak weight by this amount
  Default: 1.0
  

  -overlap_chainbreak <Boolean>

  use the overlap chainbrak term in stage4
  Default: false
  

  -sep_switch_accelerate <Real>

  constraints and chainbreak depend on in-chain-separation. Accelerate their enforcement 1+num_cuts()*<this_factor>
  Default: 0.4
  

  -dump_frags <Boolean>

  dump jump_fragments
  Default: false
  

  -njumps <Integer>

  number_of_jumps to select from library for each trajectory (membrane mode)
  Default: 1
  

  -max_strand_gap_allowed <Integer>

  merge strands if they less than X residues but same register
  Default: 2
  

  -contact_score <Real>

  the strand-weight will have a weight * contact_order component
  Default: 0.0
  

  -filter_templates <Boolean>

  filter hybridization protocol templates
  Default: false
  

• loops

  -loops <Boolean>

  loop modeling option group
  Default: true
  

  -cen_weights <String>

  ScoreFunction weights file for centroid phase of loop-modeling
  Default: "cen_std"
  

  -cen_patch <String>

  ScoreFunction patch for for centroid phase of loop-modeling
  Default: "score4L"
  

  -input_pdb <File>

  template pdb file
  Default: "input_pdb"
  

  -loop_file <StringVector>

  Loop definition file(s). When multiple files are given a random one will be picked each time when this parameter is requested.
  

  -extended_loop_file <File>

  loop definition file for loops to be extended (used in abrelax)
  Default: "loop_file"
  

  -mm_loop_file <File>

  loop definition file
  Default: "loop_file"
  

  -fix_natsc <Boolean>

  fix sidechains in template region in loop modeling
  Default: false
  

  -refine_only <Boolean>

  perform full atom refinement only on loops
  Default: false
  

  -fast <Boolean>

  reduce number of simulation cycles in loop modeling
  Default: false
  

  -vall_file <File>

  vall database file
  Default: "vall_file"
  

  -frag_sizes <IntegerVector>

  lengths of fragments to be used in loop modeling
  Default: ['9', '3', '1']
  

  -frag_files <FileVector>

  fragment libraries files
  Default: ['"frag9"', '"frag3"', '"frag1"']
  

  -output_pdb <File>

  output model pdb file
  Default: "output.pdb"
  

  -debug <Boolean>

  No description
  Default: false
  

  -build_initial <Boolean>

  Precede loop-modeling with an initial round of just removing the missing densities and building simple loops
  Default: false
  

  -extended <Boolean>

  Force extended on loops, independent of loop input file
  Default: false
  

  -remove_extended_loops <Boolean>

  Before building any loops, remove all loops marked as extended
  Default: false
  

  -idealize_after_loop_close <Boolean>

  Run structure through idealizer after loop_closing
  Default: true
  

  -idealize_before_loop_close <Boolean>

  Run structure through idealizer before loop_closing
  Default: true
  

  -select_best_loop_from <Integer>

  Keep building loops until N and choose best (by score)
  Default: 1
  

  -build_attempts <Integer>

  Build attempts per growth attempt
  Default: 3
  

  -grow_attempts <Integer>

  Total loop growth attempts
  Default: 7
  

  -random_grow_loops_by <Real>

  Randomly grow loops by up to this number of residues on either side.
  Default: 0.0
  

  -accept_aborted_loops <Boolean>

  accept aborted loops
  Default: false
  

  -strict_loops <Boolean>

  Do not allow growing of loops
  Default: false
  

  -superimpose_native <Boolean>

  Superimpose the native over the core before calculating looprms
  Default: false
  

  -build_specific_loops <IntegerVector>

  Numbers of the loops to be built
  

  -random_order <Boolean>

  build in random order
  Default: true
  

  -build_all_loops <Boolean>

  build all loops(no skip)
  Default: false
  

  -fa_closure_protocol <Boolean>

  Abrelax uses FASlidingWindowLoopClosure...
  Default: false
  

  -combine_rate <Real>

  Combine successive loops at this rate
  Default: 0.0
  

  -skip_initial_loop_build <Boolean>

  Skip the initial loop build step where existing loop torsions are discarded and the loop is built from scratch.
  Default: false
  

  -remodel <String>

  
  Default: "no"
  

  -intermedrelax <String>

  
  Default: "no"
  

  -refine <String>

  method for performing full-atom refinement on loops
  Default: "no"
  

  -relax <String>

  
  Default: "no"
  

  -final_clean_fastrelax <Boolean>

  Add a final fastrelax without constraints
  Default: false
  

  -relax_with_foldtree <Boolean>

  keep foldtree during relax
  Default: false
  

  -constrain_rigid_segments <Real>

  Use Coordinate constraints on the non-loop regions
  Default: 0.0
  

  -loopscores <String>

  Calculate loopscores individually for these loops (path to loopsfile)
  

  -timer <Boolean>

  Output time spent in seconds for each loop modeling job
  Default: false
  

  -vicinity_sampling <Boolean>

  only sample within a certain region of the current torsion values
  Default: false
  

  -vicinity_degree <Real>

  number of degrees to sample within current torsion values for vicinity sampling
  Default: 1.0
  

  -neighbor_dist <Real>

  CB distance cutoff for repacking, rotamer trails, and side-chain minimization during loop modeling. NOTE: values over 10.0 are effectively reduced to 10.0
  Default: 10.0
  

  -kic_max_seglen <Integer>

  maximum size of residue segments used in kinematic closure calculations
  Default: 12
  

  -kic_recover_last <Boolean>

  If true, do not recover lowest scoring pose after each outer cycle and at end of protocol in kic remodel and refine
  Default: false
  

  -kic_min_after_repack <Boolean>

  Should the kinematic closure refine protocol minimize after repacking steps
  Default: true
  

  -optimize_only_kic_region_sidechains_after_move <Boolean>

  Should we perform rotamer trials and minimization after every KIC move but only within the loops:neighbor_dist of the residues in the moved KIC segment. Useful to speed up when using very large loop definitions (like when whole chains are used for ensemble generation).
  Default: false
  

  -max_kic_build_attempts <Integer>

  Number of attempts at initial kinematic closure loop building
  Default: 10000
  

  -remodel_kic_attempts <Integer>

  Number of kic attempts per inner cycle during perturb_kic protocol
  Default: 300
  

  -max_kic_perturber_samples <Integer>

  Maximum number of kinematic perturber samples
  Default: 2000
  

  -nonpivot_torsion_sampling <Boolean>

  enables sampling of non-pivot residue torsions when the kinematic loop closure segment length is > 3
  Default: true
  

  -fix_ca_bond_angles <Boolean>

  Freezes N-CA-C bond angles in KIC loop sampling
  Default: false
  

  -kic_use_linear_chainbreak <Boolean>

  Use linear_chainbreak instead of (harmonic) chainbreak in KIC loop sampling
  Default: false
  

  -sample_omega_at_pre_prolines <Boolean>

  Sample omega in KIC loop sampling
  Default: false
  

  -allow_omega_move <Boolean>

  Allow loop omega to minimize during loop modeling
  Default: false
  

  -kic_with_cartmin <Boolean>

  Use cartesian minimization in KIC loop modeling
  Default: false
  

  -allow_takeoff_torsion_move <Boolean>

  Allow takeoff phi/psi to move during loop modeling
  Default: false
  

  -extend_length <Integer>

  Number of alanine residues to append after cutpoint in loopextend app
  Range: 0-
  Default: 0
  

  -perturb_outer_cycles <Integer>

  number of outer cycles in the perturbation (centroid) stage
  Range: 1-
  Default: 5
  

  -refine_outer_cycles <Integer>

  number of outer cycles in the fullatom refinement stage
  Range: 1-
  Default: 5
  

  -max_inner_cycles <Integer>

  maxium number of inner cycles in fullatom loop refinement
  Range: 1-
  Default: 1
  

  -repack_period <Integer>

  repack period during fullatom loop refinement
  Range: 1-
  Default: 20
  

  -remodel_init_temp <Real>

  Initial temperature for loop rebuiding. Currently only supported in kinematic (KIC) mode
  Default: 2.0
  

  -remodel_final_temp <Real>

  Final temperature for loop rebuilding. Currently only supported in kinematic (KIC) mode
  Default: 1.0
  

  -refine_init_temp <Real>

  Initial temperature for loop refinement. Currently only supported in kinematic (KIC) mode
  Default: 1.5
  

  -refine_final_temp <Real>

  Final temperature for loop refinement. Currently only supported in kinematic (KIC) mode
  Default: 0.5
  

  -gapspan <Integer>

  when automatically identifying loop regions, this is the maximum gap length for a single loop
  Range: 1-
  Default: 6
  

  -spread <Integer>

  when automatically identifying loop regions, this is the number of neighboring residues by which to extend out loop regions
  Range: 1-
  Default: 2
  

  -kinematic_wrapper_cycles <Integer>

  maximum number of KinematicMover apply() tries per KinematicWrapper apply()
  Default: 20
  

  -kic_num_rotamer_trials <Integer>

  number of RotamerTrial iterations in each KIC cycle – default is 1
  Default: 1
  

  -kic_omega_sampling <Boolean>

  Perform sampling of omega angles around 179.6 for trans, and including 0 for pre-prolines – default false, for legacy reasons
  Default: false
  

  -kic_bump_overlap_factor <Real>

  allow some atomic overlap in initial loop closures (should be remediated in subsequent repacking and minimization)
  Default: 0.36
  

  -minimize_max_iter <Integer>

  Max iteration of minimization during MC
  Default: 200
  

  -restrict_kic_sampling_to_torsion_string <String>

  restrict kinematic loop closure sampling to the phi/psi angles specified in the torsion string
  Default: ""
  

  -derive_torsion_string_from_native_pose <Boolean>

  apply torsion-restricted sampling, and derive the torsion string from the native [or, if not provided, starting] structure
  Default: false
  

  -always_remodel_full_loop <Boolean>

  always remodel the full loop segment (i.e. the outer pivots are always loop start & end) – currently this only applies to the perturb stage – EXPERIMENTAL
  Default: false
  

  -taboo_sampling <Boolean>

  enhance diversity in KIC sampling by pre-generating different torsion bins and sampling within those – this flag activates Taboo sampling in the perturb stage
  Default: false
  

  -taboo_in_fa <Boolean>

  enhance diversity in KIC sampling by pre-generating different torsion bins and sampling within those – this flag activates Taboo sampling in the first half of the full-atom stage; use in combination with -loops:taboo_sampling or -kic_leave_centroid_after_initial_closure
  Default: false
  

  -ramp_fa_rep <Boolean>

  ramp the weight of fa_rep over outer cycles in refinement
  Default: false
  

  -ramp_rama <Boolean>

  ramp the weight of rama over outer cycles in refinement
  Default: false
  

  -kic_rama2b <Boolean>

  use neighbor-dependent Ramachandran distributions in random torsion angle sampling
  Default: false
  

  -kic_leave_centroid_after_initial_closure <Boolean>

  only use centroid mode for initial loop closure – all further loop closures will be performed in full-atom
  Default: false
  

  -legacy_kic <Boolean>

  always select the start pivot first and then the end pivot – biases towards sampling the C-terminal part of the loop more (false by default)
  Default: false
  

  -alternative_closure_protocol <Boolean>

  use WidthFirstSliding...
  Default: false
  

  -chainbreak_max_accept <Real>

  accept all loops that have a lower cumulative chainbreak score (linear,quadratic(if present), and overlap)
  Default: 2.0
  

  -debug_loop_closure <Boolean>

  dump structures before and after loop closing
  Default: false
  

  -non_ideal_loop_closing <Boolean>

  allow small non-idealities at the chainbreak residue after loop-closing – requires binary silent out
  Default: false
  

  -scored_frag_cycles <Real>

  cycle-ratio for scored_frag_cycles ( loop_size<10 ) after jumping-abinitio
  Default: 1.0
  

  -short_frag_cycles <Real>

  cycle-ratio for short_frag_cycles ( loop_size<10 ) after jumping-abinitio
  Default: 1.0
  

  -rmsd_tol <Real>

  rmsd tolerance to deviate from original pose
  Default: 10000.0
  

  -chain_break_tol <Real>

  acceptable tolerance for chain break score
  Default: 0.2
  

  -random_loop <Boolean>

  randomize loop stub positions
  Default: false
  

  -stealfrags <FileVector>

  StealFragPDBS
  

  -stealfrags_times <Integer>

  StealFragPDBS how many times ?
  Default: 1
  

  -coord_cst <Real>

  restraintweight
  Default: 0.0
  

  -skip_1mers <Real>

  rate at which you should skip a 1 mer insertion
  Default: 0.0
  

  -skip_3mers <Real>

  rate at which you should skip a 3 mer insertion
  Default: 0.0
  

  -skip_9mers <Real>

  rate at which you should skip a 9 mer insertion
  Default: 0.0
  

  -loop_model <Boolean>

  loop modeling option
  Default: false
  

  -score_filter_cutoff <Real>

  value for score filter
  Default: 1.0
  

  -ccd_closure <Boolean>

  apply ccd closure
  Default: false
  

  -skip_ccd_moves <Boolean>

  when running in ccd_moves mode, dont actually do ccd_moves.. just do fragment insertions
  Default: false
  

  -no_randomize_loop <Boolean>

  Leave loop as it is
  Default: false
  

  -loops_subset <Boolean>

  pick subset of desired loops
  Default: false
  

  -num_desired_loops <Integer>

  number of desired loops
  Default: 1
  

  -loop_combine_rate <Real>

  skip rate for not combining a chosen loop
  Default: 0.0
  

  -final_score_filter <Real>

  Only output structures that score bette rthan that
  Default: 1000000.0
  

  -no_combine_if_fail <Boolean>

  combine loops if loop modeling fails
  Default: true
  

  -shorten_long_terminal_loop <Boolean>

  shorten long loops
  Default: false
  

  -backrub_trials <Integer>

  number of backrub steps to do in loop relax
  Default: 10
  

  -looprlx_cycle_ratio <Real>

  fraction of the total looprlx cycles
  Default: 1.0
  

  -extended_beta <Real>

  Extended tempfactor: stochastic extendedness: p_ext = exp( - beta * length )
  Default: -1.0
  

  -no_looprebuild <Boolean>

  do not rebuild loops
  Default: false
  

  -allow_lig_move <Boolean>

  allow ligands to move during loop modeling
  Default: false
  

  -keep_natro <File>

  list of residues where the rotamers are kept fixed
  Default: "keep_natro"
  

  -refine_design_iterations <Integer>

  iterations of refine and design
  Default: 1
  

• loops:ccd

  -ccd <Boolean>

  ccd option group
  

  -max_rama_score_increase <Real>

  Maximum increase in Ramachandran score that will be tolerated.
  Default: 2.0
  

  -max_torsion_delta_per_move <RealVector>

  Maxmimum absolute torsion deviation for a single residue in a given move. Different deviations for residues in helical, extended or coil conformations must be supplied (in that order).
  Default: ['1.0', '5.0', '10.0']
  

  -max_torsion_delta <RealVector>

  Maxmimum absolute torsion deviation for a single residue over the entire CCD closure. Different deviations for residues in helical, extended or coil conformations must be supplied (in that order).
  Default: ['10.0', '50.0', '75.0']
  

  -tolerance <Real>

  Maximum RMSD (in Angstroms) of the duplicated atoms across the cutpoint that will be considered a successful closure.
  Default: 0.08
  

  -max_cycles <Integer>

  Maximum number of CCD iterations to attempt. CCD will stop if the loop is closed in fewer cycles than the maximum.
  Default: 100
  

  -check_rama_scores <Boolean>

  Bias toward moves that improve the moving resiude's Ramachandran score.
  Default: true
  

  -rama_2b <Boolean>

  Use two-body (neighbor-dependent) Ramachandran score.
  Default: false
  

  -temperature <Real>

  Temperature (roughly in units of kT) to use when accepting a move that does not improve the Ramachandran score.
  Default: 0.25
  

• intf

  -intf <Boolean>

  intf option group
  

  -chains <String>

  Chains over which the statistics are taken, can be multiple. Example: 'AEF'. If not given, takes statistics over unique chains in the PDB.
  

• mp

  -mp <Boolean>

  mp option group
  

  -thickness <Real>

  Thickness of the membrane used by the high resolution scoring function. Overwrites default thickness of 30A.
  

  -membrane_core <Real>

  set membrane core thickness for Lazaridis-Karplus. default is 10A, i.e (-10, 10)
  

  -steepness <Real>

  Control transition region between polar and nonpoar phases for the membrane model used by the high resolution energy function. Default = 10 gives a 6A transition region.
  

  -center_start <RealVector>

  Starting point for center search. Example: 3 2 4.
  

  -center_delta <Real>

  Perturbation of center in Angstrom.
  

  -center_search_cycles <Real>

  Iterations for center search.
  

  -normal_start <RealVector>

  Base vector for normal search. Angles go off that vector.
  

  -normal_angle_start <Real>

  Starting angle from base vector for normal search. Degrees.
  

  -normal_angle_delta <Real>

  Perturbation of normal angle in degrees.
  

  -normal_search_cycles <Real>

  Number of iterations for normal search.
  

  -chain_normal_angle_max <Real>

  Maximum of normal angle wrt normal_start for chain embedding. Degrees.
  

  -pose_normal_angle_max <Real>

  Maximum of normal angle wrt normal_start for pose embedding. Degrees.
  

  -no_interpolate_Mpair <Boolean>

  from old code.
  

  -Hbond_depth_correction <Boolean>

  from old code.
  

  -TMprojection <Boolean>

  Penalty for hydrophobic mismatch on/off.
  

  -wt_TMprojection <Real>

  Weight for hydrophobic mismatch penalty.
  

  -non_helix <Boolean>

  Penalty for non-helix residues in the membrane on/off.
  

  -wt_non_helix <Real>

  Weight for non-helix penalty.
  

  -termini <Boolean>

  Penalty for termini in the membrane on/off.
  

  -wt_termini <Real>

  Weight for termini penalty.
  

  -secstruct <Boolean>

  Penalty if structure-based secondary structure doesn't match predicted one - on/off
  

  -wt_secstruct <Real>

  Weight for secondary structure penalty.
  

  -spanning <Boolean>

  Penalty if structure-based spanning doesn't match spanfile - on/off.
  

  -wt_spanning <Real>

  Weight for spanning penalty.
  

• mp:viewer

  -viewer <Boolean>

  viewer option group
  

  -thickness <Real>

  Thickness of membrane to visualize
  Default: 15
  

  -num_points <Integer>

  Number of points to define the membrane planes. x >= 3
  

• mp:visualize

  -visualize <Boolean>

  visualize option group
  

  -embedding <Boolean>

  Visualize embedding centers and normals for each pose element
  Default: true
  

  -spacing <Real>

  Spacing of virtual membrane residues representing the membrane planes
  Default: 5
  

  -width <Real>

  Width of membrane planes for n by n plane
  Default: 100
  

  -thickness <Real>

  Thickness of membrane to visualize
  Default: 15
  

  -plane_radius <Real>

  Radius of membrane planes to draw in PyMOL - part of the PyMOL viewer plugin
  

• mp:scoring

  -scoring <Boolean>

  scoring option group
  

  -hbond <Boolean>

  Hydrogen bonding energy correction for membrane proteins
  

• mp:setup

  -setup <Boolean>

  setup option group
  

  -spanfiles <StringVector>

  Spanning topology file from Octopus
  

  -spans_from_structure <Boolean>

  Uses spanning topology computed from the PDB; requires the protein to be transformed into the membrane coordinate frame!
  

  -lipsfile <String>

  List of lips files by chain
  Default: "mypdb.lips4"
  

  -center <RealVector>

  membrane center x,y,z
  

  -normal <RealVector>

  membrane normal x,y,z
  

  -membrane_rsd <Real>

  membrane residue number
  

  -transform_into_membrane <Boolean>

  score_jd2: transform protein into fixed membrane before scoring; spanfile required
  

  -position_from_topo <Boolean>

  determine a membrane position from the transmembrane spans of the protein
  

  -optimize1 <Boolean>

  Optimize position in membrane for partner 1 using membrane scorefunction.
  Default: false
  

  -optimize2 <Boolean>

  Optimize position in membrane for partner 2 using membrane scorefunction.
  Default: false
  

• mp:lipid_acc

  -lipid_acc <Boolean>

  lipid_acc option group
  

  -angle_cutoff <Real>

  Cutoff for CA-CB-COM angle to identify lipid accessible residues, in degrees. <90 faces towards COM, >90 faces away from COM.
  Default: 65
  

  -slice_width <Real>

  Width of the slice in Angstrom to compute hull.
  Default: 10.0
  

  -shell_radius <Real>

  Radius of shell from outermost atoms that are still counted as boundary, i.e. how thick is lipid-exposed layer from the outside.
  Default: 5.0
  

  -dist_cutoff <Real>

  Distances between boundary atoms longer than this cutoff (in 2D) will be cut in. Anything larger will be kept as boundary atoms.
  Default: 5.0
  

  -tm_alpha <Boolean>

  Is the main secondary structure in the membrane helical?
  Default: true
  

• mp:transform

  -transform <Boolean>

  transform option group
  

  -optimize_embedding <Boolean>

  Use the scorefunction to optimize the embedding after an initial coarse grained setting
  

• mp:assembly

  -assembly <Boolean>

  assembly option group
  

  -TM_pose_number <Integer>

  Number of the PDB file in the -in:file:l list which is located in the membrane. Integer
  

  -poses <StringVector>

  Filenames of the PDB files to consider. StringVector.
  

• mp:dock

  -dock <Boolean>

  dock option group
  

  -weights_cen <String>

  Scorefunction for low-resolution step.
  

  -weights_fa <String>

  Scorefunction for high-resolution step.
  

  -lowres <Boolean>

  Use centroid score function for finding interface.
  

  -allow_flips <Boolean>

  Allow partner 2 to flip in the membrane during global search. Default: yes.
  

  -flexible_bb <Boolean>

  Do a flexible backbone docking: runs relax before and after docking.
  

  -flexible_sc <Boolean>

  Do a flexible sidechain docking: repacks before and after docking.
  

  -slide_threshold <Real>

  Theshold for scoreterm to define partner closeness in SlideIntoContact.
  

• mp:quickrelax

  -quickrelax <Boolean>

  quickrelax option group
  

  -angle_max <Real>

  Maximum allowed change in dihedral angles. Typical values around 1.
  

  -nmoves <String>

  Number of moves allowed. Typical value is close to the number of residues in the protein: [nres] is allowed value.
  

  -repack_again <Boolean>

  Do an additional round of sidechain repacking, simultaneously including all sidechains.
  

• mp:mutate_relax

  -mutate_relax <Boolean>

  mutate_relax option group
  

  -mutation <String>

  Single mutation: Format: One-letter code / residue number / one-letter code. Example: A163F
  

  -mutant_file <String>

  Input file containing mutations
  

  -nmodels <Integer>

  Number of models to produce per construct. Typically between 50 and 1,000.
  

  -repack_mutation_only <Boolean>

  Boolean - Only repack the mutated residue(s), no relax.
  

  -repack_radius <Real>

  Float - Repack within a radius of X Angstrom of the mutated residue(s).
  

  -relax <Boolean>

  Boolean - Do a full relax run with both backbone minimization and repacking.
  

• mp:benchmark

  -benchmark <Boolean>

  benchmark option group
  

• mp:benchmark:ideal_helix

  -ideal_helix <Boolean>

  ideal_helix option group
  

  -helix_start <Real>

  Start position for ideal helix dihedral angles
  

  -helix_end <Real>

  End position for ideal helix dihedral angles
  

• mp:benchmark:tilt_angle

  -tilt_angle <Boolean>

  tilt_angle option group
  

  -output <String>

  Path to tilt angle vs. score output file
  

• mp:output

  -output <Boolean>

  output option group
  

  -normalize_to_thk <Boolean>

  Output an additional MEM resdiue data in the PDB where the membrane normal is scaled to match the current membrane thickness (Makes sense for IMM Models
  

• membrane

  -membrane <Boolean>

  membrane option group
  

  -normal_cycles <Integer>

  number of membrane normal cycles
  Default: 100
  

  -normal_mag <Real>

  magnitude of membrane normal angle search (degrees)
  Default: 5
  

  -center_mag <Real>

  magnitude of membrane normal center search (Angstroms)
  Default: 1
  

  -smooth_move_frac <Real>

  No description
  Default: 0.5
  

  -no_interpolate_Mpair <Boolean>

  No description
  Default: false
  

  -Menv_penalties <Boolean>

  No description
  Default: false
  

  -Membed_init <Boolean>

  No description
  Default: false
  

  -Fa_Membed_update <Boolean>

  No description
  Default: false
  

  -center_search <Boolean>

  perform membrane center search
  Default: false
  

  -normal_search <Boolean>

  perform membrane normal search
  Default: false
  

  -center_max_delta <Integer>

  magnitude of maximum membrane width deviation during membrane center search (Angstroms)
  Default: 5
  

  -normal_start_angle <Integer>

  magnitude of starting angle during membrane normal search (degrees)
  Default: 10
  

  -normal_delta_angle <Integer>

  magnitude of angle deviation during membrane normal search (degrees)
  Default: 10
  

  -normal_max_angle <Integer>

  magnitude of maximum angle deviation during membrane normal search (degrees)
  Default: 40
  

  -debug <Boolean>

  No description
  Default: false
  

  -fixed_membrane <Boolean>

  fix membrane position, by default the center is at [0,0,0] and membrane normal is the z-axis
  Default: false
  

  -membrane_center <RealVector>

  membrane center x,y,z
  

  -membrane_normal <RealVector>

  membrane normal x,y,z
  

  -view <Boolean>

  viewing pose during protocol
  Default: false
  

  -Mhbond_depth <Boolean>

  membrane depth dependent correction to the hbond potential
  Default: false
  

  -thickness <Real>

  one leaflet hydrocarbon thickness for solvation calculations (Angstroms)
  Default: 15
  

• mistakes

  -mistakes <Boolean>

  mistakes option group
  

  -restore_pre_talaris_2013_behavior <Boolean>

  Restore the set of defaults that were in place before the Talaris2013 parameters were made default. This is an umbrella flag and sets the following flags if they are not set on the command line to some other value -mistakes::chemical::pre_talaris2013_geometries true -corrections::score::dun10 false -corrections::score::use_bicubic_interpolation false -correctionsscore:hb_sp2_chipen false -corrections::score::hb_fade_energy false -corrections::score::hbond_measure_sp3acc_BAH_from_hvy false -corrections::score::lj_hbond_hdis 1.95 -corrections::score::lj_hbond_OH_donor_dis 3.0 -corrections::chemical::expand_st_chi2sampling false -score::weights pre_talaris_2013_standard.wts -score::patch score12.wts_patch -score::analytic_etable_evaluation false -score::hbond_params score12_params -score::smooth_fa_elec false -score::elec_min_dis 1.5 -chemical::set_atom_properties fa_standard:ONH2:LK_DGFREE:-10.0 fa_standard:NH2O:LK_DGFREE:-10.0 fa_standard:Narg:LK_DGFREE:-11.0 fa_standard:OH:LK_DGFREE:-6.77
  Default: false
  

• mistakes:chemical

  -chemical <Boolean>

  chemical option group
  

  -pre_talaris2013_geometries <Boolean>

  Use the version of the fa_standard geometries that were active before the Talaris2013 parameters were taken as default
  Default: false
  

• MonteCarlo

  -MonteCarlo <Boolean>

  MonteCarlo option group
  

  -temp_initial <Real>

  initial temperature for Monte Carlo considerations
  Range: 0.001-
  Default: 2
  

  -temp_final <Real>

  final temperature for Monte Carlo considerations
  Range: 0.001-
  Default: 0.6
  

• optimization

  -optimization <Boolean>

  optimization option group
  

  -default_max_cycles <Integer>

  max cycles for MinimizerOptions
  Default: 2000
  

  -armijo_min_stepsize <Real>

  min stepsize in armijo minimizer
  Default: 1e-8
  

  -scale_normalmode_dampen <Real>

  dampening scale over normal mode index, used for NormalModeMinimizer
  Default: 0.05
  

  -lbfgs_M <Integer>

  number of corrections to approximate the inverse hessian matrix.
  Default: 128
  

  -scale_d <Real>

  max cycles for MinimizerOptions
  Default: 1
  

  -scale_theta <Real>

  max cycles for MinimizerOptions
  Default: 1
  

  -scale_rb <Real>

  max cycles for MinimizerOptions
  Default: 10
  

  -scale_rbangle <Real>

  max cycles for MinimizerOptions
  Default: 1
  

  -scmin_nonideal <Boolean>

  Do we allow sidechain nonideality during scmin (e.g. rtmin and min_pack)
  Default: false
  

  -scmin_cartesian <Boolean>

  Toggle Cartesian-space minimization during scmin (e.g. rmin and min_pack)
  Default: false
  

  -nonideal <Boolean>

  Permit bond geometries to vary from ideal values
  Default: false
  

  -old_sym_min <Boolean>

  Use the old approach to symmetric minimization
  Default: false
  

  -debug_inaccurate_G <Boolean>

  Debug innacurate G messages
  Default: false
  

• orbitals

  -orbitals <Boolean>

  orbitals option group
  

  -Hpol <Boolean>

  look at only polar hydrogen interactions
  Default: false
  

  -Haro <Boolean>

  look at only aromatic hydrogen interactions
  Default: false
  

  -bb_stats <Boolean>

  look at orbital backbone stats
  Default: false
  

  -sc_stats <Boolean>

  look at orbital sc stats
  Default: false
  

• pose_metrics

  -pose_metrics <Boolean>

  pose_metrics option group
  

  -atomic_burial_cutoff <Real>

  maximum SASA that is allowed for an atom to count as buried for the BuriedUnsatisfiedPolarsCalculator
  Default: 0.3
  

  -sasa_calculator_probe_radius <Real>

  the probe radius used in the SASA calculator (and thus implicitly in the BuriedUnsatisfiedPolarsCalculator
  Default: 1.4
  

  -interface_cutoff <Real>

  distance in angstroms (def. 10.0) for calculating what residues are at an interface via InterfaceNeighborDefinitionCalculator
  Default: 10.0
  

  -min_sequence_separation <Integer>

  minimum number of sequence positions that two residues need to be apart to count as nonlocal in the NonlocalContactsCalculator
  Default: 6
  

  -contact_cutoffE <Real>

  maximum interaction energy allowed between two residues to count as a contact in the NonlocalContactsCalculator
  Default: -1.0
  

  -neighbor_by_distance_cutoff <Real>

  distance in angstroms (def. 10.0) for calculating neighbors of a residue via NeighborByDistanceCalculator
  Default: 10.0
  

  -inter_group_neighbors_cutoff <Real>

  distance in angstroms (def. 10.0) for calculating interfaces between domains with InterGroupNeighborsCalculator
  Default: 10.0
  

  -semiex_water_burial_cutoff <Real>

  water hbond states fraction cutiff for SemiExplicitWaterUnsatisfiedPolarsCalculator (0.0,1.0)
  Default: 0.25
  

• pose_metrics:shobuns

  -shobuns <Boolean>

  shobuns option group
  

  -tgt_amino <String>

  Target amino acid type
  Default: "_none_"
  

  -tgt_atom <String>

  Target atom name
  Default: "_none_"
  

  -tgt_res <File>

  File specifying a subset of target residues
  Default: ""
  

  -sho_cutoff <Real>

  max SHO value for an atom to be considered solvent exposed
  Default: 4.9
  

• rigid

  -rigid <Boolean>

  rigid option group
  

  -chainbreak_bias <Real>

  Strength of bias applied to the translation component of rigid body moves to close chainbreak
  Default: 0.00
  

  -close_loops <Boolean>

  Perform loop closure at the end of medal
  Default: true
  

  -fragment_cycles <Integer>

  Number of fragment insertion/rigid body cycles
  Default: 10000
  

  -log_accepted_moves <Boolean>

  Write accepted moves to silent file output
  Default: false
  

  -max_ca_ca_dist <Real>

  Maximum distance between consecutive CA atoms before chunk partitioning occurs
  Default: 5.0
  

  -patch <File>

  Patch file containing energy terms and their respective weights
  

  -residues_backbone_move <Integer>

  Number of residues perturbed by a backbone move
  Default: 5
  

  -rotation <Real>

  Rotation magnitude
  Default: 2.5
  

  -sampling_prob <File>

  Normalized, per-residue sampling probabilities
  

  -score <String>

  Centroid-level score function
  Default: "score3"
  

  -sequence_separation <Integer>

  Maximum sequence separation for scoring chainbreaks
  Default: 20
  

  -small_cycles <Integer>

  Number of small/shear cycles
  Default: 8000
  

  -stages <Integer>

  Number of stages over which to interpolate ramped values
  Default: 4
  

  -temperature <Real>

  Monte Carlo temperature
  Default: 2.0
  

  -translation <Real>

  Translation magnitude
  Default: 0.5
  

• sasa

  -sasa <Boolean>

  sasa option group
  

  -method <String>

  The method used to calculate sasa. More will hopefully be added in the future.
  Default: "LeGrand"
  

  -include_hydrogens_explicitly <Boolean>

  Include hydrogens explicitly in the calculation. Explicit vs implicit calculations use different radii sets. These default sets can be controlled via cmd line. Historically, calculations included hydrogens implicitly. Some protocols may overwrite this setting to their needs.
  Default: true
  

  -probe_radius <Real>

  Probe radius used by SasaCalc. Default is radius of water. 1.2 is also commonly used.
  Default: 1.4
  

  -include_probe_radius_in_atom_radii <Boolean>

  This is typically done in calculation of SASA, and in fact is one of the defining features of SASA. Turn this off to calculate the Surface Area instead.
  Default: true
  

  -include_only_C_S_in_hsasa <Boolean>

  Include only carbon or sulfer in hsasa calculation. This is typical. Only revert to false if excluding polar atoms by charge or everything will be counted as hydrophobic. Note hydrogens are dealt with automatically.
  Default: true
  

  -exclude_polar_atoms_by_charge_in_hsasa <Boolean>

  Polar carbons and other atoms should not be included in hydrophobic hSASA - though historically they were. Set this to false to get historic hsasa
  Default: false
  

  -polar_charge_cutoff <Real>

  Charge cutoff (abs value) to use on heavy atoms if excluding hydrophobic atoms from hSASA calculation by charge. The default is optimized for protein atom types (which excludes only carbonyl and carboxyl carbons. By default only carbon and sulfer are excluded.
  Default: .4
  

  -implicit_hydrogen_radii_set <String>

  The radii set to use when including hydrogens implicitly instead of explicitly. Chothia 1976 radii are used by the program Naccess. chothia=naccess
  Default: "chothia"
  

  -explicit_hydrogen_radii_set <String>

  The radii set to use when including hydrogens explicitly. Default is reduce, which was generally agreed upon at Minicon 2014 and come from original data from Bondi (1964) and Gavezzotti (1983) . LJ are the Rosetta leonard-jones radii, which are not quite exactly from Charmm. Legacy radii were optimized for a no-longer-in-Rosetta scoreterm (Jerry Tsai et al 2003)
  Default: "reduce"
  

• symmetry

  -symmetry <Boolean>

  symmetry option group
  

  -symmetry_definition <String>

  Text file describing symmetry setup
  

  -reweight_symm_interactions <Real>

  Scale intersubunit interactions by a specified weight
  Default: 1.0
  

  -initialize_rigid_body_dofs <Boolean>

  Initialize the RB dofs from the symmetry definition file?
  Default: false
  

  -detect_bonds <Boolean>

  allow new cross subunit bond formation
  Default: true
  

  -perturb_rigid_body_dofs <RealVector>

  (As in docking) Do a small perturbation of the symmetric DOFs: -perturb_rigid_body_dofs ANGSTROMS DEGREES
  

  -symmetric_rmsd <Boolean>

  calculate the rmsd symmetrically by checking all chain orderings
  

• abinitio

  -abinitio <Boolean>

  Ab initio mode
  

  -membrane <Boolean>

  will use the membrane abinitio protocol. sequential insertion of TMH
  Default: false
  

  -use_loophash_filter <Boolean>

  use loophash filter to determine if SSEs too far away
  

  -loophash_filter_acceptance_rate <Real>

  fraction at which want to accept poses from loophash filter if no loophash hits found
  

  -kill_hairpins <File>

  setup hairpin killing in score (kill hairpin file or psipred file)
  

  -kill_hairpins_frequency <Real>

  automated hairpin killing frequency (for use with psipred file)
  Default: 0.2
  

  -smooth_cycles_only <Boolean>

  Only smooth cycles in abinitio protocol
  Default: false
  

  -relax <Boolean>

  Do a relax after abinitio = abrelax ?
  

  -final_clean_relax <Boolean>

  Do a final relax without constraints
  

  -fastrelax <Boolean>

  Do a fastrelax after abinitio = abfastrelax ?
  

  -multifastrelax <Boolean>

  Do a fastrelax after abinitio = abfastrelax ?
  

  -debug <Boolean>

  No description
  Default: false
  

  -clear_pose_cache <Boolean>

  always clear extra-scores away before output
  Default: false
  

  -explicit_pdb_debug <Boolean>

  always dump pdb (not silent ) files during abinitio stages
  Default: false
  

  -use_filters <Boolean>

  use RG, contact-order and sheet filters
  Default: false
  

  -increase_cycles <Real>

  Increase number of cycles at each stage of fold_abinitio (or pose_abinitio) by this factor
  Range: 0.001-
  Default: 1.0
  

  -number_3mer_frags <Integer>

  Number of top 3mer fragments to use in fold_abinitio protocol
  Range: 0-
  Default: 200
  

  -number_9mer_frags <Integer>

  Number of top 9mer fragments to use in fold_abinitio protocol
  Range: 0-
  Default: 25
  

  -temperature <Real>

  Temperature used in fold_abinitio
  Default: 2.0
  

  -rg_reweight <Real>

  Reweight contribution of radius of gyration to total score by this scale factor
  Default: 1.0
  

  -rsd_wt_helix <Real>

  Reweight env,pair,cb for helix residues by this factor
  Default: 1.0
  

  -rsd_wt_strand <Real>

  Reweight env,pair,cb for strand residues by this factor
  Default: 1.0
  

  -rsd_wt_loop <Real>

  Reweight env,pair,cb for loop residues by this factor
  Default: 1.0
  

  -skip_convergence_check <Boolean>

  this option turns off the convergence check in stage3 (score 2/5)
  

  -stage1_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage1 abinitio
  

  -stage2_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage2 abinitio
  

  -stage3a_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage3a abinitio
  

  -stage3b_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage3b abinitio
  

  -stage4_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage4 abinitio
  

  -stage5_patch <FileVector>

  Name of weights patch file (without extension .wts) to use during stage5 abinitio
  

  -steal_3mers <Boolean>

  stealing: use 3mers from native
  Default: false
  

  -steal_9mers <Boolean>

  stealing: use 9mers from native
  Default: false
  

  -no_write_failures <Boolean>

  dont write failed structures to silent-out
  Default: false
  

  -relax_failures <Boolean>

  relax failures anyway
  Default: false
  

  -relax_with_jumps <Boolean>

  switch to allow relax even if loops are not closed
  Default: false
  

  -process_store <Boolean>

  run process_decoy on each structure in the structure store
  Default: false
  

  -fix_residues_to_native <IntegerVector>

  these residues torsions are copied from native and fixed
  Default: 0
  

  -return_full_atom <Boolean>

  return a full-atom structure even if no relax is done
  Default: false
  

  -detect_disulfide_before_relax <Boolean>

  run detect_disulfides() before relax
  Default: false
  

  -close_loops <Boolean>

  close loops
  Default: false
  

  -bGDT <Boolean>

  compute gdtmmm
  Default: true
  

  -dump_frags <Boolean>

  for control purposes... dump fragments
  Default: false
  

  -jdist_rerun <Boolean>

  go through intput structures and evaluate ( pca, rmsd, cst-energy )
  Default: false
  

  -perturb <Real>

  add some perturbation (gaussian) to phi/psi of native
  Default: 0.0
  

  -rerun <Boolean>

  go through intput structures and evaluate ( pca, rmsd, cst-energy )
  Default: false
  

  -rmsd_residues <IntegerVector>

  give start and end residue for rmsd calcul.
  Default: -1
  

  -start_native <Boolean>

  start from native structure (instead of extended)
  Default: false
  

  -cyclic_peptide <Boolean>

  set up cyclic peptide (N-to-C cyclization) constraints for abinitio runs
  Default: false
  

  -debug_structures <Boolean>

  write structures to debug-out files
  Default: false
  

  -log_frags <File>

  fragment insertions (each trial) will be logged to file
  Default: ""
  

  -only_stage1 <Boolean>

  useful for benchmarks sets cycle of all higher stages to 0
  Default: false
  

  -end_bias <Real>

  set the endbias for Fragment moves
  Default: 30.0
  

  -apply_end_bias <Boolean>

  eliminate the endbias for Fragment moves
  Default: true
  

  -symmetry_residue <Integer>

  hacky symmetry mode for dimers, fragments are inserted at i and i + SR - 1
  Default: -1
  

  -vdw_weight_stage1 <Real>

  vdw weight in stage1
  Default: 1.0
  

  -override_vdw_all_stages <Boolean>

  apply vdw_weight_stage1 for all stages
  Default: false
  

  -recover_low_in_stages <IntegerVector>

  say default: 2 3 4 recover_low happens in stages 2 3 4
  Default: 0
  

  -skip_stages <IntegerVector>

  say: 2 3 4, and it will skip stages 2 3 4
  Default: 0
  

  -close_chbrk <Boolean>

  Chain break closure during classic abinito
  Default: false
  

  -include_stage5 <Boolean>

  stage5 contains small moves only
  Default: false
  

  -close_loops_by_idealizing <Boolean>

  close loops by idealizing the structure after stage 4
  Default: false
  

  -optimize_cutpoints_using_kic <Boolean>

  optimize around cutpoints using kinematic relax
  Default: false
  

  -optimize_cutpoints_margin <Integer>

  
  Default: 5
  

• abinitio:star

  -star <Boolean>

  star option group
  

  -initial_dist_cutoff <Real>

  Maximum distance cutoff for restraints that constrain aligned residues to their initial positions
  Default: 8.0
  

  -min_unaligned_len <Integer>

  Minimum length of an unaligned region
  Default: 3
  

• abrelax

  -abrelax <Boolean>

  ab initio relax mode
  

  -fail_unclosed <Boolean>

  structures which don't close loops are reported as FAIL_DO_NOT_RETRY
  Default: false
  

• AnchoredDesign

  -AnchoredDesign <Boolean>

  AnchoredDesign option group
  

  -anchor <File>

  anchor specification file
  Default: "anchor"
  

  -allow_anchor_repack <Boolean>

  allow repacking of anchor (default is to prevent)
  Default: false
  

  -vary_cutpoints <Boolean>

  vary loop cutpoints. Picks new cutpoints at start of each nstruct
  Default: false
  

  -no_frags <Boolean>

  use no fragments. Overrides passing an old-style fragment file. Skips new-style fragment generation.
  Default: false
  

  -debug <Boolean>

  debug mode (extra checks and pdb dumps)
  Default: false
  

  -show_extended <Boolean>

  dump pre-perturb PDB to check if loop torsions are extended and/or sequence is fuzzed; debugging only
  Default: false
  

  -refine_only <Boolean>

  refine only mode (skip perturbation step)
  Default: false
  

  -perturb_show <Boolean>

  dump perturbed centroid pdbs as well as final results
  Default: false
  

  -perturb_cycles <Integer>

  perturbation phase runs for <input> cycles
  Default: 5
  

  -perturb_temp <Real>

  perturbation phase temperature for monte carlo
  Default: 0.8
  

  -perturb_CCD_off <Boolean>

  CCD-style loop remodeling off in perturb phase (meaning, KIC only)
  Default: false
  

  -perturb_KIC_off <Boolean>

  KIC-style loop remodeling off in perturb phase (meaning, CCD only)
  Default: false
  

  -refine_CCD_off <Boolean>

  CCD-style loop remodeling off in refine phase (meaning, KIC only)
  Default: false
  

  -refine_KIC_off <Boolean>

  KIC-style loop remodeling off in refine phase (meaning, CCD only)
  Default: false
  

  -refine_cycles <Integer>

  refinement phase runs for <input> cycles
  Default: 5
  

  -refine_temp <Real>

  refinement phase temperature for monte carlo
  Default: 0.8
  

  -refine_repack_cycles <Integer>

  refinement phase runs repack every <input> cycles
  Range: 2-
  Default: 20
  

  -rmsd <Boolean>

  Calculate result structure CA RMSD from starting structure
  Default: false
  

  -unbound_mode <Boolean>

  Ignore the anchor, as if this were loop modeling
  Default: false
  

  -chainbreak_weight <Real>

  Chainbreak term weight
  Default: 2.0
  

• AnchoredDesign:filters

  -filters <Boolean>

  filters option group
  

  -score <Real>

  do not print trajectories with scores greater than this total scorefunction value
  Default: 0
  

  -sasa <Real>

  do not print trajectories with sasas less than this interface delta sasa value
  Default: 500
  

  -omega <Boolean>

  filter out non-trans omegas
  Default: false
  

• AnchoredDesign:akash

  -akash <Boolean>

  akash option group
  

  -dyepos <Integer>

  dye position
  Default: 0
  

• AnchoredDesign:testing

  -testing <Boolean>

  testing option group
  

  -VDW_weight <Real>

  centroid VDW weight; testing if 2 better than 1
  Range: 0-
  Default: 1.0
  

  -anchor_via_constraints <Boolean>

  allow anchor&jump to move; anchor held in place via constraints - you must specify constraints!
  Default: false
  

  -delete_interface_native_sidechains <Boolean>

  benchmarking option. delete input sidechains as prepacking step before running centroid or fullatom phases. use if also using use_input_sc and doing benchmarking. use_input_sc is used because of sidechain minimization, not to maintain input sidechains.
  

  -RMSD_only_this <File>

  Perform only RMSD calculations without modifying input. Only used for re-running metrics during benchmarking/debugging.
  

  -anchor_noise_constraints_mode <Boolean>

  Hold the anchor loosely (via constraints), not rigidly. Automatically generate the constraints from the starting pose. Mildly randomize the anchor's placement before modeling (up to 1 angstrom in x,y,z from initial placement.) Only compatible with single-residue anchors. Used to meet a reviewer's commentary.
  Default: false
  

  -super_secret_fixed_interface_mode <Boolean>

  hold the anchor-containing loop fixed. Currently in testing.
  Default: false
  

  -randomize_input_sequence <Boolean>

  randomizes the input sequence by packing with a null scorefunction; uses the AnchoredDesign-specified packer task (obeys resfile, etc).
  Default: false
  

• antibody

  -antibody <Boolean>

  Antibody option group
  

  -input_ab_scheme <String>

  The numbering scheme of the PDB file.
  Default: "Chothia_Scheme"
  

  -output_ab_scheme <String>

  Output numbering scheme supported by most antibody apps that output pdbs. Please see documentation.
  Default: "Chothia_Scheme"
  

  -cdr_definition <String>

  The CDR definition to use. Current Options are: Chothia, Aroop, North, Kabat, Martin
  Default: "Aroop"
  

  -light_chain <String>

  Type of light chain if known. Only used for design for now.
  Default: "unknown"
  

  -check_cdr_chainbreaks <Boolean>

  Check CDRs of input antibody for chainbreaks upon initializing RosettaAntibody and RosettaAntibodyDesign. Chainbreaks found will result in the model not proceeding. A peptide bond in the loop is considered broken if its C-N bond is > 2.0 A
  Default: true
  

  -check_cdr_pep_bond_geom <Boolean>

  Check CDRs of input antibody for bad peptide bond geometry. This checks Ca-C-N and C-N-Ca bond angles for -large- deviations from the min max values found in a recent analysis of protein geometry - Conformation dependence of backbone geometry in proteins. Structure -. If found, the model will not proceed. Use FastRelax with bond angle min to fix issues. These issues usually arise from poorly resolved crystal loops or incorrectly solved structures. Many older antibody structures have some of these issues.
  Default: false
  

  -numbering_scheme <String>

  Deprecated Numbering Scheme option
  Default: "Chothia_Scheme"
  

  -graft_l1 <Boolean>

  Graft CDR L1 from template
  Default: false
  

  -l1_template <String>

  Choose specified template for CDR L1 grafting
  Default: "l1.pdb"
  

  -graft_l2 <Boolean>

  Graft CDR L2 from template
  Default: false
  

  -l2_template <String>

  Choose specified template for CDR L2 grafting
  Default: "l2.pdb"
  

  -graft_l3 <Boolean>

  Graft CDR L3 from template
  Default: false
  

  -l3_template <String>

  Choose specified template for CDR L3 grafting
  Default: "l3.pdb"
  

  -graft_h1 <Boolean>

  Graft CDR H1 from template
  Default: false
  

  -h1_template <String>

  Choose specified template for CDR H1 grafting
  Default: "h1.pdb"
  

  -graft_h2 <Boolean>

  Graft CDR H2 from template
  Default: false
  

  -h2_template <String>

  Choose specified template for CDR H2 grafting
  Default: "h2.pdb"
  

  -graft_h3 <Boolean>

  Graft CDR H3 from template
  Default: false
  

  -h3_template <String>

  Choose specified template for CDR H3 grafting
  Default: "h3.pdb"
  

  -light_heavy_template <String>

  Choose specified template for VL-VH orientation
  Default: ""
  

  -frl_template <String>

  Choose specified template for light chain framework
  Default: ""
  

  -frh_template <String>

  Choose specified template for heavy chain framework
  Default: ""
  

  -run_snugdock <Boolean>

  Run Snugdock after Antibody_H3/RAbD?
  Default: false
  

  -h3_no_stem_graft <Boolean>

  Graft CDR H3 from template, use stem to superimpose, but do not copy the stem
  Default: false
  

  -packonly_after_graft <Boolean>

  Only do packing after grafting, do not do minimization
  Default: false
  

  -stem_optimize <Boolean>

  turn on/off the option to optimize the grafted stems
  Default: true
  

  -stem_optimize_size <Integer>

  define the size of the stem to optimize
  Default: 4
  

  -preprocessing_script_version <String>

  Rosetta 2 using Perl script has errors for grafting
  Default: "R3_Python"
  

  -model_h3 <Boolean>

  Model CDR H3 from scratch using fragments
  Default: false
  

  -snugfit <Boolean>

  Adjust relative orientation of VL-VH
  Default: false
  

  -refine_h3 <Boolean>

  Refine CDR H3 in high resolution
  Default: true
  

  -h3_filter <Boolean>

  filter decoys having neither kink nor extend form
  Default: true
  

  -h3_filter_tolerance <Real>

  maximum number of tries for the filter
  Default: 5
  

  -cter_insert <Boolean>

  insert kind or extend Ab fragments to CDR H3
  Default: true
  

  -flank_residue_min <Boolean>

  minimize flank residues of CDR H3 during high-reso refinement
  Default: true
  

  -sc_min <Boolean>

  minimize the side chain after finishing the rotamer packing
  Default: false
  

  -rt_min <Boolean>

  minimize the rotamer each packing
  Default: false
  

  -bad_nter <Boolean>

  the n-terminal is bad because of bad H3 grafting
  Default: true
  

  -extend_h3_before_modeling <Boolean>

  extend the H3 to forget the intial H3 configuration
  Default: true
  

  -idealize_h3_stems_before_modeling <Boolean>

  idealize the H3 stem, H3 grafting does not copy the coordinates which makes the grafting bad
  Default: true
  

  -remodel <String>

  Choose a perturb method to model H3 in centroid mode
  Default: "legacy_perturb_ccd"
  

  -refine <String>

  Choose a refine method to model H3 in high-resol model
  Default: "legacy_perturb_ccd"
  

  -centroid_refine <String>

  Choose a refine method to refine a loop in centroid mode
  Default: "refine_kic"
  

  -constrain_cter <Boolean>

  The option to turn on/off the cterminal constrain penalty in loop scoring function
  Default: false
  

  -constrain_vlvh_qq <Boolean>

  The option to turn on/off the VL-VH QQ H-bond in docking scoring function
  Default: false
  

  -auto_generate_kink_constraint <Boolean>

  Generate the kink constraint on-the-fly
  Default: false
  

  -all_atom_mode_kink_constraint <Boolean>

  Enable the kink constraint in the all-atom phase of the simulation
  Default: false
  

  -snug_loops <Boolean>

  Allow CDR loop backbone flexibility during minimization
  Default: false
  

  -input_fv <File>

  input antibody variable (Fv) region
  Default: "FR02.pdb"
  

  -camelid <Boolean>

  Camelid input with only heavy (VH) chain
  Default: false
  

  -camelid_constraints <Boolean>

  Display constraints file for use with camelid H3 modeler
  Default: false
  

  -use_mean_cluster_cst_data <Boolean>

  Use CDR Dihedral cluster-based constraints which have the means as the actual cluster means. Setting this to false will use constraints that have the means set as cluster center data.
  Default: true
  

  -force_use_of_cluster_csts_with_outliers <Boolean>

  Force the use of cluster dihedral constraints to use ones with outliers.
  Default: false
  

  -cluster_csts_stats_cutoff <Integer>

  Value for cluster-based dihedral csts -> general dihedral csts switch. If number of total structures used for cluster-based constraints is less than this value, general dihedral constraints will be used. More data = better predictability.
  Default: 10
  

  -general_dihedral_cst_phi_sd <Real>

  Standard deviation to use for phi while using general dihedral circular harmonic constraints
  Default: 16.0
  

  -general_dihedral_cst_psi_sd <Real>

  Standard deviation to use for psi while using general dihedral circular harmonic constraints
  Default: 16.0
  

  -allow_omega_mismatches_for_north_clusters <Boolean>

  Skip first grouping Cis and Trans for clusters in which a Cis/Trans designation currently does not exist.
  Default: false
  

  -prefix <String>

  Base/dir name prefix for antibody grafting output, split on /. By default this is grafting/.
  Default: "grafting/"
  

  -grafting_database <String>

  Path to the Antibody Grafting Database from Rosetta tools repository. By default this option is empty and grafting_database is looked at ../../tools/antibody and then $ROSETTA/tools/antibody
  Default: ""
  

  -blastp <String>

  Path to NCBI-Blast+ executable
  Default: "blastp"
  

  -exclude_homologs <Boolean>

  Filter BLAST matches by sequence identity? (false by default)
  Default: false
  

  -exclude_homologs_cdr_cutoff <Real>

  Sequence identity cutoff for complementarity determining regions (80 percent is default).
  Default: 80.0
  

  -exclude_homologs_fr_cutoff <Real>

  Sequence identity cutoff for framework regions (80 percent is default).
  Default: 80.0
  

  -ocd_cutoff <Real>

  Orientational coordinate distance cutoff for templates. Introduces diversity when using multi-template grafting (0.5 is default).
  Default: 0.5
  

  -n_multi_templates <Integer>

  Number of multiple templates to use during grafting. Default is 10.
  Default: 10
  

• antibody:design

  -design <Boolean>

  design option group
  

  -view <Boolean>

  Enable viewing of the antibody design run. Must have built using extras=graphics and run with antibody_designer.graphics executable
  Default: false
  

  -base_cdr_instructions <String>

  The Default/Baseline instructions file. Should not need to be changed.
  Default: "/sampling/antibodies/design/default_instructions.txt"
  

  -cdr_instructions <String>

  Path to CDR Instruction File
  

  -antibody_database <String>

  Path to the current Antibody Database, updated weekly. Download from http://dunbrack2.fccc.edu/PyIgClassify/
  Default: "/sampling/antibodies/antibody_database_rosetta_design.db"
  

  -paper_ab_db <Boolean>

  Force the use the Antibody Database with data from the North clustering paper. This is included in Rosetta. If a newer antibody database is not found, we will use this. The full ab db is available at http://dunbrack2.fccc.edu/PyIgClassify/
  Default: false
  

  -paper_ab_db_path <String>

  Path to the North paper ab_db path. Only used if -paper_ab_db option is passed
  Default: "/sampling/antibodies/antibody_database_rosetta_design_north_paper.db"
  

  -seq_design_cdrs <StringVector>

  Enable these CDRs for Sequence-Design. (Can be set here or in the instructions file. Overrides any set in instructions file if given)
  

  -graft_design_cdrs <StringVector>

  Enable these CDRs for Graft-Design. (Can be set here or in the instructions file. Overrides any set in instructions file if given)
  

  -primary_cdrs <StringVector>

  Manually set the CDRs which can be chosen in the outer cycle. Normally, we pick any that are sequence or graft -designing.
  

  -mintype <String>

  The default mintype for all CDRs. Individual CDRs may be set via the instructions file
  Default: "min"
  

  -disallow_aa <StringVector>

  Disallow certain amino acids while sequence-designing (could still be in the graft-designed sequence, however). Useful for optimizing without, for example, cysteines and prolines. Applies to all sequence design profiles and residues from any region (cdrs, framework, antigen). You can control this per-cdr (or only for the CDRs) through the CDR-instruction file. A resfile is also accepted if you wish to limit specific positions directly.
  

  -top_designs <Integer>

  Number of top designs to keep (ensemble). These will be written to a PDB and each move onto the next step in the protocol.
  Default: 1
  

  -high_mem_mode <Boolean>

  If false, we load the CDRSet (CDRs loaded from the database that could be grafted) on-the-fly for a CDR if it has more than 50 graft-design members. If true, then we cache the CDRSet before the start of the protocol. Typically, this will really only to come into play when designing all CDRs. For de-novo design of 5/6 CDRs, without limiting the CDRSet in the instructions file, you will need 3-4 gb per process for this option.
  Default: false
  

  -cdr_set_cache_limit <Integer>

  If high_mem_mode is false, this is the limit of CDRSet cacheing we do before we begin load them on-the-fly instead. If high_mem_mode is true, then we ignore this setting. If you have extremely low memory per-process, lower this number
  Default: 300
  

  -design_protocol <String>

  Set the main protocol to use. Note that deterministic is currently only available for the grafting of one CDR.
  Default: "even_cluster_mc"
  

  -run_relax <Boolean>

  Run Dualspace Relax on each ensemble after designing (after snugdock if run). Also output pre-relaxed structures
  Default: false
  

  -run_interface_analyzer <Boolean>

  Run the Interface Analyzer and add the information to the resulting score function for each top design output.
  Default: true
  

  -paratope <StringVector>

  Use these CDRs as the paratope. Default is all of them. Currently only used for constraints. Note that these site constraints are only used during docking unless -enable_full_protocol_atom_pair_cst is set.
  

  -epitope <StringVector>

  Use these residues as the antigen epitope. Default is to auto-identify them within the set interface distance at protocol start if epitope constraints are enabled. Currently only used for constraints. PDB Numbering. Optional insertion code. Example: 1A 1B 1B:A. Note that these site constraints are only used during docking unless -enable_full_protocol_atom_pair_cst is set.
  Default: []
  

  -use_epitope_constraints <Boolean>

  Enable use of epitope constraints to add SiteConstraints between the epitope and paratope. Note that paratope constraints are always used. Note that these site constraints are only used during docking unless -global_atom_pair_cst_scoring is set.
  Default: false
  

  -dihedral_cst_weight <Real>

  Weight to use for CDR CircularHarmonic cluster-based or general constraints that are automatically added to each structure and updated after each graft. Set to zero if you dont want to use these constraints. Note that they are not used for the backrub mintype. Overrides weight/patch settings.
  Default: .3
  

  -atom_pair_cst_weight <Real>

  Weight to use for Epitope/Paratope SiteConstraints. Paratope Side contraints are always used. Set to zero to completely abbrogate these constraints. Overrides weight/patch settings.
  Default: 0.01
  

  -global_dihedral_cst_scoring <Boolean>

  Use the dihedral cst score throughout the protocol, including final scoring of the poses instead of just during minimization step
  Default: false
  

  -global_atom_pair_cst_scoring <Boolean>

  Use the atom pair cst score throughout the protocol, including final scoring of the poses instead of just during docking. Typically, the scoreterm is set to zero for scorefxns other than docking to decrease bias via loop lengths, relax, etc. It may indeed help to target a particular epitope quicker during monte carlo design if epitope constraints are in use, as well for filtering final models on score towards a particular epitope if docking.
  Default: true
  

  -do_dock <Boolean>

  Run a short lowres + highres docking step in the inner cycles. (dock/min). Recommended 2 inner cycles for better coverage. (dock/min/dock/min). Inner/Outer loops for highres are hard coded, while low-res can be changed through regular low_res options. If sequence design is enabled, will design regions/CDRs set during the high-res dock. Recommended to
  Default: false
  

  -outer_cycle_rounds <Integer>

  Rounds for outer loop of the protocol (not for deterministic_graft ). Each round chooses a CDR and designs. One run of 100 cycles with relax takes about 12 hours. If you decrease this number, you will decrease your run time significantly, but your final decoys will be higher energy. Make sure to increase the total number of output structures (nstruct) if you use lower than this number. Typically about 500 - 1000 nstruct is more than sufficient. Full DeNovo design will require significantly more rounds and nstruct. If you are docking, runs take about 30 percent longer.
  Default: 25
  

  -inner_cycle_rounds <Integer>

  Number of times to run the inner minimization protocol after each graft. Higher (2-3) rounds recommended for pack/min/backrub mintypes or if including dock in the protocol.
  Default: 1
  

  -dock_cycle_rounds <Integer>

  Number of rounds for any docking. If you are seeing badly docked structures, increase this value.
  Default: 1
  

  -interface_dis <Real>

  Interface distance cutoff. Used for repacking of interface, epitope detection, etc.
  Default: 8.0
  

  -neighbor_dis <Real>

  Neighbor distance cutoff. Used for repacking after graft, minimization, etc.
  Default: 6.0
  

  -use_outliers <Boolean>

  Include outlier data for GraftDesign, profile-based sequence design stats, and cluster-based dihedral constraints. Outliers are defined as having a dihedral distance of > 40 degrees and an RMSD of >1.5 A to the cluster center. Use to increase sampling of small or rare clusters.
  Default: false
  

  -use_H3_graft_outliers <Boolean>

  Include outliers when grafting H3. H3 does not cluster well, so most structures have high dihedral distance and RMSD to the cluster center. Due to this, cluster-based dihedral constraints for H3 are not used. Sequence profiles can be used for clusters, but not usually.
  Default: true
  

  -use_only_H3_kinked <Boolean>

  Remove any non-kinked CDRs from the CDRSet if grafting H3. For now, the match is based on the ramachandran area of the last two residues of the H3. Kinked in this case is defined as having AB or DB regions at the end. Will be improved for detection.
  Default: false
  

  -design_antigen <Boolean>

  Design antigen residues during sequence design. Intelligently. Typically, only the neighbor antigen residues of designing cdrs or interfaces will be co-designed. Useful for specific applications.
  Default: false
  

  -design_framework <Boolean>

  Design framework residues during sequence design. Typically done with only neighbor residues of designing CDRs or during interface minimization.
  Default: false
  

  -conservative_framework_design <Boolean>

  If designing Framework positions, use conservative mutations instead of all of them.
  Default: true
  

  -design_H3_stem <Boolean>

  Enable design of the first 2 and last 3 residues of the H3 loop if sequence designing H3. These residues play a role in the extended vs kinked H3 conformation. Designing these residues may negatively effect the overall H3 structure by potentially switching a kinked loop to an extended and vice versa. Rosetta may get it right. But it is off by default to err on the cautious side of design. Sequence designing H3 may be already risky.
  Default: false
  

  -design_proline <Boolean>

  Enable proline design. Profiles for proline are very good, but designing them is a bit risky. Enable this if you are feeling daring.
  Default: false
  

  -sample_zero_probs_at <Real>

  Value for probabilstic design. Probability that a normally zero prob will be chosen as a potential residue each time packer task is called. Increase to increase variablility of positions.
  Default: 0
  

  -force_mutate_framework_for_cluster <Boolean>

  Force framework mutations that maintain certain clusters. Currently L1-11-1 vs L1-11-2. See North cluster paper for these dependencies, or checkout rosetta/database/sampling/antibodies/design/cluster_framework_mutations.txt
  Default: true
  

  -seq_design_stats_cutoff <Integer>

  Value for probabilistic -> conservative sequence design switch. If number of total sequences used for probabilistic design for a particular cdr cluster being designed is less than this value, conservative design will occur. More data = better predictability.
  Default: 10
  

  -seq_design_profile_samples <Integer>

  If designing using profiles, this is the number of times the profile is sampled each time packing done. Increase this number to increase variability of designs - especially if not using relax as the mintype.
  Default: 1
  

  -idealize_graft_cdrs <Boolean>

  Idealize the CDR before grafting. May help or hinder.
  Default: false
  

  -add_backrub_pivots <StringVector>

  Additional backrub pivot residues if running backrub as the MinType. PDB Numbering. Optional insertion code. Example: 1A 1B 1B:A. Can also specify ranges: 1A-10:A. Note no spaces in the range.
  

  -inner_kt <Real>

  KT used in the inner min monte carlo after each graft.
  Default: 1.0
  

  -outer_kt <Real>

  KT used for the outer graft Monte Carlo. Each graft step will use this value
  Default: 1.0
  

  -random_start <Boolean>

  Start graft design (currently) with a new set of CDRs from the CDRSets as to not bias the run with native CDRs.
  Default: false
  

  -adapt_graft <Boolean>

  Adapt the grafting algorithm to increase rate of closed grafts. Takes more time. Grafts that cannot be closed may not be very compatable with the framework in the first place.
  Default: true
  

  -enable_adapt_graft_cartesian <Boolean>

  Cartesian minimization seems to be causing numerous bugs since the Lukis AST pointer rewrite. These only happen on the cluster and it is very difficult to reproduce them. Until this is fixed, we can skip the cartesian adaptation where cartesian minimization would run when the graft could not close properly. Exceptions are wrapped so that when it does fail we skip the graft. Set this to false to disable its use
  Default: false
  

  -remove_antigen <Boolean>

  Remove the antigen from the pose before doing any design on it
  Default: false
  

  -add_graft_log_to_pdb <Boolean>

  Add the full graft log to the output pose. Must also pass -pdb_comments option.
  Default: true
  

  -mutate_framework_for_cluster <Boolean>

  Mutate the framework to maintain certain clusters post-graft.
  Default: false
  

• task_operations

  -task_operations <Boolean>

  task_operations option group
  

  -cons_design_data_source <String>

  Data source used for the ConservativeDesignOperation. This guides the set of allowed mutations. Higher blosum means higher conservation (numbers indicate sequence similarity cutoffs.
  Default: "blosum62"
  

• assembly

  -assembly <Boolean>

  assembly option group
  

  -pdb1 <File>

  pdb1 file
  

  -pdb2 <File>

  pdb2 file
  

• backrub

  -backrub <Boolean>

  backrub option group
  

  -pivot_residues <IntegerVector>

  residues for which contiguous stretches can contain segments (internal residue numbers, defaults to all residues)
  Default: utility::vector1<int>()
  

  -pivot_atoms <StringVector>

  main chain atoms usable as pivots
  Default: utility::vector1<std::string>(1, "CA")
  

  -min_atoms <Integer>

  minimum backrub segment size (atoms)
  Default: 3
  

  -max_atoms <Integer>

  maximum backrub segment size (atoms)
  Default: 34
  

  -ntrials <Integer>

  number of Monte Carlo trials to run
  Default: 1000
  

  -sc_prob <Real>

  probability of making a side chain move
  Default: 0.25
  

  -sm_prob <Real>

  probability of making a small move
  Default: 0
  

  -sc_prob_uniform <Real>

  probability of uniformly sampling chi angles
  Default: 0.1
  

  -sc_prob_withinrot <Real>

  probability of sampling within the current rotamer
  Default: 0.0
  

  -mc_kt <Real>

  value of kT for Monte Carlo
  Default: 0.6
  

  -mm_bend_weight <Real>

  weight of mm_bend bond angle energy term
  Default: 1.0
  

  -initial_pack <Boolean>

  force a repack at the beginning regardless of whether mutations are set in the resfile
  Default: false
  

  -minimize_movemap <File>

  specify degrees of freedom for minimization
  

  -trajectory <Boolean>

  record a trajectory
  Default: false
  

  -trajectory_gz <Boolean>

  gzip the trajectory
  Default: false
  

  -trajectory_stride <Integer>

  write out a trajectory frame every N steps
  Default: 100
  

• batch_relax

  -batch_relax <Boolean>

  batch_relax option group
  

  -batch_size <Integer>

  Size of batches - note that thsie affects memory usage significantly
  Default: 100
  

• bbg

  -bbg <Boolean>

  bbg option group
  

  -factorA <Real>

  Control how big the move would be(acceptance rate), default 1.0
  Default: 1.0
  

  -factorB <Real>

  Control how local the move would be(folded 10.0, unfolded 0.1), default 10.0
  Default: 10.0
  

  -ignore_improper_res <Boolean>

  Skip improper residues (proline)
  Default: false
  

  -fix_short_segment <Boolean>

  Do not apply small mover to short segments, for loop
  Default: false
  

• boinc

  -boinc <Boolean>

  boinc option group
  

  -graphics <Boolean>

  The boinc client uses this option for the windowed graphics
  Default: false
  

  -fullscreen <Boolean>

  The boinc client uses this option for the screensaver full screen graphics
  Default: false
  

  -max_fps <Integer>

  Maximum frames per second, overrides user preference.
  Default: 0
  

  -max_cpu <Integer>

  Maximum cpu percentage, overrides user preferecne.
  Default: 0
  

  -noshmem <Boolean>

  for testing graphics without shared memory.
  Default: false
  

  -cpu_run_time <Integer>

  Target cpu run time in seconds
  Default: 10800
  

  -max_nstruct <Integer>

  Maximum number of output models (failed or successful) for a given client
  Default: 99
  

  -cpu_frac <Real>

  Percentage of CPU time used for graphics
  Default: 10.0
  

  -frame_rate <Real>

  Number of frames per second for graphics
  Default: 10.0
  

  -watchdog <Boolean>

  Turn watchdog on
  Default: false
  

  -watchdog_time <Integer>

  Time interval in seconds used by watchdog to check if run is stuck or going too long (default every 5 minutes)
  Default: 300
  

  -cpu_run_timeout <Integer>

  Maximum time the WU may exceed the users WU time settings. Default is 4 hours. Used by watchdog.
  Default: 14400
  

  -description_file <File>

  work unit description file
  Default: "rosetta_description.txt"
  

  -score_cut_pct <Real>

  score cut done on the local nodes by percentage, required to return centroid models
  

  -score_cut_fl <File>

  temp file where output is stored in
  Default: "score_cut_tmp.out"
  

  -score_cut_smart_throttle <Boolean>

  makes absolutely sure you are generating < 1 model per 60 seconds.(set to 65 sec to be safe)
  

• broker

  -broker <Boolean>

  broker option group
  

  -setup <FileVector>

  setup file for topology-broker
  Default: "NO_SETUP_FILE"
  

  -rb_mover_stage1_weight <Real>

  weight of RB mover in abinitio stage 1
  Default: 5.0
  

  -large_frag_mover_stage1_weight <Real>

  weight of fragment mover in abinitio stage 1
  Default: 1.0
  

  -small_frag_mover_stage1_weight <Real>

  weight of fragment mover in abinitio stage 1
  Default: 1.0
  

• bunsat_calc2

  -bunsat_calc2 <Boolean>

  bunsat_calc2 option group
  

  -sasa_burial_cutoff <Real>

  Minimum SASA to be considered exposed
  Default: 0.01
  

  -layered_sasa <Boolean>

  Use the variable distance solvent SASA calculator for finding buried unsats
  Default: true
  

  -generous_hbonds <Boolean>

  Use generous hbond criteria
  Default: true
  

  -AHD_cutoff <Real>

  Minimum AHD angle for secondary geometry based h-bond detection
  Default: 120
  

  -dist_cutoff <Real>

  max dist
  Default: 3.0
  

  -hxl_dist_cutoff <Real>

  hxl max dist
  Default: 3.5
  

  -sulph_dist_cutoff <Real>

  max sulph dist
  Default: 3.3
  

  -metal_dist_cutoff <Real>

  max metal dist
  Default: 2.7
  

• canonical_sampling

  -canonical_sampling <Boolean>

  canonical_sampling option group
  

• canonical_sampling:probabilities

  -probabilities <Boolean>

  probabilities option group
  

  -sc <Real>

  probability of making a side chain move
  Default: 0.25
  

  -localbb <Real>

  probability of making a small move
  Default: 0.75
  

  -sc_prob_uniform <Real>

  probability of uniformly sampling chi angles
  Default: 0.1
  

  -sc_prob_withinrot <Real>

  probability of sampling within the current rotamer
  Default: 0.9
  

  -sc_prob_perturbcurrent <Real>

  probability of perturbing the current rotamer
  Default: 0.0
  

  -MPI_sync_pools <Boolean>

  use MPI to synchronize pools and communicate between nodes
  Default: false
  

  -MPI_bcast <Boolean>

  use broadcasting in syncing
  Default: false
  

  -fast_sc_moves <Boolean>

  use the fast SidechainMCMover
  Default: false
  

  -fast_sc_moves_ntrials <Real>

  specify the number of ntrials for each call of scmover apply
  Default: 1000
  

  -no_jd2_output <Boolean>

  do not write to silent-file specified by -out:file:silent
  Default: false
  

  -use_hierarchical_clustering <Boolean>

  use the HierarchicalLevel class
  Default: false
  

  -backrub <Real>

  set the probability of executing a backrub move when making a backbone move
  Default: 0.5
  

  -conrot <Real>

  set relative probability of executing a conrot move when making a backbone move
  Default: 0.0
  

• canonical_sampling:sampling

  -sampling <Boolean>

  sampling option group
  

  -no_detailed_balance <Boolean>

  preserve detailed balance
  Default: false
  

  -ntrials <Integer>

  number of Monte Carlo trials to run
  Default: 1000
  

  -mc_kt <Real>

  value of kT for Monte Carlo
  Default: 0.6
  

  -interval_pose_dump <Integer>

  dump a pose out every x steps
  Default: 1000
  

  -interval_data_dump <Integer>

  dump data out every x steps
  Default: 100
  

  -output_only_cluster_transitions <Boolean>

  output only cluster transitions
  Default: false
  

  -transition_threshold <Real>

  if rmsd to known_structures larger than X, add a new structure to pool
  Default: 2.0
  

  -max_files_per_dir <Integer>

  distribute traj and transition files into subdirectories with max N entries
  Default: 1000
  

  -save_loops_only <Boolean>

  save only loop conformation to pool
  Default: false
  

  -dump_loops_only <Boolean>

  dump only loop conformation in silent-files
  Default: false
  

• canonical_sampling:out

  -out <Boolean>

  out option group
  

  -new_structures <File>

  
  Default: "discovered_decoys.out"
  

• casp

  -casp <Boolean>

  casp option group
  

  -opt_radius <Real>

  optimization radius for repacking and minimization
  

  -repack <Boolean>

  should we repack the structure?
  

  -sc_min <Boolean>

  should we sidechain minimize the structure?
  

  -sequential <Boolean>

  should mutations be considered in sequence or all together?
  

  -num_iterations <Real>

  number of iterations to perform
  

  -refine_res <String>

  specifies file that contains which residues to refine
  

• chemically_conjugated_docking

  -chemically_conjugated_docking <Boolean>

  chemically_conjugated_docking option group
  

  -UBQpdb <File>

  ubiquitin structure, or the structure for the attached thing that is moving
  Default: "1UBQ.pdb"
  

  -E2pdb <File>

  E2 structure, or the structure of the thing that is attached to (has cysteine) and does not move; should be one chain
  Default: "2OB4.pdb"
  

  -E2_residue <Integer>

  E2 catalytic cysteine (PDB numbering) (where the ubiquitin gets attached; assumed to be on the first chain of E2pdb
  Default: 85
  

  -SASAfilter <Real>

  filter out structures with interface dSASA less than this
  Default: 1000
  

  -scorefilter <Real>

  filter out structures with total score greater than this
  Default: 10
  

  -publication <Boolean>

  output statistics used in publication. TURN OFF if not running (original Saha et al.) publication demo.
  Default: false
  

  -n_tail_res <Integer>

  Number of c-terminal ~tail~ residues to make flexible (terminus inclusive)
  Default: 3
  

  -two_ubiquitins <Boolean>

  Mind-blowing - use two ubiquitins (assembled for a K48 linkage) to try to examine the transition state. Don't use this option unless trying to reproduce publication XXXX
  Default: false
  

  -extra_bodies <FileVector>

  extra structures to add before modeling. Should be in the coordinate frame of the non-moving partner. Will not move during modeling. Will be detected as part of the nonmoving body for repacking purposes.
  Default: ""
  

  -UBQ2_lys <Integer>

  which Lys on the second UB will be conjugated
  Default: 48
  

  -UBQ2_pdb <File>

  PDB for second ubiquitin (second moving chain). Only active if -two_ubiquitins is used; inactive otherwise. Optional; defaults to value of -UBQpdb if not passed.
  

  -dont_minimize_omega <Boolean>

  disable minimization of omega angles near thioester in MoveMap; not present in original publications (Saha; Baker)
  Default: false
  

  -pdz <Boolean>

  For the UBQ_Gp_LYX-Cterm executable, if -publication is already on, switch to the PDZ center of mass instead of ubiquitin center of mass for the extra statistics calculations. Don't use this option unless trying to reproduce publication XXXX
  Default: false
  

  -GTPasepdb <File>

  GTPase structure, or the structure of the thing that is attached to (has cysteine) and does not move; should be one chain
  Default: "2OB4.pdb"
  

  -GTPase_residue <Integer>

  GTPase lysine (PDB numbering) (where the ubiquitin gets attached; assumed to be on the first chain of GTPase_pdb
  Default: 85
  

• chunk

  -chunk <Boolean>

  chunk option group
  

  -pdb2 <File>

  file for chunk2
  

  -loop2 <File>

  rigid region for chunk2
  

• cluster

  -cluster <Boolean>

  cluster option group
  

  -lite <Boolean>

  uses light-weight method of outputting cluster-centers, useful for when there's a HUGE amount of data!
  Default: false
  

  -input_score_filter <Real>

  Only read in structures below a certain energy
  Default: 1000000.0
  

  -output_score_filter <Real>

  Only read in structures below a certain energy
  Default: 1000000.0
  

  -exclude_res <IntegerVector>

  Residue numbers to be excluded from cluster RMS calculation
  Default: -1
  

  -thinout_factor <Real>

  Ignore this fraction of decoys in the first round !
  Default: -1
  

  -radius <Real>

  Cluster radius
  Default: 3.0
  

  -limit_cluster_size <Integer>

  For each cluster only retain top N
  Default: -1
  

  -limit_cluster_size_percent <Real>

  0 to 1. For each cluster only retain top N %
  

  -random_limit_cluster_size_percent <Real>

  0 to 1. For each cluster only retain random N %
  

  -limit_clusters <Integer>

  Only retain largest N clusters
  Default: 100
  

  -limit_total_structures <Integer>

  Only retain the first N structures (ordered by cluster number)
  Default: -1
  

  -max_total_cluster <Integer>

  Only ever make N clusters or less
  Default: 1000
  

  -gdtmm <Boolean>

  Cluster by gdtmm instead of RMS
  Default: false
  

  -skip_align <Boolean>

  Cluster without aligning the structures
  Default: false
  

  -max_rms_matrix <Integer>

  Maximum number of structures to use to calculate the full RMSD matrix
  Default: 400
  

  -rna_P <Boolean>

  Calculate rmsd from backbone phosphate positions only
  Default: false
  

  -sort_groups_by_energy <Boolean>

  Sort clusters by energy
  Default: false
  

  -sort_groups_by_size <Boolean>

  Sort clusters by energy
  Default: false
  

  -remove_singletons <Boolean>

  Get rid of single-member clusters
  Default: false
  

  -export_only_low <Boolean>

  Print only the lowest energy member
  Default: false
  

  -remove_highest_energy_member <Boolean>

  Remove highest energy member from each cluster
  Default: false
  

  -idealize_final_structures <Boolean>

  Run an idealization over the resulting structures
  Default: false
  

  -limit_dist_matrix <Integer>

  Only calculate full matrix for a subset of structres. Then simply assign structures to nearest cluster
  Default: -1
  

  -make_ensemble_cst <Boolean>

  Create a set of constraints describing the variablity in each cluster of each residue.
  Default: false
  

  -hotspot_hash <Boolean>

  Cluster hotspot hashing results. Each input PDB must contain both the target and the newly docked hotspot (which should be the last residue in the pose).
  Default: false
  

  -loops <Boolean>

  Cluster the loop specified with the -loops:loop_file option
  Default: false
  

  -population_weight <Real>

  Order Clusters by (1-p)*score - p*size whpere p = population_weight
  Default: 0.09
  

  -template_scores <String>

  imple textfile containing template names (in caps) and scores.
  

  -K_level <Integer>

  Hierarchical cluster level number
  Default: 1
  

  -K_radius <RealVector>

  Radius list of different level of cluster
  Default: utility::vector1<float>(1, 2.0)
  

  -K_n_cluster <IntegerVector>

  How many clusters in each level
  Default: utility::vector1<int>(1, 10000)
  

  -K_style <StringVector>

  Which K-cluster engine to use
  Default: utility::vector1<std::string>(9, "GKC")
  

  -K_n_sub <Integer>

  Number of clusters in subdir
  Default: 100
  

  -K_deque_size <Integer>

  Size of subcluster deque
  Default: 20
  

  -K_deque_level <Integer>

  Provide deque in top level
  Default: 1
  

  -K_redundant <Boolean>

  Keep all the higher level center structure in sub-pools
  Default: true
  

  -K_not_fit_xyz <Boolean>

  Do not rotate xyz when calculate rmsd
  Default: false
  

  -K_save_headers <Boolean>

  Save headers in silent file
  Default: false
  

  -score_diff_cut <Real>

  score difference cut for RNA and SWA clustering
  Default: 1000000.0
  

  -auto_tune <Boolean>

  autotune rmsd for clustering between 0.1A up to 2.0A, for SWA clusterer
  Default: false
  

  -write_centers <Boolean>

  Write out a silent file with the cluster centers
  Default: false
  

• cluster:energy_based_clustering

  -energy_based_clustering <Boolean>

  energy_based_clustering option group
  

  -prerelax <Boolean>

  Should imported structures be subjected to a round of fast relaxation? Default false.
  Default: false
  

  -relax_rounds <Integer>

  The number of fastrelax rounds to apply if the -cluster:energy_based_clustering:prerelax option is used. Default 1.
  Default: 1
  

  -cluster_by <String>

  What should I use as the basis for clustering? Options are bb_cartesian (xyz coordinates of backbone atoms) and bb_dihedral (phi, psi, omega angles). Default is bb_cartesian.
  Default: "bb_cartesian"
  

  -use_CB <Boolean>

  If clustering by backbone Cartesian coordinates, should beta carbons be included? Default false. Note that if this option is used, none of the input structures can contain glycine.
  Default: false
  

  -cluster_radius <Real>

  The radius for clustering, in Angstroms for Cartesian clustering and degrees for dihedral clustering. Default 1.0.
  Default: 1.0
  

  -residues_to_ignore <IntegerVector>

  List of residues to ignore in alignments for clustering. Default empty list.
  

  -chains_to_ignore <IntegerVector>

  List of chains to ignore in alignments for clustering. Default empty list.
  

  -limit_structures_per_cluster <Integer>

  Maximum number of structures to output per cluster. Default no limit (0).
  Default: 0
  

  -limit_clusters <Integer>

  Maximum number of clusters to output. Default no limit (0).
  Default: 0
  

  -cyclic <Boolean>

  If true, constraints are added to make a peptide bond between the N- and C-termini. If false (default), the termini are free. Default false.
  Default: false
  

  -cyclic_symmetry <Integer>

  If provided, structures that do not have the desired symmetry are filtered out. Set to 2 for C2 or S2 symmetry, 3 for C3 symmetry, 4 for C4 or S4 symmetry, etc. Unused (0) if not specified. Can only be used with the -cluster:energy_based_clustering:cyclic flag.
  Default: 0
  

  -cyclic_symmetry_mirroring <Boolean>

  If true, then SN symmetry is used instead of CN. Unused if not specified. Can only be used with the -cluster:energy_based_clustering:cyclic and -cluster:energy_based_clustering:cyclic_symmetry flags.
  Default: false
  

  -cyclic_symmetry_threshold <Real>

  The angle threshold, in degrees, for determining whether a cyclic peptide is symmetric. Can only be used with the -cluster:energy_based_clustering:cyclic and -cluster:energy_based_clustering:cyclic_symmetry flags. Defaults to 10.0 degrees.
  Default: 10.0
  

  -cluster_cyclic_permutations <Boolean>

  If true, all cyclic permutations are tried when comparing two structures for clustering. Requires -cluster:energy_based_clustering:cyclic true. Default false.
  Default: false
  

  -cyclic_permutation_offset <Integer>

  1 by default, meaning that every cyclic permutation is clustered if -cluster:energy_based_clustering:cluster_cyclic_permutations is true. Values X > 1 mean that cyclic permutations shifted by X residues will be clustered.
  Default: 1
  

  -mutate_to_ala <Boolean>

  If true, the input structures will be converted to a chain of alanines (L- or D-) before scoring. Default false.
  Default: false
  

  -disulfide_positions <IntegerVector>

  A space-separated list of positions that are disulfide-bonded. For example, -cluster:energy_based_clustering:disulfide_positions 3 8 6 23 would mean that residues 3 and 8 are disulfide-bonded, as are residues 6 and 23. Defaults to an empty list of the option is not specified, in which case disulfides are auto-detected.
  

  -homooligomer_swap <Boolean>

  If the structures contain multiple chains with identical sequence, setting this to true will test all permutations of chains when clustering. Default false.
  Default: false
  

  -silent_output <Boolean>

  Write output to a silent file instead of to separate PDBs. This will create two files: one that only contains the first member of each cluster, and one that contains everything. Default false.
  Default: false
  

  -cst_file <FileVector>

  An optional, user-specified list of one or more constraints files. Default unused.
  

  -extra_rms_atoms <StringVector>

  A list of additional atoms to use in the RMSD calculation, each in the format residue:atomname separated by whitespace. For example, -extra_rms_atoms 7:SG 12:CG 12:CD 12:CE 12:NZ 14:OG. Default empty list.
  

  -rebuild_all_in_dihedral_mode <Boolean>

  If true, full poses are rebuilt for output when clustering in dihedral mode. If false, only backbones are written out. True by default.
  Default: true
  

• partial_thread

  -partial_thread <Boolean>

  partial_thread option group
  

  -skip_repack <Boolean>

  Do not repack sidechain missing density and idealize/optimize h-bonds
  Default: false
  

• cm

  -cm <Boolean>

  cm option group
  

• cm:sanitize

  -sanitize <Boolean>

  sanitize option group
  

  -num_fragments <Integer>

  Use the top k fragments at each position during sanitization
  Default: 25
  

  -cst_weight_pair <Real>

  atom_pair_constraint weight
  Default: 1.0
  

  -cst_weight_coord <Real>

  coordinate_constraint weight
  Default: 1.0
  

• cm

  -start_models_only <Boolean>

  Make starting models only!
  Default: false
  

  -aln_format <String>

  No description
  Default: "grishin"
  

  -recover_side_chains <Boolean>

  recover side-chains
  Default: false
  

  -steal_extra_residues <FileVector>

  list of template extra residues (ie ligands) to add to query pose in comparative modeling
  

  -loop_mover <String>

  No description
  Default: "quick_ccd"
  

  -loop_close_level <Integer>

  level of aggressiveness to use in closing loops. The integers that follow flags specify how aggressively loops are rebuilt. Each option implies all non-zero levels below it, so that loop_close_level 2 implies level 1 as well. Meaning of the options are: NO_REBUILD 0 don't rebuild loops at all REBUILD_UNALIGNED 1 rebuild loops around unaligned regions REBUILD_CHAINBREAK 2 rebuild loops around chainbreaks REBUILD_EXHAUSTIVE 3 rebuild loops around regions with a chainbreak until no chainbreaks remain
  Default: 0
  

  -min_loop_size <Integer>

  Minimum size of loops to remodel when building threading models.
  Default: 5
  

  -max_loop_rebuild <Integer>

  Maximum number of times to try to rebuild a loop before giving up.
  Default: 10
  

  -loop_rebuild_filter <Real>

  Maximum score a structure must have after loop rebuilding.
  Default: 0
  

  -aln_length_filter_quantile <Real>

  Only use alignment lengths longer than the Xth quantile. e.g. setting this to 0.75 will only use the 25% longest alignments
  Default: 0.0
  

  -aln_length_filter <Integer>

  Only use alignment longer or equal to this length
  Default: -1
  

  -seq_score <StringVector>

  sequence-based scoring scheme used for generating alignments
  Default: utility::vector1<std::string>(1,"Simple")
  

  -aligner <String>

  algorithm for making sequence alignments
  

  -min_gap_open <Real>

  gap opening penalty for sequence alignments (usually negative)
  Default: -2.0
  

  -max_gap_open <Real>

  gap opening penalty for sequence alignments (usually negative)
  Default: -2.0
  

  -min_gap_extend <Real>

  gap extension penalty for sequence alignments (usually negative)
  Default: -0.2
  

  -max_gap_extend <Real>

  gap extension penalty for sequence alignments (usually negative)
  Default: -0.2
  

  -nn <Integer>

  number of neighbors to include in constraint derivation
  Default: 500
  

  -ev_map <FileVector>

  Input file that maps pdbChains to blast e-values
  

  -hh_map <FileVector>

  Input file that maps pdbChains to hhsearch probabilities
  

  -seeds <IntegerVector>

  list of tags used as seed parents at prv iteration
  

  -quota_per_silent <RealVector>

  quota for picking input structures associated with -in:file:silent
  

  -similarity_cut <Real>

  Distance cut on the structure population, used for CSA (in S-score)
  

  -similarity_limit <Real>

  Distance cut for initial filtering (in S-score)
  

  -refsimilarity_cut <Real>

  Lower threshold on model-to-template GDT-HA where it starts to get penalty
  Default: 25
  

• cm:hybridize

  -hybridize <Boolean>

  hybridize option group
  

  -starting_template <IntegerVector>

  Define starting templates
  

  -realign_domains <Boolean>

  domain parse and realign the starting templates
  Default: true
  

  -realign_domains_stage2 <Boolean>

  realign the starting templates to the pose after stage1
  Default: true
  

  -add_non_init_chunks <Integer>

  add (on average) this many non-template chunks
  Default: 0
  

  -stage1_increase_cycles <Real>

  Scale stage 1 cycles
  Default: 1.0
  

  -stage2_increase_cycles <Real>

  Scale stage 2 cycles
  Default: 1.0
  

  -stage2min_increase_cycles <Real>

  Scale minimizer cycles after stage 2
  Default: 1.0
  

  -stage1_probability <Real>

  Probability of hybridizing in stage 1, 0=never, 1=always
  Default: 1.0
  

  -skip_stage2 <Boolean>

  skip cartesian fragment hybridize stage
  Default: false
  

  -no_global_frame <Boolean>

  no global-frame fragment insertions
  Default: false
  

  -linmin_only <Boolean>

  linmin only in stage 2
  Default: false
  

  -relax <Integer>

  if n==1, perform relax at end; if n>1 perform batch relax over n centroids
  Default: 0
  

  -frag_weight_aligned <Real>

  Probability of fragment insertion in the aligned region
  Default: 0.
  

  -max_registry_shift <Integer>

  maximum registry shift
  Default: 0
  

  -frag_1mer_insertion_weight <Real>

  weight for 1mer fragment insertions where fragments are not allowed vs. template chunk insertions in stage1
  Default: 0.0
  

  -small_frag_insertion_weight <Real>

  weight for small fragment insertions where large fragments are not allowed vs. template chunk insertions in stage1
  Default: 0.0
  

  -big_frag_insertion_weight <Real>

  weight for big fragment insertions vs. template chunk insertions in stage1
  Default: 0.5
  

  -auto_frag_insertion_weight <Boolean>

  automatically set the weight for fragment insertions vs. template chunk insertions in stage1
  Default: true
  

  -stage1_1_cycles <Integer>

  Number of cycles for ab initio stage 1 in Stage1
  Default: 2000
  

  -stage1_2_cycles <Integer>

  Number of cycles for ab initio stage 2 in Stage1
  Default: 2000
  

  -stage1_3_cycles <Integer>

  Number of cycles for ab initio stage 3 in Stage1
  Default: 2000
  

  -stage1_4_cycles <Integer>

  Number of cycles for ab initio stage 4 in Stage1
  Default: 400
  

  -stage2_temperature <Real>

  Monte Carlo temperature in the stage2
  Default: 2.0
  

  -stage1_4_cenrot_score <String>

  Switch to cenrot model in stage1_4
  Default: "score_cenrot_cm_stage1_4.wts"
  

  -include_loop_ss_chunks <Boolean>

  include loop secondary structure chunks from templates
  Default: false
  

• contactMap

  -contactMap <Boolean>

  contactMap option group
  

  -prefix <String>

  Prefix of contactMap filename
  Default: "contact_map_"
  

  -distance_cutoff <Real>

  Cutoff Backbone distance for two atoms to be considered interacting
  Default: 10.0
  

  -region_def <String>

  Region definition for comparison eg: 1-10:20-30,40-50,A:ligand=X
  Default: ""
  

  -row_format <Boolean>

  Flag whether to output in row instead of matrix format
  Default: false
  

  -distance_matrix <Boolean>

  Output a distance matrix instead of a contact map
  Default: false
  

• coupled_moves

  -coupled_moves <Boolean>

  coupled_moves option group
  

  -ntrials <Integer>

  number of Monte Carlo trials to run
  Default: 1000
  

  -number_ligands <Integer>

  number of ligands in the pose
  Default: 1
  

  -mc_kt <Real>

  value of kT for Monte Carlo
  Default: 0.6
  

  -boltzmann_kt <Real>

  value of kT for Boltzmann weighted moves
  Default: 0.6
  

  -mm_bend_weight <Real>

  weight of mm_bend bond angle energy term
  Default: 1.0
  

  -trajectory <Boolean>

  record a trajectory
  Default: false
  

  -trajectory_gz <Boolean>

  gzip the trajectory
  Default: false
  

  -trajectory_stride <Integer>

  write out a trajectory frame every N steps
  Default: 100
  

  -trajectory_file <String>

  name of trajectory file
  Default: "traj.pdb"
  

  -output_fasta <String>

  name of FASTA output file
  Default: "sequences.fasta"
  

  -output_stats <String>

  name of stats output file
  Default: "sequences.stats"
  

  -ligand_mode <Boolean>

  if true, model protein ligand interaction
  Default: false
  

  -initial_repack <Boolean>

  start simulation with repack and design step
  Default: true
  

  -min_pack <Boolean>

  use min_pack for initial repack and design step
  Default: false
  

  -save_sequences <Boolean>

  save all unique sequences
  Default: true
  

  -save_structures <Boolean>

  save structures for all unique sequences
  Default: false
  

  -ligand_prob <Real>

  probability of making a ligand move
  Default: 0.1
  

  -fix_backbone <Boolean>

  do not make any backbone moves
  Default: false
  

  -uniform_backrub <Boolean>

  select backrub rotation angle from uniform distribution
  Default: false
  

  -bias_sampling <Boolean>

  if true, bias rotamer selection based on energy
  Default: true
  

  -bump_check <Boolean>

  if true, use bump check in generating rotamers
  Default: true
  

  -ligand_weight <Real>

  weight for residue - ligand interactions
  Default: 1.0
  

  -output_prefix <String>

  prefix for output files
  Default: ""
  

• cp

  -cp <Boolean>

  cp option group
  

  -cutoff <Real>

  designable neighbor cutoff
  Default: 16
  

  -relax_sfxn <String>

  score function for final relaxation step
  Default: "score12_full"
  

  -pack_sfxn <String>

  score function for mutational trials
  Default: "gauss"
  

  -minimizer_score_fxn <String>

  score function for initial minimization
  Default: "score12_full"
  

  -output <String>

  file where we want to dump the final pose
  Default: "final_mutant.pdb"
  

  -ncycles <Integer>

  how many cycles to run refinement for
  Default: 0
  

  -max_failures <Integer>

  how many failures to tolerate at each iteration before quitting
  Default: 1
  

  -print_reports <Boolean>

  print reports to text file?
  Default: false
  

  -vipReportFile <String>

  File to print reports to
  Default: "reports.txt"
  

  -exclude_file <String>

  Optional input file to specify positions that should not be mutated
  Default: "cp_excludes"
  

  -relax_mover <String>

  relax w/o constraints=relax, w constraints=cst_relax
  Default: "relax"
  

  -skip_relax <Boolean>

  Skip relax step... may reduce accurate identification of mutations
  Default: false
  

  -local_relax <Boolean>

  Limit relax step to neighbors
  Default: false
  

  -print_intermediate_pdbs <Boolean>

  Output a pdb file for each consecutive mutation
  Default: false
  

  -use_unrelaxed_starting_points <Boolean>

  For subsequent iterations, uses mutation before relaxation
  Default: false
  

  -easy_vip_acceptance <Boolean>

  For all iterations, use initial energy for acceptance test
  Default: false
  

• cryst

  -cryst <Boolean>

  cryst option group
  

  -mtzfile <String>

  mtz file
  

  -crystal_refine <Boolean>

  Turns on crystal-refinement-specific options
  Default: false
  

  -refinable_lattice <Boolean>

  In MakeLatticeMover, are the lattice dimensions refineable?
  Default: true
  

  -interaction_shell <Real>

  In MakeLatticeMover, what is default interaction shell?
  Default: 12.0
  

• csa

  -csa <Boolean>

  csa option group
  

  -useZ <Boolean>

  Use absolute zaxis for scoring csa
  

• cutoutdomain

  -cutoutdomain <Boolean>

  cutoutdomain option group
  

  -start <Integer>

  start residue
  Default: 1
  

  -end <Integer>

  end residue
  Default: 2
  

• cyclization

  -cyclization <Boolean>

  cyclization option group
  

  -chains_to_cyclize <IntegerVector>

  The chain number to cyclize
  

  -num_min_rebuild <Integer>

  The number of time to iterate between minimization and rebuilding the connection dependant atom positions
  Default: 3
  

  -add_constraints <Boolean>

  The add constraints to maintain cycle geometry
  Default: true
  

• cyclic_peptide

  -cyclic_peptide <Boolean>

  cyclic_peptide option group
  

  -cyclization_type <String>

  The type of cyclization for the peptide (e.g. N-to-C amide bond, terminal disulfide, isopeptide N-terminal lariat, etc.
  Default: "n_to_c_amide_bond"
  

  -rand_checkpoint_file <String>

  The name of the checkpoint file used for the random number generator. Defaults to rng.state.gz. Not used if the -cyclic_peptide:checkpoint_job_identifier flag isn't used.
  Default: "rng.state.gz"
  

  -checkpoint_file <String>

  The name of the checkpoint file. Defaults to checkpoint.txt. Not used if the -cyclic_peptide:checkpoint_job_identifier flag isn't used.
  Default: "checkpoint.txt"
  

  -checkpoint_job_identifier <String>

  A unique job name for checkpointing. If none is provided, jobs are not checkpointed.
  Default: ""
  

  -default_rama_sampling_table <String>

  A custom rama table used for sampling, applied by default to all residues unless the –cyclic_peptide:rama_sampling_table_by_res flag overrides this. Default unused (in which case the default rama tables for each residue type are used).
  Default: ""
  

  -rama_sampling_table_by_res <StringVector>

  Custom rama tables that are to be used for sampling on a per-residue basis. These must be specified as pairs of [residue_index table_name]. For example: -rama_sampling_table_by_res 2 flat_symm_gly_ramatable 3 flat_symm_pro_ramatable. Specified values override the -default_rama_sampling_table at the relevant positions.
  

  -sequence_file <String>

  Filename of a file specfying the sequence, as a series of whitespace-separated full residue names (e.g. ALA LYS DARG DPRO HYP). Required input for the simple_cycpep_predict app.
  

  -genkic_closure_attempts <Integer>

  How many closure attempts should we make for each job attempted by the simple_cycpep_predict app? Default 1,000.
  Default: 1000
  

  -genkic_min_solution_count <Integer>

  How many solutions should genKIC find before picking one when used in the simple_cycpep_predict app? Default 1.
  Default: 1
  

  -cyclic_permutations <Boolean>

  Should cyclic permutations of the sequence be considered when setting up the kinematic closure? Default true.
  Default: true
  

  -use_rama_filter <Boolean>

  Should GenKIC solutions be filtered based on rama score in the simple_cycpep_predict app? True by default.
  Default: true
  

  -rama_cutoff <Real>

  The maximum rama score value that's permitted in the accepted GenKIC solutions if the use_rama_filter option is passed to the simple_cycpep_predict app. Default 0.8.
  Default: 0.8
  

  -high_hbond_weight_multiplier <Real>

  In parts of the simple_cycpep_predict protocol involving upweighting of the backbone hbond terms, by what factor should backbone hbond energy be upweighted? Default 10.0.
  Default: 10.0
  

  -min_genkic_hbonds <Real>

  The minimum number of backbone hbonds for a solution to pass during GenKIC closure in the simple_cycpep_predict app. Default 3.
  Default: 3.0
  

  -min_final_hbonds <Real>

  The minimum number of backbone hbonds for a solution to pass after final relaxtion in the simple_cycpep_predict app. Default 0 (report only).
  Default: 0.0
  

  -total_energy_cutoff <Real>

  An absolute energy threshold, above which solutions are discarded. Unused if not specified.
  Default: 0.0
  

  -hbond_energy_cutoff <Real>

  The mainchain hbond energy threshold for something to be counted as a hydrogen bond in the simple_cycpep_predict app. Default -0.25.
  Default: -0.25
  

  -do_not_count_adjacent_res_hbonds <Boolean>

  When counting hydrogen bonds to a residue, should we skip hydrogen bonds to adjacent residues? Default true.
  Default: true
  

  -fast_relax_rounds <Integer>

  The number of rounds of FastRelax to perform at each FastRelax step in the simple_cycpep_predict protocol. Note that there are two such steps: a high-hbond initial FastRelax applied to all GenKIC solutions, and a regular scorefunction final FastRelax applied to the best GenKIC solution. Default 3.
  Default: 3
  

  -count_sc_hbonds <Boolean>

  Should sidechain-backbone and sidechain-sidechain hydrogen bonds be counted in the total hydrogen bond count in the simple_cycpep_predict protocol? Default false.
  Default: false
  

  -require_disulfides <Boolean>

  If true, accepted conformations must permit disulfides to be formed. All permutations of disulfides will be considered, between all disulfide-forming residues. Default false.
  Default: false
  

  -disulf_cutoff_prerelax <Real>

  If require_disulfides is true, this is the maximum disulfide energy per disulfide bond that is allowed prior to relaxation. If the energy exceeds this value, the solution is rejected. Default 15.0.
  Default: 15.0
  

  -disulf_cutoff_postrelax <Real>

  If require_disulfides is true, this is the maximum disulfide energy per disulfide bond that is allowed following relaxation. If the energy exceeds this value, the solution is rejected. Default 0.5.
  Default: 0.5
  

  -user_set_alpha_dihedrals <RealVector>

  Allows the user to specify the dihedrals values at one or more alpha-amino acid positions in the peptide. The flag must be followed by groups of four numbers, where the first is the sequence position and the second, third, and fourth are the phi, psi, and omega values, respectively. Not used if not specified.
  

  -user_set_alpha_dihedral_perturbation <Real>

  A small, random perturbation added to all dihedral values set with the -user_set_alpha_dihedrals value. Zero if not specified.
  Default: 0.0
  

  -filter_oversaturated_hbond_acceptors <Boolean>

  If true, sampled conformations with more than the allowed number of hydrogen bonds to an acceptor are discarded. True by default.
  Default: true
  

  -hbond_acceptor_energy_cutoff <Real>

  The hydrogen bond energy above which we do not count a hydrogen bond. Default -0.1.
  Default: -0.1
  

  -sample_cis_pro_frequency <Real>

  The fraction of the time that omega=0 degrees is sampled at positions preceding L-proline or D-proline. Defaults to 0.3. Set this to 0.0 to prevent all cis-pro sampling.
  Default: 0.3
  

  -design_peptide <Boolean>

  If true, then design is attempted for every conformation sampled that passes filters. Default false.
  Default: false
  

  -allowed_residues_by_position <File>

  A text file that lists allowed amino acid resides at each position in the peptide. Each line must be a whiltespace-separated list of full amino acid names, with the positon index at the start of the line. Optionally, a DEFAULT setting may be provided (where DEFAULT replaces the position index), which is applied to all positions in the absence of a line describing what's allowed at that position. In the absence of a DEFAULT line, non-specified positions are repacked with no design. Not used if not specified (in which case all D- and L-amino acids except cysteine, glycine, and methionine are allowed at all positions).
  

  -prohibit_D_at_negative_phi <Boolean>

  If design is allowed, should D-amino acid residues be prohibited at positions with negative phi values? Default true.
  Default: true
  

  -prohibit_L_at_positive_phi <Boolean>

  If design is allowed, should L-amino acid residues be prohibited at positions with positive phi values? Default true.
  Default: true
  

  -L_alpha_comp_file <File>

  If design is allowed, this is the (optional) aa_composition file used for the right-handed (L-amino acid) alpha-helical region of Ramachandran space. Unused if not specified.
  

  -D_alpha_comp_file <File>

  If design is allowed, this is the (optional) aa_composition file used for the left-handed (D-amino acid) alpha-helical region of Ramachandran space. Unused if not specified.
  

  -L_beta_comp_file <File>

  If design is allowed, this is the (optional) aa_composition file used for the negative-phi (L-amino acid) beta-strand region of Ramachandran space. Unused if not specified.
  

  -D_beta_comp_file <File>

  If design is allowed, this is the (optional) aa_composition file used for the positive-phi (D-amino acid) beta-strand region of Ramachandran space. Unused if not specified.
  

  -angle_relax_rounds <Integer>

  The number of rounds of FastRelax to perform with flexible bond angles after each standard FastRelax step in the simple_cycpep_predict protocol. Default 0 (unused).
  Default: 0
  

  -angle_length_relax_rounds <Integer>

  The number of rounds of FastRelax to perform with flexible bond angles and bond lengths after each standard FastRelax step in the simple_cycpep_predict protocol. Default 0 (unused).
  Default: 0
  

  -cartesian_relax_rounds <Integer>

  The number of rounds of Cartesian FastRelax to perform after each standard FastRelax step in the simple_cycpep_predict protocol. Default 0 (unused).
  Default: 0
  

  -use_classic_rama_for_sampling <Boolean>

  If true, classic Ramachandran tables are used for sampling instead of the RamaPrePro tables. Default false (i.e. newer RamaPrePro tables are used by default).
  Default: false
  

  -lariat_sidechain_index <Integer>

  If a lariat cyclization type is specified (e.g. nterm_isopeptide_lariat, cterm_isopeptide_lariat), then this is the residue that provides the side-chain that connects to the N- or C-terminus of the peptide. If not specified, the residue of appropriate type closest to the other end is used.
  Default: 0
  

  -sidechain_isopeptide_indices <IntegerVector>

  If the sidechain_isopeptide cyclization type is specified, these are the indices of the residues that are linked by a sidechain-sidechain isopeptide bond to make the loop. If not specified, the residues furthest apart of appropriate types are used. Note that exactly two indices must be given.
  

  -TBMB_positions <IntegerVector>

  If provided, then these positions will be linked by a 1,3,5-tris(bromomethyl)benzene crosslinker. 3N positions must be specified, and every group of three will be linked. Unused if not specified.
  

  -use_TBMB_filters <Boolean>

  If true, then filters are applied based on distance between TBMB cysteines and on constraints to discard GenKIC solutions that can't be crosslinked easily. True by default.
  Default: true
  

  -TBMB_sidechain_distance_filter_multiplier <Real>

  A multiplier for the distance cutoff for TBMB cysteines. Higher values result in more permissive filtering. Default 1.0.
  Default: 1.0
  

  -TBMB_constraints_energy_filter_multiplier <Real>

  A multiplier for the constraints energy for TBMB cysteines. Higher values result in more permissive filtering. Default 1.0.
  Default: 1.0
  

  -link_all_cys_with_TBMB <Boolean>

  If true, then all cysteine residues in the peptide are linked with 1,3,5-tris(bromomethyl)benzene. There must be exactly three cysteine residues for this flag to be used, and it cannot be used with the -TBMB_positions flag. False/unused by default.
  Default: false
  

  -TMA_positions <IntegerVector>

  If provided, then these positions will be linked by a trimesic acid crosslinker. The positions must have sidechain primary amines (i.e. be one of lysine [LYS], ornithine [ORN], 2,4-diaminobutyric acid [DAB], or 2,3-diaminopripionic acid [DPP]. There must be 3N positions specified, and every group of three will be linked. Unused if not specified.
  

  -use_TMA_filters <Boolean>

  If true, then filters are applied based on distance between TMA-conjugated sidechains and on constraints to discard GenKIC solutions that can't be crosslinked easily. True by default.
  Default: true
  

  -TMA_sidechain_distance_filter_multiplier <Real>

  A multiplier for the distance cutoff for side-chains linked by trimseic acid (TMA). Higher values result in more permissive filtering. Default 1.0.
  Default: 1.0
  

  -TMA_constraints_energy_filter_multiplier <Real>

  A multiplier for the constraints energy for side-chains linked by trimseic acid (TMA). Higher values result in more permissive filtering. Default 1.0.
  Default: 1.0
  

  -require_symmetry_repeats <Integer>

  If this option is used, then only backbones that are cN (or cN/m, if mirror symmetry is required) symmetric will be accepted. For example, if set to 2, then only c2-symmetric backbones will be accepted. Unused if not specified.
  Default: 1
  

  -require_symmetry_mirroring <Boolean>

  If this option is used, then only backbones with mirror symmetry are accepted. Must be used with the -cyclic_peptide:require_symmetry_repeats flag.
  Default: false
  

  -require_symmetry_angle_threshold <Real>

  The cutoff, in degrees, to use when comparing mainchain torsion values to determine whether symmetry repeats are truely symmetric. Defaults to 10 degrees.
  Default: 10.0
  

  -require_symmetry_perturbation <Real>

  If provided, this is the magnitude of the perturbation to apply when copying mainchain dihedrals for symmetric sampling. Allows slightly asymmetric conformations to be sampled. Default is 0.0 (no perturbation).
  Default: 0.0
  

  -MPI_processes_by_level <IntegerVector>

  The number of processes at each level of the parallel communications hierarchy, used only by the MPI version. For example, '1 10 100' would mean that one emperor would talk to 10 masters, which would talk to 100 slaves (implying that each master is assigned 100 slaves). Similarly, '1 100' would mean that one master would talk directly to 100 slaves. Required for the MPI version.
  

  -MPI_batchsize_by_level <IntegerVector>

  The number of jobs sent at a time by each communication level to its children. Given N levels, N-1 values must be specified. For example, given 3 communications levels, '100 10' would mean that the emperor sends 100 jobs at a time to each master, which sends 10 jobs at a time to each slave. Must be specified for the simple_cycpep_predict application in MPI mode.
  

  -MPI_sort_by <String>

  The MPI version of the simple_cycpep_predict app has the option of writing out the top N% of solutions. This determines the sort metric.
  Default: "energy"
  

  -MPI_choose_highest <Boolean>

  When outputing the top N% of solutions, should I choose the ones with the higest score for the metric chosen (energy, rmsd, hbonds, etc.) or lowest? Default false (chose lowest).
  Default: false
  

  -MPI_output_fraction <Real>

  The fraction of total structures that will be written out. This is used in conjunction with 'MPI_sort_by' to output the top N% of job outputs. For example, '-MPI_output_fraction 0.05 -MPI_sort_by rmsd' means that the 5% of structures with the lowest RMSD values will be written out.
  Default: 1.0
  

  -MPI_stop_after_time <Integer>

  If this option is used, the emperor node will send a stop signal after an elapsed period of time, given in seconds. Slaves jobs currently running will continue, but intermediate masters will not assign any more work. Useful on HPC clusters with time limits, to ensure that jobs completed are collected at the end. Unused if not specified.
  

  -MPI_pnear_lambda <Real>

  In MPI mode a goodness-of-funnel metric is automatically calculated at the end (PNear). This value may be thought of as the probability, from 0 to 1, of the peptide being in the target conformation at any given time. The parameter lambda controls the bredth of the Gaussian (in RMSD units – Angstroms) that is used to determine whether a state is native-like or not. Default 0.5 A.
  Default: 0.5
  

  -MPI_pnear_kbt <Real>

  In MPI mode a goodness-of-funnel metric is automatically calculated at the end (PNear). This value may be thought of as the probability, from 0 to 1, of the peptide being in the target conformation at any given time. The parameter kbt is the Boltzmann temperature that determines the extent to which higher energy states are likely to be sampled. Default 1.0 Rosetta energy units.
  Default: 1.0
  

  -threads_per_slave <Integer>

  In the multi-threaded MPI compilation, this is the number of threads to launch per slave process. Note that emperor and master-layer processes do not launch threads. A value of 1 (the default) means that only standard hierarchical process-based parallelism will be used. In non-MPI or non-threaded compilations, this option is unused.
  Default: 1
  

• dc

  -dc <Boolean>

  dc option group
  

  -useZ <Boolean>

  Use absolute zaxis for scoring dc
  

• ddg

  -ddg <Boolean>

  ddg option group
  

  -opt_input_structure <Boolean>

  No description
  Default: false
  

  -pack_until_converge <Boolean>

  No description
  Default: false
  

  -no_constraints <Boolean>

  No description
  Default: false
  

  -use_rotamer_constraints_to_native <Boolean>

  No description
  Default: false
  

  -suppress_checkpointing <Boolean>

  boinc specific options to suppress checkpointing behavior
  Default: false
  

  -wt_only <Boolean>

  option added to minirosetta app in order to produce only refinement in wt structures
  

  -mut_only <Boolean>

  options added to minirosetta app in order to produce refinement in only mutant structure
  

  -output_silent <Boolean>

  No description
  

  -minimization_scorefunction <String>

  No description
  

  -minimization_patch <String>

  No description
  

  -min_cst <Boolean>

  Following sidechain optimization in the packer, should we then proceed to minimize the backbone at all. Constraints will be used to keep the structure from moving too far.
  Default: true
  

  -lowest_x_decoys <Integer>

  No description
  

  -local_opt_only <Boolean>

  No description
  Default: false
  

  -print_per_res_diff <Boolean>

  No description
  Default: false
  

  -mean <Boolean>

  No description
  

  -min <Boolean>

  No description
  

  -no_bb_movement <Boolean>

  No description
  Default: false
  

  -initial_repack <Boolean>

  No description
  Default: false
  

  -interface_ddg <Integer>

  Calculate ddGs across an interface? Uses jump # specified for determining interface.
  Default: 0
  

  -ens_variation <Real>

  No description
  Default: 0.5
  

  -sc_min_only <Boolean>

  No description
  Default: true
  

  -rna_all_prot_sc_min_only <Boolean>

  No description
  Default: false
  

  -min_cst_weights <String>

  No description
  Default: "talaris2013"
  

  -opt_radius <Real>

  No description
  Default: 8.0
  

  -output_dir <String>

  No description
  Default: "./"
  

  -last_accepted_pose_dir <String>

  No description
  Default: "./"
  

  -min_with_cst <Boolean>

  Used in ensemble generation
  Default: false
  

  -temperature <Real>

  because I really dont know what the monte carlo temperature should be set to
  Default: 10
  

  -ramp_repulsive <Boolean>

  set fa_rep to 0.1, 0.33 of original value when minimizing in the minimization phase following packing
  Default: false
  

  -mut_file <String>

  alternate specification for mutations. File format described in fix_bb_monomer_ddg.cc above the read_in_mutations function
  

  -out_pdb_prefix <String>

  specifies the prefix assigned to output so that no overwriting happens
  

  -constraint_weight <Real>

  because that other option isnt working
  Default: 1.0
  

  -harmonic_ca_tether <Real>

  default CA tether for harmonic constraints
  Default: 2.0
  

  -iterations <Integer>

  specifies the number of iterations of refinement
  Default: 20
  

  -out <String>

  create output file of predicted ddgs
  Default: "ddg_predictions.out"
  

  -debug_output <Boolean>

  specify whether or not to write a whole bunch of debug statements to standard out
  Default: false
  

  -dump_pdbs <Boolean>

  specify whether or not to dump repacked wild-type and mutant pdbs
  Default: true
  

  -weight_file <String>

  specifies the weight-files to be used in calculations
  Default: "ddg.wts"
  

  -cst_dist_cutoff <Real>

  the cutoff distance for generating harmonic csts between residues
  Default: 9.0
  

• DenovoProteinDesign

  -DenovoProteinDesign <Boolean>

  DenovoProteinDesign option group
  

  -redesign_core <Boolean>

  redesign core of pdb
  Default: false
  

  -redesign_loops <Boolean>

  redesign loops of pdb
  Default: false
  

  -redesign_surface <Boolean>

  redesign surface of pdb
  Default: false
  

  -redesign_complete <Boolean>

  complete redesign of pdb
  Default: false
  

  -optimize_loops <Boolean>

  do serious loop modeling at the end of designrelax mover
  

  -secondary_structure_file <File>

  has fasta file format - describes secondary structure of desired target with H/C/E
  

  -hydrophobic_polar_pattern <File>

  has fasta file format - describes hydrophobic(B) polar(P) pattern
  

  -use_template_sequence <Boolean>

  use the template pdbs sequence when creating starting structures
  Default: false
  

  -use_template_topology <Boolean>

  use templates phi/psi in loops and begin/end helix/sheet generate only template like starting structures
  Default: false
  

  -create_from_template_pdb <File>

  create starting structure from a template pdb, follow with pdb name
  

  -create_from_secondary_structure <Boolean>

  create starting structure from a file that contains H/C/E to describe topology or B/P pattern, has fasta file format
  Default: false
  

• dna

  -dna <Boolean>

  dna option group
  

• dna:specificity

  -specificity <Boolean>

  specificity option group
  

  -exclude_dna_dna <Boolean>

  No description
  Default: true
  

  -params <RealVector>

  vector of real-valued params
  

  -frag_files <FileVector>

  files to collect frags from
  

  -only_repack <Boolean>

  No description
  Default: false
  

  -design_DNA <Boolean>

  No description
  Default: false
  

  -soft_rep <Boolean>

  No description
  Default: false
  

  -dump_pdbs <Boolean>

  No description
  Default: false
  

  -fast <Boolean>

  No description
  Default: false
  

  -randomize_motif <Boolean>

  No description
  Default: false
  

  -Wfa_elec <Real>

  No description
  Default: 0
  

  -Wdna_bs <Real>

  No description
  Default: 0
  

  -Wdna_bp <Real>

  No description
  Default: 0
  

  -minimize_tolerance <Real>

  No description
  Default: 0.001
  

  -weights_tag <String>

  No description
  

  -weights_tag_list <String>

  No description
  

  -min_type <String>

  No description
  Default: "lbfgs_armijo_nonmonotone"
  

  -mode <String>

  No description
  

  -score_function <String>

  No description
  

  -pre_minimize <Boolean>

  No description
  Default: false
  

  -post_minimize <Boolean>

  No description
  Default: false
  

  -pre_pack <Boolean>

  No description
  Default: false
  

  -nloop <Integer>

  No description
  Default: 20
  

  -n_inner <Integer>

  No description
  

  -n_outer <Integer>

  No description
  

  -nstep_water <Integer>

  No description
  Default: 0
  

  -moving_jump <Integer>

  No description
  Default: 0
  

  -motif_begin <Integer>

  No description
  Default: 0
  

  -motif_size <Integer>

  No description
  Default: 0
  

  -pdb_pos <StringVector>

  list of one or more positions in the input pdb, eg: -pdb_pos 125:A 127:A 4:C
  Default: ""
  

  -methylate <StringVector>

  list of one or more positions in the input pdb to be methylated, eg: -methylate 125:A 127:A 4:C
  Default: ""
  

  -dna_backbone_torsion_sdevs <RealVector>

  No description
  

  -dna_sugar_torsion_sdev <Real>

  No description
  Default: 4.0
  

  -dna_chi_torsion_sdev <Real>

  No description
  Default: 15.0
  

  -lk_ball_wtd_tag <String>

  No description
  

  -lk_ball_for_bb <Boolean>

  No description
  Default: true
  

  -lk_ball_ramp_width_A2 <Real>

  No description
  Default: 3.9
  

  -lk_ball_overlap_gap <Real>

  No description
  Default: 0.0
  

  -lk_ball_overlap_width_A2 <Real>

  No description
  Default: 5.0
  

  -lk_ball_water_fade <Real>

  No description
  Default: 1.0
  

  -lk_ball_wtd_prefactors <RealVector>

  6 scale factors that are applied to the lk_ball_wtd per-atom weights; the order is <donor-iso> <donor-ball> <acceptor-iso> <acceptor-ball> <don+acc-iso> <don+acc-ball>; where <don+acc> means atom-types that are both donors and acceptors (SP3 hybridized OH for example)
  

  -lk_ball_waters_sp2 <RealVector>

  The geometry of sp2 acceptor waters in lk_ball. Format: ( <length_A> <angle_degrees> <torsion_degrees> )+ Default: 2.65 120 0 2.65 120 180. No limit on #, but all three params must be specified for each
  

  -lk_ball_waters_sp3 <RealVector>

  The geometry of sp3 acceptor waters in lk_ball. Format: ( <length_A> <angle_degrees> <torsion_degrees> )+ Default: 2.65 109 120 2.65 109 240. No limit on #, but all three params must be specified for each
  

  -lk_ball_waters_ring <RealVector>

  The geometry of ring acceptor waters in lk_ball. Format: ( <length_A> <angle_degrees> <torsion_degrees> )+ Default: 2.65 180 0. No limit on #, but all three params must be specified for each
  

  -lk_ball_waters_donor <Real>

  The geometry of donor waters in lk_ball. Length along N-H vector
  

  -lk_ball_bridge_angle_widthscale <Real>

  The width scaling on the angular component of lk_ball_bridge (lower = tighter)
  Default: 0.0
  

• dna:design

  -design <Boolean>

  design option group
  

  -output_unbound_pdb <Boolean>

  write out an unbound pdb if doing binding score calculations
  Default: false
  

  -z_cutoff <Real>

  distance along DNA-axis from designing DNA bases to allow amino acids to design
  Range: 0-
  Default: 3.5
  

  -protein_scan <String>

  single-residue scanning of protein residue types for binding and specificity scores
  Default: "ACDEFGHIKLMNPQRSTVWY"
  

  -checkpoint <String>

  write/read checkpoint files for higher-level protocols that proceed linearly for long periods of time. Provide a checkpoint filename after this option.
  Default: ""
  

  -minimize <Boolean>

  Perform minimization in DNA design mode.
  Default: false
  

  -dna_defs <StringVector>

  
  Default: ""
  

  -dna_defs_file <String>

  
  Default: ""
  

  -nopdb <Boolean>

  use this flag to disable pdb output
  Default: false
  

  -designable_second_shell <Boolean>

  No description
  Default: false
  

  -base_contacts_only <Boolean>

  No description
  Default: false
  

  -probe_specificity <Integer>

  Rapidly estimate the explicit specificity of DNA designs during fixed-backbone repacking
  Default: 1
  

  -reversion_scan <Boolean>

  Try to revert spurious mutations after designing
  Default: false
  

  -binding <Boolean>

  compute a protein-DNA binding energy
  Default: false
  

  -Boltz_temp <Real>

  temperature for Boltzmann calculations
  Default: 0.6
  

  -repack_only <Boolean>

  Do not allow protein sequences to mutate arbitrarily
  Default: false
  

  -sparse_pdb_output <Boolean>

  Output only coordinates that change relative to the input structure
  Default: false
  

• dna:design:specificity

  -specificity <Boolean>

  specificity option group
  

  -output_structures <Boolean>

  output structures for each sequence combination
  Default: false
  

  -include_dna_potentials <Boolean>

  include DNA potentials in calculations of DNA sequence specificity
  Default: false
  

• dna:design:reversion

  -reversion <Boolean>

  reversion option group
  

  -dscore_cutoff <Real>

  limit for acceptable loss in energy
  Default: 1.5
  

  -dspec_cutoff <Real>

  limit for acceptable loss in specificity
  Default: -0.05
  

• DisulfideInsertion

  -DisulfideInsertion <Boolean>

  DisulfideInsertion option group
  

  -peptide_chain <Integer>

  The number of peptide chain for which to perform a DisulfideInsertion check
  Default: 1
  

  -n_cyd_seqpos <Integer>

  The sequential position of the residue in the n-ter of the putative disulfide; 0 signals the peptide n-ter
  Default: 0.0
  

  -c_cyd_seqpos <Integer>

  The sequential position of the residue in the c-ter of the putative disulfide; 0 signals the peptide c-ter
  Default: 0.0
  

  -max_dslf_pot <Real>

  The maximum allowed match score for disulfide rotation and translation
  Default: 2.0
  

  -max_dslf_energy <Real>

  The maximum allowed change in disulfide energy upon peptide disulfide bridge formation
  Default: 1.0
  

  -min_dslf_dist_multiplier <Real>

  A multiplier for the minimum allowed distance between residues that might form a disulfide.
  Default: 1.0
  

  -max_dslf_dist_multiplier <Real>

  A multiplier for the maximum allowed distance between residues that might form a disulfide.
  Default: 1.0
  

  -scorefxn <String>

  The scorefunction to be used in disulfideInsertion
  

  -constraint_weight <Real>

  Weight of the constraints on disulfide bonds formed by the DisulfideInsertionMover; EXPERIMENTAL
  Default: 0.0
  

• docking

  -kick_relax <Boolean>

  Add relax step at the end of symmetric docking
  Default: false
  

  -docking <Boolean>

  Docking option group
  

  -view <Boolean>

  Decide whether to use the viewer (graphical) or not
  Default: false
  

  -no_filters <Boolean>

  Toggle the use of filters
  Default: false
  

  -design_chains <StringVector>

  Pass in the one-letter chain identifiers, separated by space, for each chain to design: -design_chains A B
  

  -recover_sidechains <File>

  usually side-chains are taken from the input structure if it is fullatom - this overrides this behavior and takes sidechains from the pdb-file
  

  -partners <String>

  defines docking partners by ChainID, example: docking chains L+H with A is -partners LH_A
  Default: "_"
  

  -docking_local_refine <Boolean>

  Do a local refinement of the docking position (high resolution)
  Default: false
  

  -low_res_protocol_only <Boolean>

  Run only low resolution docking, skip high resolution docking
  Default: false
  

  -randomize1 <Boolean>

  Randomize the first docking partner.
  Default: false
  

  -randomize2 <Boolean>

  Randomize the second docking partner.
  Default: false
  

  -use_ellipsoidal_randomization <Boolean>

  Modify docking randomization to use ellipsoidal rather than spherical method.
  Default: false
  

  -spin <Boolean>

  Spin a second docking partner around axes from center of mass of partner1 to partner2
  Default: false
  

  -tilt <RealVector>

  tilt the docking partners at a random angle : -tilt PARTNER1_MAX_DEGREES PARTNER2_MAX_DEGREES.
  

  -tilt1_center <String>

  resID around which rotation of partner1 is centered (default: center of mass of partner 1
  Default: ""
  

  -tilt2_center <String>

  resID around which rotation of partner2 is centered (default: center of mass of partner 2
  Default: ""
  

  -dock_pert <RealVector>

  Do a small perturbation with partner two: -dock_pert ANGSTROMS DEGREES. Good values for protein docking are 3 A and 8 deg.
  

  -uniform_trans <Real>

  No description
  

  -center_at_interface <Boolean>

  Perform all initial perturbations with the center of rotation at the interface between partners instead of at the center of mass of the oppposite partner.
  Default: false
  

  -dock_mcm_first_cycles <Integer>

  Perfrom 4 cycles to let the filter decide to continue.
  Default: 4
  

  -dock_mcm_second_cycles <Integer>

  If the first cycle pass the fliter, continue 45 cycles.
  Default: 45
  

  -docking_centroid_outer_cycles <Integer>

  Outer cycles during cking rigid body adaptive moves.
  Default: 10
  

  -docking_centroid_inner_cycles <Integer>

  Inner cycles during docking rigid body adaptive moves.
  Default: 50
  

  -dock_min <Boolean>

  Minimize the final fullatom structure.
  Default: false
  

  -flexible_bb_docking <String>

  How to do flexible backbone docking, if at all. Choices include fixedbb, ccd, alc, and backrub.
  Default: "fixedbb"
  

  -flexible_bb_docking_interface_dist <Real>

  Distance between chains required to define a residue as having flexible backbone (ie. loop).
  Default: 10.0
  

  -ensemble1 <String>

  turns on ensemble mode for partner 1. String is multi-model pdb file
  Default: ""
  

  -ensemble2 <String>

  turns on ensemble mode for partner 2. String is multi-model pdb file
  Default: ""
  

  -dock_mcm_trans_magnitude <Real>

  The magnitude of the translational perturbation during mcm in docking.
  Default: 0.1
  

  -dock_mcm_rot_magnitude <Real>

  The magnitude of the rotational perturbation during mcm in docking.
  Default: 5.0
  

  -minimization_threshold <Real>

  Threhold for Rosetta to decide whether to minimize jump after a rigid_pert
  Default: 15
  

  -temperature <Real>

  Temperature setting for the mc object during rigid-body docking
  Default: 0.8
  

  -repack_period <Integer>

  full repack period during dockingMCM
  Default: 8
  

  -extra_rottrial <Boolean>

  extra rotamer trial after minimization
  Default: false
  

  -dock_rtmin <Boolean>

  does rotamer trials with minimization, RTMIN
  Default: false
  

  -sc_min <Boolean>

  does sidechain minimization of interface residues
  Default: false
  

  -norepack1 <Boolean>

  Do not repack the side-chains of partner 1.
  Default: false
  

  -norepack2 <Boolean>

  Do not repack the side-chains of partner 2.
  Default: false
  

  -bb_min_res <IntegerVector>

  Minimize backbone at these positions.
  

  -sc_min_res <IntegerVector>

  Minimize backbone at these positions.
  

  -dock_ppk <Boolean>

  docking prepack mode
  Default: false
  

  -max_repeats <Integer>

  If a decoy does not pass the low- and high-resolution filters, how many attempts to make before failur
  Default: 1000
  

  -dock_lowres_filter <RealVector>

  manually sets the lowres docking filter: -dock_lowres_filter <INTERCHAIN_CONTACT cutoff>=""> <INTERCHAIN_VDW cutoff>=""> <RESTRAINT cutoff>="">. Default values for protein docking are 10.0 and 1.0
  

  -multibody <IntegerVector>

  List of jumps allowed to move during docking
  

  -ignore_default_docking_task <Boolean>

  Allows the user to define another task to give to Docking and will ignore the default DockingTask. Task will default to designing everything if no other TaskFactory is given to docking.
  Default: false
  

  -low_patch <String>

  Name of weights patch file (without extension .wts) to use during rigid body
  

  -high_patch <String>

  Name of weights patch file (without extension .wts) to use during docking
  

  -high_min_patch <String>

  Name of weights patch file (without extension .wts) to use during
  

  -pack_patch <String>

  Name of weights patch file (without extension .wts) to use during packing
  

  -use_legacy_protocol <Boolean>

  Use the legacy high resolution docking algorithm for output compatibility.
  Default: false
  

  -docklowres_trans_magnitude <Real>

  The magnitude of the translational perturbation during lowres in docking.
  Default: 0.7
  

  -docklowres_rot_magnitude <Real>

  The magnitude of the rotational perturbation during lowres in docking.
  Default: 5.0
  

• docking:ligand

  -ligand <Boolean>

  docking:ligand option group
  

  -protocol <String>

  Which protocol to run?
  Default: "abbreviated"
  

  -soft_rep <Boolean>

  Use soft repulsive potential?
  Default: false
  

  -tweak_sxfn <Boolean>

  Apply default modifications to the score function?
  Default: true
  

  -old_estat <Boolean>

  Emulate Rosetta++ electrostatics? (higher weight, ignore protein-protein)
  Default: false
  

  -random_conformer <Boolean>

  Start from a random ligand rotamer chosen from the library
  Default: false
  

  -improve_orientation <Integer>

  Do N cycles of randomization to minimize clashes with backbone
  

  -mutate_same_name3 <Boolean>

  Allow ligand to 'design' to residue types with same name3? Typically used for protonation states / tautomers.
  Default: false
  

  -subset_to_keep <Real>

  When selecting a subset of ligand poses, what fraction (number if > 1.0) to keep?
  Default: 0.05
  

  -min_rms <Real>

  When selecting a subset of ligand poses, all must differ by at least this amount.
  Default: 0.8
  

  -max_poses <Integer>

  When selecting a subset of ligand poses, select as most this many.
  Default: 50
  

  -minimize_ligand <Boolean>

  Allow ligand torsions to minimize?
  Default: false
  

  -harmonic_torsions <Real>

  Minimize with harmonic restraints with specified stddev (in degrees)
  Default: 10.0
  

  -use_ambig_constraints <Boolean>

  Use ambiguous constraints to restrain torsions instead of adding and removing constraints
  Default: false
  

  -shear_moves <Integer>

  Do N pseudo-shear moves on ligand torsions per MCM cycle
  Default: 0
  

  -minimize_backbone <Boolean>

  Allow protein backbone to minimize? Restrained except near ligand.
  Default: false
  

  -harmonic_Calphas <Real>

  Minimize with harmonic restraints with specified stddev (in Angstroms)
  Default: 0.2
  

  -tether_ligand <Real>

  Restrain ligand to starting point with specified stddev (in Angstroms)
  

  -start_from <RealVector>

  One or more XYZ locations to choose for the ligand: -start_from X1 Y1 Z1 -start_from X2 Y2 Z2 ...
  

  -option_file <String>

  Name of Ligand Option File for use with multi_ligand_dock application
  

  -ligand_ensemble <Real>

  Weight for correlation adjustment in ligand ensemble docking, ignores ligand-ligand interactions if value is not zero
  Default: 0
  

• docking:ligand:grid

  -grid <Boolean>

  docking:ligand:grid option group
  

  -grid_kin <File>

  Write kinemage version of generated grid to named file
  

  -grid_map <File>

  Write grid to named file as electron density in BRIX (aka `O'-map) format
  

• DomainAssembly

  -DomainAssembly <Boolean>

  DomainAssembly option group
  

  -da_setup <Boolean>

  run DomainAssembly setup routine
  Default: false
  

  -da_setup_option_file <File>

  input list of pdbs and linker sequences
  Default: "--"
  

  -da_setup_output_pdb <File>

  PDB file output by DomainAssemblySetup
  Default: "--"
  

  -da_linker_file <File>

  input file with linker definitions
  Default: "--"
  

  -da_require_buried <File>

  Input file containing residues to be buried in the domain interface
  Default: "--"
  

  -da_start_pdb <File>

  input pdb for linker optimization
  Default: "--"
  

  -run_fullatom <Boolean>

  Run fullatom stage of the protocol
  Default: false
  

  -run_centroid <Boolean>

  Run centroid stage of the protocol
  Default: false
  

  -run_centroid_abinitio <Boolean>

  Run centroid abinitio stage of the protocol
  Default: true
  

  -da_nruns <Integer>

  number of runs
  Default: 1
  

  -da_start_pdb_num <Integer>

  starting number for output pdb files
  Default: 1
  

  -da_linker_file_rna <File>

  input file with moveable RNA definitions
  Default: "--"
  

  -residues_repack_only <String>

  Residues not to be redesigned under any circumstances
  

  -da_eval_pose_map <File>

  input file that maps pose coordinates to structurally related positions of native pose
  

• dump_trajectory

  -dump_trajectory <Boolean>

  dump_trajectory option group
  

  -prefix <String>

  Prefix to use when dumping trajectories with dump_trajectory ScoreType.
  Default: "traj"
  

  -gz <Boolean>

  Dump trajectories in .pdb.gz format.
  Default: false
  

• edensity

  -edensity <Boolean>

  edensity option group
  

  -debug <Boolean>

  No description
  Default: false
  

  -mapfile <String>

  No description
  

  -mapreso <Real>

  No description
  Default: 0.0
  

  -grid_spacing <Real>

  No description
  Default: 0.0
  

  -centroid_density_mass <Real>

  No description
  Default: 0.0
  

  -sliding_window <Integer>

  No description
  Default: 1
  

  -cryoem_scatterers <Boolean>

  No description
  Default: false
  

  -force_apix <Real>

  force pixel spacing to take a particular value
  Default: 0.0
  

  -fastdens_wt <Real>

  wt of fast edens score
  Default: 0.0
  

  -fastdens_params <RealVector>

  parameters for fastdens scoring
  

  -legacy_fastdens_score <Boolean>

  use the pre-June 2013 normalization for scoring
  Default: false
  

  -sliding_window_wt <Real>

  wt of edens sliding-window score
  Default: 0.0
  

  -score_sliding_window_context <Boolean>

  when using sl. win. density fit, include neighbor atoms (slows trajectory)
  Default: false
  

  -whole_structure_ca_wt <Real>

  wt of edens centroid (CA-only) scoring
  Default: 0.0
  

  -whole_structure_allatom_wt <Real>

  wt of edens centroid (allatom) scoring
  Default: 0.0
  

  -debug_derivatives <Boolean>

  calculate numeric derivatives for density terms and compare with analytical
  Default: false
  

  -realign <String>

  how to initially align the pose to density
  Default: "no"
  

  -membrane_axis <String>

  the membrane normal axis
  Default: "Z"
  

  -atom_mask <Real>

  override default (=3.2A) atom mask radius to this value (hi-res scoring)
  Default: 3.2
  

  -atom_mask_min <Real>

  override the 3 sigma minimum value which takes precedence over atom_mask value (hi-res scoring)
  Default: 2.0
  

  -ca_mask <Real>

  override default (=6A) CA mask radius to this value (low-res scoring)
  Default: 6.0
  

  -score_symm_complex <Boolean>

  If set, scores the structure over the entire symmetric complex; otherwise just use controlling monomer
  Default: false
  

  -sc_scaling <Real>

  Scale sidechain density by this amount (default same as mainchain density)
  Default: 1.0
  

  -n_kbins <Integer>

  Number of B-factor bins
  Default: 1
  

  -unmask_bb <Boolean>

  Only include sidechain atoms in atom mask
  Default: false
  

  -render_density <Boolean>

  render electron density in graphics mode build
  Default: false
  

• enzdes

  -enzdes <Boolean>

  enzdes option group
  

  -checkpoint <String>

  write/read checkpoint files to the desired filename.
  Default: ""
  

  -enz_score <Boolean>

  prevent repacking in enzyme design calculation
  Default: false
  

  -enz_repack <Boolean>

  prevent redesign in enzyme design calculation
  Default: false
  

  -cst_opt <Boolean>

  pre design constraint minimization
  Default: false
  

  -cst_predock <Boolean>

  docks a ligand relative the catalytic residue
  Default: false
  

  -trans_magnitude <Real>

  rigid body translation in Angstrom
  Default: 0.1
  

  -rot_magnitude <Real>

  rigid body rotation in deg
  Default: 2
  

  -dock_trials <Real>

  number of docking trials
  Default: 100
  

  -cst_min <Boolean>

  after design minimization, constraints turned off
  Default: false
  

  -cst_design <Boolean>

  invokes actual design
  Default: false
  

  -design_min_cycles <Integer>

  determines how many iterations of designing/minimizing are done during a design run
  Default: 1
  

  -make_consensus_mutations <Boolean>

  Invokes mutations back to sequence profile consensus throughout whole protein in EnzdesFixBB protocol. sequence profile file must be specified through -in:pssm option.
  Default: false
  

  -bb_min <Boolean>

  allows backbone of active site residues to move during cst_opt and cst_min. In the cst_opt stage, residue Cas will be constrained to their original positions.
  Default: false
  

  -bb_min_allowed_dev <Real>

  distance by which Cas are allowed to move during backbone minimization before a penalty is assigned.
  Default: 0.5
  

  -loop_bb_min_allowed_dev <Real>

  distance by which Cas are allowed to move during backbone minimization before a penalty is assigned. Applied only for loops as determined by DSSP.
  Default: 0.5
  

  -minimize_ligand_torsions <Real>

  degrees by which ligand torsions are allowed to rotate before a penalty is assigned. Only those torsions which have diversity in the conformational ensemble are allowed this std dev. rest are constrained to 0.1
  Default: 10.0
  

  -minimize_all_ligand_torsions <Real>

  allows constrained minimization of all ligand torsions using stddev.
  Default: 10.0
  

  -chi_min <Boolean>

  allows chi values of active site residues to move during cst_opt and cst_min.
  Default: false
  

  -min_all_jumps <Boolean>

  allows all jumps in the pose to minimize during cst_opt and cst_min. By default only ligand-associated jumps minimize
  Default: false
  

  -cst_dock <Boolean>

  ligand docking after design. By default, constraints (except covalent connections will be turned off for this stage.
  Default: false
  

  -run_ligand_motifs <Boolean>

  run ligand motif search and add motif rotamers to packer
  Default: false
  

  -enz_debug <Boolean>

  invokes various debug routines around the enzdes code
  Default: false
  

  -cstfile <File>

  file that contains all necessary constraints for an enzyme design calculation
  Default: "constraints.cst"
  

  -enz_loops_file <File>

  file that contains definitions of loop regions
  Default: "eloops.els"
  

  -flexbb_protocol <Boolean>

  triggers flexible backbone design
  Default: false
  

  -remodel_protocol <Boolean>

  triggers remodel protocol design
  Default: false
  

  -kic_loop_sampling <Boolean>

  Generate alternate loop conformations using KIC loop closure instead of backrub
  Default: false
  

  -dump_loop_samples <String>

  yes/no? Create loop pdb files named loopreg_[regionid]_[whichsample].pdb for the chosen loop samples; if 'quit_afterwards' is given, then the program exits after all loops have been generated
  Default: "no"
  

  -fix_catalytic_aa <Boolean>

  preventing catalytic aa from repacking
  Default: false
  

  -additional_packing_ligand_rb_confs <Integer>

  Ligand Rotamers will be built at additional random rigid body positions during packing
  Default: 0
  

  -ex_catalytic_rot <Integer>

  convenience option to use higher number of rotamers for catalytic residues. The chosen level will be applied to all chis of every catalytic residue.
  Default: 1
  

  -single_loop_ensemble_size <Integer>

  number of conformations generated for each of the independent loops in a flexbb calculation
  Default: 100
  

  -loop_generator_trials <Integer>

  number of trials of that the respective loop generator(backrub/kinematic kic) does in enzdes flexbb
  Default: 200
  

  -no_catres_min_in_loopgen <Boolean>

  prevents minimization of catalytic residues when generating loop ensembles
  Default: false
  

  -mc_kt_low <Real>

  low monte carlo limit for ensemble generation using backrub
  Default: 0.6
  

  -mc_kt_high <Real>

  high monte carlo limit for ensemble generation using backrub
  Default: 0.9
  

  -min_cacb_deviation <Real>

  Fragment uniqueness filter. On by default. Minimum CA/CB average deviation that at least one residue must have from all other already-included fragments for a new fragment to be included
  Default: 0.3
  

  -max_bb_deviation <Real>

  Fragment smoothness filter. Off by default. Upper limit on the backbone average deviation a new fragment may have to its most-similar fragment that has already been included in the fragment set.
  Default: 0.1
  

  -max_bb_deviation_from_startstruct <Real>

  Fragment native-proximity Filter. Always on. Maximum tolerated backbone average deviation from the starting backbone for a fragment that to be included in the fragment set.
  Default: 1.5
  

  -remodel_trials <Integer>

  how often each loop is being remodeled in the enzdes_remodel mover
  Default: 100
  

  -remodel_secmatch <Boolean>

  if constrained interactions are missing in the pose during remodel, the SecondaryMatcher will be used to try to find them in the remodeled region. very experimental at this point
  Default: false
  

  -dump_inverse_rotamers <Boolean>

  in case of remodel secmatching against inverse rotamers, these rotamers will be dumped before the protocol starts for visual inspection by the user
  Default: false
  

  -remodel_aggressiveness <Real>

  determines the aggressiveness with which a given loop is remodeled. legal values between 0 and 1, where 1 is aggressive and 0 conservative.
  Default: 0.1
  

  -favor_native_res <Real>

  a bonus energy assigned to the native res during a design calculation
  Default: 0.5
  

  -detect_design_interface <Boolean>

  automatically detect design/repack region around ligand(s)
  Default: false
  

  -include_catres_in_interface_detection <Boolean>

  if option -detect_design_interface is active, invoking this option causes all residues that are within the specified cuts of any catalytic residue are also set to designing/repacking
  Default: false
  

  -arg_sweep_interface <Boolean>

  Use protein-DNA design-like interface detection, involving generation of arginine rotamers at each position, checking to see if argininte can make interaction with ligand.
  Default: false
  

  -arg_sweep_cutoff <Real>

  Interaction cutoff distance from arginine to ligand when performing arginine sweep interface detection.
  Default: 3.7
  

  -cut1 <Real>

  option to specify redesign cutoff 1 in enzdes calculation
  Default: 0.0
  

  -cut2 <Real>

  option to specify redesign cutoff 2 in enzdes calculation
  Default: 0.0
  

  -cut3 <Real>

  option to specify repack cutoff 1 in enzdes calculation
  Default: 10.0
  

  -cut4 <Real>

  option to specify repack cutoff 2 in enzdes calculation
  Default: 10.0
  

  -lig_packer_weight <Real>

  specifies the weights for protein ligand interaction during packing (and only packing!! )
  Default: 1.0
  

  -no_unconstrained_repack <Boolean>

  no unconstrained repacking after the design stage
  Default: false
  

  -secmatch_Ecutoff <Real>

  the maximum constraint energy at which a residue is accepted in the secondary matcher
  Default: 1.0
  

  -change_lig <File>

  Can be used with the secondary matching protocol if different incarnations of the ligand are used for design and primary matching. The file needs to contain information on what atoms to superimpose.
  Default: "ligchange_file.txt"
  

  -process_ligrot_separately <String>

  In the EnzdesFixBB protocol, causes the protocol to be executed separately for all non_bb clashing ligand rotamers.
  Default: "default_lig"
  

  -start_from_random_rb_conf <Boolean>

  In the EnzdesFixBB protocol, if there are additional ligand rigid body conformations available (from a multimodel pdb), a random one of these will be the starting point for the protocol.
  Default: false
  

  -bb_bump_cutoff <Real>

  option to specify the maximum allowed backbone energie when replacing a new residue type
  Default: 2.0
  

  -sc_sc_bump_cutoff <Real>

  option to specify the maximum allowed energy between two newly placed sidechains in the secondary matcher
  Default: 2.0
  

  -no_packstat_calculation <Boolean>

  will determine whether the computationally intensive packstat calculation will be done at the end of a run
  Default: false
  

  -compare_native <String>

  triggers comparison of every designed structure to its respective native pdb. the value of the option needs to be a directory path that contains all the native pdb files
  Default: "./"
  

  -final_repack_without_ligand <Boolean>

  if a scorefile is requested, this option triggers every structure to be repacked without the ligand. the resulting structure will be output in a multimodel pdb, and differences in energy and rmsd are added to the scorefile.
  Default: false
  

  -dump_final_repack_without_ligand_pdb <Boolean>

  If option -final_repack_without_ligand is active, this option will cause the repacked structure to be separately dumped.
  Default: false
  

  -parser_read_cloud_pdb <Boolean>

  read cloud format PDB for enzdes in rosetta scripts
  Default: false
  

• fast_loops

  -fast_loops <Boolean>

  fast_loops option group
  

  -window_accept_ratio <Real>

  windows with more than x percent of good loops in fast-loop sampling are used for scored-sampling
  Default: 0.01
  

  -nr_scored_sampling_passes <Integer>

  good windows go into scored-sampling N times
  Default: 4
  

  -nr_scored_fragments <Integer>

  scored loops sampled per good window each pass
  Default: 20
  

  -min_breakout_good_loops <Integer>

  stop doing scored sampling if N or more good loops have been found
  Default: 5
  

  -min_breakout_fast_loops <Integer>

  stop doing fast sampling if N or more good loops have been found
  Default: 80
  

  -min_good_loops <Integer>

  treat as failure if less good-loops than
  Default: 0
  

  -min_fast_loops <Integer>

  treat as failure if less fast-loops than
  Default: 3
  

  -vdw_delta <Real>

  accept as good loop if vdw-score < vdw-score-start+vdw-delta
  Default: 0.5
  

  -give_up <Integer>

  if N scored_frag_attemps didnt give any good loop – jump out
  Default: 1000
  

  -chainbreak_max <Real>

  accept only loops that have a maximum chainbreak score of... (sum of linear_chainbreak / chainbreak and overlap_chainbreak
  Default: 0.2
  

  -fragsample_score <File>

  Scorefunction used durgin scored-frag sampling
  Default: "loop_fragsample.wts"
  

  -fragsample_patch <File>

  Patch weights for scorefunction used during scored-frag sampling
  

  -overwrite_filter_scorefxn <File>

  force Scorefunction to be used during filter stage (instead last score of sampling protocol)
  

  -patch_filter_scorefxn <File>

  apply patch to Scorefunction used during filter stage
  

  -filter_cst_file <File>

  use these constraints to filter loops — additional to whatever is in pose already
  

  -filter_cst_weight <Real>

  weight for constraints versus normal score (might contain additional constraints)
  Default: 1.0
  

  -fast_relax_sequence_file <File>

  use this FastRelax protocol for loop-selection
  

• flexpack

  -flexpack <Boolean>

  flexpack option group
  

• flexpack:annealer

  -annealer <Boolean>

  annealer option group
  

  -inner_iteration_scale <Real>

  Scale up or down the number of inner iterations in the flexpack annealer
  

  -outer_iteration_scale <Real>

  Scale up or down the number of outer iterations in the flexpack annealer
  

  -fixbb_substitutions_scale <Real>

  Scale up or down the number of fixed-backbone rotamer substitutions in the flexpack annealer
  

  -pure_movebb_substitutions_scale <Real>

  Scale up or down the number of backbone moves
  

  -rotsub_movebb_substitutions_scale <Real>

  Scale up or down the number of rotamer substitions with backbone moves
  

• flexPepDocking

  -flexPepDocking <Boolean>

  flexPepDocking option group
  

  -params_file <String>

  parameters file that describe the complex details, like anchor residues, etc.
  

  -peptide_anchor <Integer>

  Set the peptide anchor residue mannualy (instead of using the center of mass
  Range: 1-
  Default: 1
  

  -receptor_chain <String>

  chain-id of receptor protein
  

  -peptide_chain <String>

  chain-id of peptide protein
  

  -pep_fold_only <Boolean>

  Only fold a peptide, without docking (no input receptor is expected in this case).
  Default: false
  

  -lowres_abinitio <Boolean>

  Do a preemptive ab-initio low-resolution peptide docking
  Default: false
  

  -lowres_preoptimize <Boolean>

  Do a preemptive optimization in low resolution
  Default: false
  

  -flexPepDockingMinimizeOnly <Boolean>

  Just do simple minimization on input structure
  Default: false
  

  -extend_peptide <Boolean>

  start the protocol with the peptide in extended conformation
  Default: false
  

  -place_peptide_on_binding_site <Boolean>

  places peptide on the binding using SiteConstraints
  Default: false
  

  -sample_pcs <Integer>

  number of principle components to use for initial peptide placement and flipping
  Range: 0-
  Default: 0
  

  -SlideIntoContact <Boolean>

  Slides peptide toward or away from receptor to remove clashes
  Default: false
  

  -recalculate_foldtree <Boolean>

  recalculates foldtree after random RB perturbation
  Default: false
  

  -pep_refine <Boolean>

  High-resolution peptide refinement over receptor surface, equivalent to the obsolete -rbMCM -torsionsMCM flags
  Default: false
  

  -rbMCM <Boolean>

  Do rigid body mcm in the main loop of the protocol (obsolete)
  Default: false
  

  -torsionsMCM <Boolean>

  Do torsions (small/shear mcm in the main loop of the protocol (obsolete)
  Default: false
  

  -peptide_loop_model <Boolean>

  Do cycles of random loop modeling to peptide backbone
  Default: false
  

  -backrub_peptide <Boolean>

  Adds a backrub stage to the protocol
  Default: false
  

  -boost_fa_atr <Boolean>

  while ramping up the fa_rep, start from high atr and lower to normal
  Default: true
  

  -ramp_fa_rep <Boolean>

  Whether to ramp the full-atom repulsive score during the protocol
  Default: true
  

  -ramp_rama <Boolean>

  Whether to ramp the Ramachandran score during the protocol
  Default: false
  

  -flexpep_score_only <Boolean>

  just reads in the pose and scores it
  Default: false
  

  -ref_startstruct <File>

  Alternative start structure for scoring statistics, instead of the original start structure (useful as reference for rescoring previous runs)
  

  -use_cen_score <Boolean>

  when in score_only mode, uses centroid weights to score
  Default: false
  

  -design_peptide <Boolean>

  Add a desing stage to each cycle of the RB-torsions perturbations
  Default: false
  

  -rep_ramp_cycles <Integer>

  Number of cycles for the ramping up of repulsion term
  Range: 0-
  Default: 10
  

  -mcm_cycles <Integer>

  Number of cycles for the mcm procedures (rb/torsions)
  Range: 0-
  Default: 8
  

  -random_phi_psi_preturbation <Real>

  Size of random perturbation of peptide's phi/psi
  Range: 0.0-
  Default: 0.0
  

  -smove_angle_range <Real>

  Defines the perturbations size of small/sheer moves
  Range: 0.0-
  Default: 6.0
  

  -min_receptor_bb <Boolean>

  Whether to include protein backbone in minimization
  Default: false
  

  -random_trans_start <Real>

  Size of random perturbation of peptide's rigid body translation
  Range: 0.0-
  Default: 0.0
  

  -random_rot_start <Real>

  Size of random perturbation of peptide's rigid body rotation
  Range: 0.0-
  Default: 0.0
  

  -flexpep_prepack <Boolean>

  Prepack an initial structure and exit
  Default: false
  

  -flexpep_noprepack1 <Boolean>

  Do not repack the side-chains of partner 1 ( = globular protein).
  Default: false
  

  -flexpep_noprepack2 <Boolean>

  Do not repack the side-chains of partner 2 ( = peptide).
  Default: false
  

  -score_filter <Real>

  Only output decoys with scores lower than this filter.
  Default: 10000.0
  

  -hb_filter <Integer>

  Only output decoys with more h-bonds than this filter.
  Range: 0-
  Default: 0
  

  -hotspot_filter <Integer>

  Only output decoys with more hotspots than this filter.
  Range: 0-
  Default: 0
  

  -frag5 <String>

  5-mer fragments for ab-initio flexPepDock
  

  -frag9_weight <Real>

  Relative weight of 9-mers in ab-initio
  Range: 0-
  Default: 0.1
  

  -frag5_weight <Real>

  relative weight of 5-mers in ab-initio
  Range: 0-
  Default: 0.25
  

  -frag3_weight <Real>

  Relative weight of 3-mers in ab-initio
  Range: 0-
  Default: 1.0
  

  -pSer2Asp_centroid <Boolean>

  convert pSer to Asp during centroid mode
  Default: false
  

  -pSer2Glu_centroid <Boolean>

  convert pSer to Glu during centroid mode
  Default: false
  

  -dumpPDB_abinitio <Boolean>

  dump PDB during Monte-Carlo ab-initio
  Default: false
  

  -dumpPDB_lowres <Boolean>

  dump PDB during Monte-Carlo low-res
  Default: false
  

  -dumpPDB_hires <Boolean>

  dump PDB during Monte-Carlo hi-res
  Default: false
  

• FloppyTail

  -FloppyTail <Boolean>

  FloppyTail option group
  

  -flexible_start_resnum <Integer>

  starting residue for the flexible region, using PDB numbering
  Default: 180
  

  -flexible_stop_resnum <Integer>

  stop residue for the flexible region, using PDB numbering. If unspecified, it assumes the end of the pose.
  Default: 0
  

  -flexible_chain <String>

  chain ID for flexible region
  Default: "C"
  

  -shear_on <Real>

  fraction of perturb moves when shear turns on (0.5 = halfway through)
  Default: 1.0/3.0
  

  -pair_off <Boolean>

  turn off Epair electrostatics term. Used once for a simple side experiment, not meant for general use.
  Default: false
  

  -publication <Boolean>

  output statistics used in publication. TURN OFF if not running publication demo.
  Default: false
  

  -C_root <Boolean>

  Reroot the fold_tree to the C-terminus. If your flexible region is N-terminal, or closer to the first half of the pose, this will speed computation.
  Default: false
  

  -COM_root <Boolean>

  Reroot the fold_tree to the center of mass. This allows you to flop the N- & C-termini simultaneously.
  Default: false
  

  -force_linear_fold_tree <Boolean>

  Force a linear fold tree. Used in combination with C_root and reordering the chains in your input PDB to ensure you get exactly the right kinematics
  Default: false
  

  -debug <Boolean>

  debug mode (extra checks and pdb dumps)
  Default: false
  

  -cen_weights <String>

  Use a different/custom scorefunction for centroid step
  

  -perturb_show <Boolean>

  dump perturbed centroid pdbs as well as final results
  Default: false
  

  -perturb_cycles <Integer>

  perturbation phase runs for <input> cycles
  Default: 5
  

  -perturb_temp <Real>

  perturbation phase temperature for monte carlo
  Default: 0.8
  

  -refine_cycles <Integer>

  refinement phase runs for <input> cycles
  Default: 5
  

  -refine_temp <Real>

  refinement phase temperature for monte carlo
  Default: 0.8
  

  -refine_repack_cycles <Integer>

  refinement phase runs repack every <input> cycles
  Range: 2-
  Default: 20
  

• FloppyTail:short_tail

  -short_tail <Boolean>

  short_tail option group
  

  -short_tail_fraction <Real>

  what fraction of the flexible segment is used in the short-tail section of refinement (not compatible with non-terminal flexible regions)
  Default: 1.0
  

  -short_tail_off <Real>

  fraction of refine cycles where movemap reverts to full tail (0.5 = halfway through)
  Default: 0.0
  

• flxbb

  -flxbb <Boolean>

  flxbb option group
  

  -view <Boolean>

  viewing pose during protocol
  

  -ncycle <Integer>

  number of cycles of design and relax
  

  -constraints_sheet <Real>

  weight constraints between Ca atoms in beta sheet
  

  -constraints_sheet_include_cacb_pseudotorsion <Boolean>

  puts an additional constraint on two residues paired in a beta-sheet to ensure their CA-CB vectors are pointing the same way.
  Default: false
  

  -constraints_NtoC <Real>

  weight constraints between N- and C- terminal CA atoms
  

  -filter_trial <Integer>

  number of filtering trial
  

  -filter_type <String>

  filter type name, currently only packstat is available
  

  -blueprint <File>

  blueprint file
  

  -movemap_from_blueprint <Boolean>

  viewing pose during protocol
  

• flxbb:layer

  -layer <String>

  design core, boundary, and surface with different aa types
  Default: "normal"
  

• fold_and_dock

  -fold_and_dock <Boolean>

  fold_and_dock option group
  

  -move_anchor_points <Boolean>

  move the anchor points that define symmetric coordinate system during symmetry fragment insertion
  Default: false
  

  -set_anchor_at_closest_point <Boolean>

  set the anchor points that define symmetric coordinate system to the nearest point between two consecutive chains during fragment insertion
  Default: false
  

  -rotate_anchor_to_x <Boolean>

  rotate the anchor residue to the x-axis before applying rigid body transformations
  Default: true
  

  -trans_mag_smooth <Real>

  translation perturbation size for smooth refinement
  Default: 0.1
  

  -rot_mag_smooth <Real>

  rotational perturbation size for smooth refinement
  Default: 1.0
  

  -rb_rot_magnitude <Real>

  rotational perturbation size for rigid body pertubations
  Default: 8.0
  

  -rb_trans_magnitude <Real>

  translational perturbation size rigid body pertubations
  Default: 3.0
  

  -rigid_body_cycles <Integer>

  number of rigid bosy cycles during fold and dock fragment insertion
  Default: 50
  

  -move_anchor_frequency <Real>

  Frequency of slide-anchor moves
  Default: 1.0
  

  -rigid_body_frequency <Real>

  The fraction of times rigid body cycles are applied during fragment assembly moves
  Default: 0.2
  

  -rigid_body_disable_mc <Boolean>

  Dissallow moves to be accepted locally by MC criteria within the rigid body mover
  Default: false
  

  -slide_contact_frequency <Real>

  The fraction of times subunits are slided together during fragment assembly moves
  Default: 0.1
  

• fold_cst

  -fold_cst <Boolean>

  fold_cst option group
  

  -constraint_skip_rate <Real>

  if e.g., 0.95 it will randomly select 5% if the constraints each round – full-cst score in extra column
  Default: 0
  

  -violation_skip_basis <Integer>

  local skip_rate is viol/base
  Default: 100
  

  -violation_skip_ignore <Integer>

  no skip for numbers below this level
  Default: 10
  

  -keep_skipped_csts <Boolean>

  final score only with active constraints
  Default: false
  

  -no_minimize <Boolean>

  No minimization moves in fold_constraints protocol. Useful for testing wheather fragment moves alone can recapitulate a given structure.
  Default: false
  

  -force_minimize <Boolean>

  Minimization moves in fold_constraints protocol also if no constraints present
  Default: false
  

  -seq_sep_stages <RealVector>

  give vector with sequence_separation after stage1, stage3 and stage4
  Default: 0
  

  -reramp_cst_cycles <Integer>

  in stage2 do xxx cycles where atom_pair_constraint is ramped up
  Default: 0
  

  -reramp_start_cstweight <Real>

  drop cst_weight to this value and ramp to 1.0 in stage2 – needs reramp_cst_cycles > 0
  Default: 0.01
  

  -reramp_iterations <Integer>

  do X loops of annealing cycles
  Default: 1
  

  -skip_on_noviolation_in_stage1 <Boolean>

  if constraints report no violations — skip cycles
  Default: false
  

  -stage1_ramp_cst_cycle_factor <Real>

  spend x*<standard cycles>=""> on each step of sequence separation
  Default: 0.25
  

  -stage2_constraint_threshold <Real>

  stop runs that violate this threshold at end of stage2
  Default: 0
  

  -ignore_sequence_seperation <Boolean>

  usually constraints are switched on according to their separation in the fold-tree
  Default: false
  

  -no_recover_low_at_constraint_switch <Boolean>

  dont recover low when max_seq_sep is increased
  Default: false
  

  -ramp_coord_cst <Boolean>

  ramp coord csts just like chainbreak-weights during fold-cst
  Default: false
  

• fold_from_loops

  -fold_from_loops <Boolean>

  fold_from_loops option group
  

  -native_ca_cst <Boolean>

  derive constraints from the native topology
  Default: false
  

  -swap_loops <File>

  pdb of the target loops
  Default: "--"
  

  -checkpoint <String>

  write/read checkpoint files for nstruct. Provide a checkpoint filename after this option.
  Default: ""
  

  -ca_csts_dev <Real>

  standard deviation allowed to each constraint
  Default: 0.5
  

  -add_relax_cycles <Integer>

  additional relax cycles
  Default: 2
  

  -loop_mov_nterm <Integer>

  Movable region inside the provided loop(nterm)
  Default: 0
  

  -loop_mov_cterm <Integer>

  Moveable region inside the provided loop(cterm)
  Default: 0
  

  -ca_rmsd_cutoff <Real>

  Filter the decoys to pass the relax-design stage
  Default: 5.0
  

  -res_design_bs <IntegerVector>

  enumerate the residues to be designed within the fixed binding site
  

  -clear_csts <File>

  input loops file with ranges free of CA csts
  Default: "--"
  

  -output_centroid <Boolean>

  output centroid structures befor the design stage
  Default: false
  

  -add_cst_loop <Boolean>

  add CA csts of motif to constraint set
  Default: false
  

• frags

  -frags <Boolean>

  frags option group
  

  -j <Integer>

  Number of threads to use
  

  -filter_JC <Boolean>

  Filter J-coupling values in the dynamic range
  Default: false
  

  -bounded_protocol <Boolean>

  makes the picker use bounded protocol to select fragments. This is teh default behavior
  Default: true
  

  -keep_all_protocol <Boolean>

  makes the picker use keep-all protocol to select fragments. The default is bounded protocol
  Default: false
  

  -quota_protocol <Boolean>

  quota protocol implies the use of a QuotaCollector and a QuotaSelelctor, no matter what user set up by other flags.
  Default: false
  

  -nonlocal_pairs <Boolean>

  identifies and outputs nonlocal fragment pairs.
  Default: false
  

  -fragment_contacts <Boolean>

  identifies and outputs fragment contacts.
  Default: false
  

  -p_value_selection <Boolean>

  the final fragment selection will b based on p-value rather than on a total score for the given fragment
  Default: false
  

  -n_frags <Integer>

  number of fragments per position
  Default: 200
  

  -allowed_pdb <File>

  provides a text file with allowed PDB chains (five characters per entry, e.g.'4mbA'). Only these PDB chains from Vall will be used to pick fragments
  

  -ss_pred <StringVector>

  provides one or more files with secondary structure prediction (PsiPred SS2 format) , to be used by secondary structure scoring and quota selector. Each file name must be followed by a string ID.
  

  -spine_x <File>

  provides phi and psi torsion angle predictions and solvent accessibility prediction from Spine-X
  

  -depth <File>

  provides residue depth values from DEPTH
  

  -denied_pdb <File>

  provides a text file with denied PDB chains (five characters per entry, e.g.'4mbA'). This way close homologs may be excluded from fragment picking.
  

  -frag_sizes <IntegerVector>

  sizes of fragments to pick from the vall
  Default: ['9', '3', '1']
  

  -write_ca_coordinates <Boolean>

  Fragment picker will store CA Cartesian coordinates in output fragment files. By default only torsion coordinates are stored.
  Default: false
  

  -write_scores <Boolean>

  Fragment picker will write scores in output fragment files.
  Default: false
  

  -annotate <Boolean>

  read the annotation from the rosetta++ fragment file
  Default: false
  

  -nr_large_copies <Integer>

  make N copies for each standard 9mer (or so) fragment
  Default: 1
  

  -n_candidates <Integer>

  number of fragment candidates per position; the final fragments will be selected from them
  Default: 200
  

  -write_rama_tables <Boolean>

  Fragment picker will spit out sequence specific ramachandran score tables for your viewing pleasure. These ramachandran tables are based on the secondary structure predictions fed into RamaScore, and you may occasionally want to look at what the program has defined.
  Default: false
  

  -rama_C <Real>

  Constant in RamaScore equation, command line is for optimization tests
  Default: 0.0
  

  -rama_B <Real>

  Constant in RamaScore equation, command line is for optimization tests
  Default: 1.0
  

  -sigmoid_cs_A <Real>

  Constant in CSScore equation, command line is for optimization tests
  Default: 2.0
  

  -sigmoid_cs_B <Real>

  Constant in CSScore equation, command line is for optimization tests
  Default: 4.0
  

  -seqsim_H <Real>

  Secondary structure type prediction multiplier, for use in fragment picking
  Default: 1.0
  

  -seqsim_E <Real>

  Secondary structure type prediction multiplier, for use in fragment picking
  Default: 1.0
  

  -seqsim_L <Real>

  Secondary structure type prediction multiplier, for use in fragment picking
  Default: 1.0
  

  -rama_norm <Real>

  Used to multiply rama table values after normalization, default (0.0) means use raw counts (unnormalized)
  Default: 0.0
  

  -describe_fragments <String>

  Writes scores for all fragments into a file
  Default: ""
  

  -picking_old_max_score <Real>

  maximal score allowed for fragments picked by the old vall (used by RosettaRemodel).
  Default: 1000000.0
  

  -write_sequence_only <Boolean>

  Fragment picker will output fragment sequences only. This option is for creating structure based sequence profiles using the FragmentCrmsdResDepth score.
  Default: false
  

  -output_silent <Boolean>

  Fragment picker will output fragments into a silent file.
  Default: false
  

  -output_index <Boolean>

  Fragment picker will output fragments into an index file.
  Default: false
  

  -score_output_silent <Boolean>

  Fragment picker will output fragments into a silent file. Scores of relaxed fragments are added to the silent file.
  Default: false
  

• frags:scoring

  -scoring <Boolean>

  scoring option group
  

  -config <File>

  scoring scheme used for picking fragments
  Default: ""
  

  -profile_score <String>

  scoring scheme used for profile-profile comparison
  Default: "L1"
  

• frags:picking

  -picking <Boolean>

  picking option group
  

  -selecting_rule <String>

  the way how fragments are selected from candidates, e.g. QuotaSelector of BestTotalScoreSelector
  Default: "BestTotalScoreSelector"
  

  -selecting_scorefxn <String>

  in the case user chose BestTotalScoreSelector to be used, this option provides a custom scoring function to be used at the selection step
  

  -quota_config_file <File>

  provides a configuration file for quota selector
  

  -query_pos <IntegerVector>

  provide sequence position for which fragments will be picked. By default fragments are picked for the whole query sequence
  

• frags:nonlocal

  -nonlocal <Boolean>

  nonlocal option group
  

  -relax_input <Boolean>

  relax input before running protocol
  

  -relax_input_with_coordinate_constraints <Boolean>

  relax input with coordinate constraints before running protocol
  

  -relax_frags_repeats <Integer>

  relax repeats for relaxing fragment pair
  

  -single_chain <Boolean>

  non-local fragment pairs will be restricted to the same chain
  

  -min_contacts_per_res <Real>

  minimum contacts per residue in fragment to be considered a fragment pair
  Default: 1.0
  

  -max_ddg_score <Real>

  maximum DDG score of fragment pair
  

  -max_rmsd_after_relax <Real>

  maximum rmsd of fragment pair after relax
  

  -output_frags_pdbs <Boolean>

  output non-local fragment pair PDBs
  

  -output_idealized <Boolean>

  output an idealized pose which can be used for generating a new VALL
  

  -output_silent <Boolean>

  output non-local fragment pairs silent file
  Default: true
  

• frags:contacts

  -contacts <Boolean>

  contacts option group
  

  -min_seq_sep <Integer>

  minimum sequence separation between contacts
  Default: 12
  

  -dist_cutoffs <RealVector>

  distance cutoffs to be considered a contact. contact counts will only be saved.
  Default: ['9.0']
  

  -centroid_distance_scale_factor <Real>

  Scaling factor for centroid distance cutoffs.
  Default: 1.0
  

  -type <StringVector>

  Atom considered for contacts
  Default: utility::vector1<std::string>(1,"ca")
  

  -neighbors <Integer>

  number of adjacent residues to a contact for finding neighboring contacts
  Default: 0
  

  -output_all <Boolean>

  output all contacts
  Default: false
  

• frags:ABEGO

  -ABEGO <Boolean>

  ABEGO option group
  

  -phi_psi_range_A <Real>

  Further filter phi&psi during frag picking process in design
  Default: 999.0
  

• holes

  -holes <Boolean>

  holes option group
  

  -dalphaball <File>

  The DAlaphaBall_surf program
  

  -params <File>

  File containing score parameters
  Default: "holes_params.dat"
  

  -h_mode <Integer>

  include H's or no... see PoseBalls.cc
  Default: 0
  

  -water <Boolean>

  include water or no
  Default: false
  

  -make_pdb <Boolean>

  make pdb with scores
  Default: false
  

  -make_voids <Boolean>

  do separate SLOW void calculation
  Default: false
  

  -atom_scores <Boolean>

  output scores for all atoms
  Default: false
  

  -residue_scores <Boolean>

  output scores for all residues (avg over atoms)
  Default: false
  

  -minimize <String>

  RosettaHoles params to use: decoy15, decoy25 or resl
  Default: "decoy15"
  

  -debug <Boolean>

  dump debug output
  Default: false
  

• hotspot

  -hotspot <Boolean>

  hotspot option group
  

  -allow_gly <Boolean>

  Allow glycines in hotspot hashing constraints?
  Default: false
  

  -allow_proline <Boolean>

  Allow prolines in hotspot hashing constraints?
  Default: false
  

  -benchmark <Boolean>

  Score existing interface?
  Default: false
  

  -residue <StringVector>

  mini residue name3 to use for hotspot hashing
  Default: utility::vector1<std::string>(1,"ALL")
  

  -hashfile <File>

  Existing hotspot hash file.
  

  -target <File>

  Target PDB of the hotspot hash. Used for both de novo hashing and making hash density maps.
  

  -target_res <Integer>

  Rosetta residue number of interest on the target PDB. Used for targeted hashing
  

  -target_dist <Real>

  Tolerated distance from the target residue. Used for targeted hashing
  Default: 20
  

  -density <File>

  Filename to write unweighted hotspot density (compared to -target PDB).
  

  -weighted_density <File>

  Filename to write score weighted hotspot density (compared to -target PDB).
  

  -rms_target <File>

  Filename to write best rms of hotspot to target complex. Suitable for pymol data2b_res
  

  -rms_hotspot <File>

  Filename to write best rms of hotspot to target complex. Suitable for rms vs E scatter plots.
  

  -rms_hotspot_res <Integer>

  Rosetta residue # to use for calculating rms_hotspot.
  

  -rescore <Boolean>

  Rescore hotspots from -hashfile based on the supplied -target PDB.
  Default: false
  

  -threshold <Real>

  Score threshold for hotspot accepts. Found hotspots must be better than or equal to threshold
  Default: -1.0
  

  -sc_only <Boolean>

  Make backbone atoms virtual to find sidechain-only hotspots?
  Default: true
  

  -fxnal_group <Boolean>

  Only use a stubs functional group for rmsd calculations.
  Default: true
  

  -cluster <Boolean>

  Cluster stubset. Will take place before colonyE.
  Default: false
  

  -colonyE <Boolean>

  Rescore hotspots from -hashfile based on colony energy.
  Default: false
  

  -length <Integer>

  Length of hotspot peptide to use for hashing. Sidechain-containing group will be in the center.
  Default: 1
  

  -envhb <Boolean>

  Use environment dependent Hbonds when scoring hotspots.
  Default: false
  

  -angle <Real>

  Maximum allowed angle between stubCA, target CoM, and stubCB. Used to determine if stub is pointing towards target. Negative numbers deactivates this check (default)
  Default: -1
  

  -angle_res <Integer>

  Residue to use for angle calculation from stubCA, <this option>="">, and stubCB. Used to determine if stub is pointing towards target. 0 uses the default, which is the targets center of mass
  Default: 0
  

• indexed_structure_store

  -indexed_structure_store <Boolean>

  indexed_structure_store option group
  

  -fragment_store <File>

  Fragment store. [.h5] file
  

  -fragment_threshold_distance <Real>

  sets the fragment threshold distance when being read in by the VallLookback score function
  Default: 0.4
  

  -store_name <String>

  name of store in hdf5
  Default: "9_mer"
  

  -exclude_homo <String>

  turns on delete homologs from hdf5 database and gives files
  

• lh

  -lh <Boolean>

  lh option group
  

  -loopsizes <IntegerVector>

  Which loopsizes to use
  Default: ['10', '15', '20']
  

  -num_partitions <Integer>

  Number of partitions to split the database into
  Default: 1
  

  -db_path <Path>

  Path to database
  Default: ""
  

  -exclude_homo <Boolean>

  Use a homolog exclusion filter
  Default: false
  

  -bss <Boolean>

  Use BinaryProteinSilentStruct instead of ProteinSilentStruct (needed for nonideal)
  Default: false
  

  -refstruct <String>

  File with a target reference structure
  Default: ""
  

  -homo_file <String>

  File containing homologs to exclude
  Default: ""
  

  -createdb_rms_cutoff <RealVector>

  RMS cutoff used for throwing out similar fragments.
  Default: ['0', '0', '0']
  

  -min_bbrms <Real>

  No description
  Default: 20.0
  

  -max_bbrms <Real>

  No description
  Default: 1400.0
  

  -min_rms <Real>

  No description
  Default: 0.5
  

  -max_rms <Real>

  No description
  Default: 4.0
  

  -filter_by_phipsi <Boolean>

  No description
  Default: true
  

  -max_radius <Integer>

  No description
  Default: 4
  

  -max_struct <Integer>

  No description
  Default: 10
  

  -max_struct_per_radius <Integer>

  No description
  Default: 10
  

  -grid_space_multiplier <Real>

  No description
  Default: 1
  

  -grid_angle_multiplier <Real>

  No description
  Default: 2.5
  

  -skim_size <Integer>

  No description
  Default: 100
  

  -rounds <Integer>

  No description
  Default: 100
  

  -jobname <String>

  Prefix (Ident string) !
  Default: "default"
  

  -max_lib_size <Integer>

  No description
  Default: 2
  

  -max_emperor_lib_size <Integer>

  No description
  Default: 25
  

  -max_emperor_lib_round <Integer>

  No description
  Default: 0
  

  -library_expiry_time <Integer>

  No description
  Default: 2400
  

  -objective_function <String>

  What to use as the objective function
  Default: "score"
  

  -expire_after_rounds <Integer>

  If set to > 0 this causes the Master to expire a structure after it has gone through this many cycles
  Default: 0
  

  -mpi_resume <String>

  Prefix (Ident string) for resuming a previous job!
  

  -mpi_feedback <String>

  No description
  Default: "no"
  

  -mpi_batch_relax_chunks <Integer>

  No description
  Default: 100
  

  -mpi_batch_relax_absolute_max <Integer>

  No description
  Default: 300
  

  -mpi_outbound_wu_buffer_size <Integer>

  No description
  Default: 60
  

  -mpi_loophash_split_size <Integer>

  No description
  Default: 50
  

  -mpi_metropolis_temp <Real>

  No description
  Default: 1000000.0
  

  -mpi_save_state_interval <Integer>

  No description
  Default: 1200
  

  -mpi_master_save_score_only <Boolean>

  No description
  Default: true
  

  -max_loophash_per_structure <Integer>

  No description
  Default: 1
  

  -prob_terminus_ramapert <Real>

  Prob. to run ramapert instead of fraginsert on terminus
  Default: 0.0
  

  -rms_limit <Real>

  How to deal with returned relaxed structures
  Default: 2.0
  

  -similarity_reference <Real>

  How to deal with returned relaxed structures
  Default: 2.0
  

  -centroid_only <Boolean>

  false
  Default: false
  

  -write_centroid_structs <Boolean>

  Output raw loophashed decoys as well as relaxed ones
  Default: false
  

  -write_all_fa_structs <Boolean>

  Write out all structures returned from batch relax
  Default: false
  

  -sandbox <Boolean>

  Sand box mode
  Default: false
  

  -create_db <Boolean>

  Make database with this loopsize
  Default: false
  

  -sample_weight_file <File>

  Holds the initial per residue sample weights
  

  -radius_size <Real>

  tune the radius for hypershell
  Default: 2
  

  -max_ref_lib_size <Integer>

  No description
  Default: 2
  

  -multi_objective_functions <StringVector>

  What to use as the objective function
  Default: utility::vector1<std::string>(1,"score")
  

  -additional_objective_functions <StringVector>

  What to add for the multi-objective function
  

  -edensity_weight_for_sampling <Real>

  weight for elec_dens_fast in WorkUnit_Samplers
  Default: 0.0
  

  -mpi_master_schfile <String>

  schedule file
  Default: ""
  

  -mpi_master_cpu_weight <IntegerVector>

  weight on number of slaves
  Default: ['0.0']
  

  -mpi_loophash_scan_type <String>

  No description
  Default: "random"
  

  -mpi_read_structure_for_emperor <Boolean>

  No description
  Default: true
  

  -mpi_packmin_init <Boolean>

  No description
  Default: false
  

  -max_sample_per_structure <Integer>

  No description
  Default: 1
  

  -loop_string <String>

  string to be parsed for loop region, e.g. 1-10,15-20,32-38
  Default: ""
  

  -seg_string <String>

  string to be parsed for segment region, e.g. 1-10,15-20,32-38
  Default: ""
  

  -loopresdef <StringVector>

  String vector that tells connectivity, e.g. peptide:1,2,3,4,5-6 SSbond:3,2,1-9,8,7,6
  Default: ['']
  

  -pert_init_loop <Boolean>

  Try perturbing loops from starting structure at the beginning
  Default: false
  

  -NMdist <Real>

  normalmodemover distance cut
  Default: 10.0
  

  -objective_dominate_cut <RealVector>

  cut for objective function domination
  Default: ['0.0', '0.0', '3.0']
  

  -objective_cut_increment <RealVector>

  objective_dominate_cut increment for every call
  Default: ['0.0', '0.0', '0.0']
  

  -similarity_method <String>

  No description
  Default: "sum"
  

  -similarity_measure <String>

  No description
  Default: "Sscore"
  

  -similarity_tolerance <Real>

  No description
  Default: 0.5
  

  -parent_selection_kT <Real>

  No description
  Default: 0.2
  

  -sim_replace_obj <String>

  No description
  Default: "goap"
  

  -ulr_mulfactor <Real>

  No description
  Default: 1.8
  

  -filter_up_to_maxlib <Boolean>

  No description
  Default: false
  

  -minimize_after_nmsearch <Boolean>

  No description
  Default: false
  

• lh:fragpdb

  -fragpdb <Boolean>

  fragpdb option group
  

  -out_path <String>

  Path where pdbs are saved
  Default: ""
  

  -indexoffset <IntegerVector>

  list of index offset pairs
  Default: ['-1']
  

  -bin <StringVector>

  list of bin keys
  Default: utility::vector1<std::string>()
  

• lh:symfragrm

  -symfragrm <Boolean>

  symfragrm option group
  

  -pdblist <FileVector>

  list of pdbs to be processed
  

• loopfcst

  -loopfcst <Boolean>

  loopfcst option group
  

  -coord_cst_weight <Real>

  use coord constraints for template
  Default: 0.0
  

  -coord_cst_all_atom <Boolean>

  use coord constraints on all atoms and not just CA
  Default: false
  

  -use_general_protocol <Boolean>

  use the new machinery around classes KinematicXXX
  Default: false
  

  -coord_cst_weight_array <File>

  use these weights (per seqpos) for coord cst in rigid regions
  Default: ""
  

  -dump_coord_cst_weight_array <File>

  dump these weights (per seqpos) for coord cst in rigid regions
  Default: ""
  

• LoopModel

  -LoopModel <Boolean>

  LoopModel option group
  

  -input_pdb <File>

  input pdb file
  Default: "LoopModel::input_pdb"
  

• make_rot_lib

  -make_rot_lib <Boolean>

  make_rot_lib option group
  

  -options_file <File>

  path to make rot lib options file
  

  -two_fold_symmetry_135_315 <IntegerVector>

  the chi number at which to apply two fold symmetry across the 135/315 axis
  

  -two_fold_symmetry_0_180 <IntegerVector>

  the chi number at which to apply two fold symmetry across the 0/180 axis
  

  -three_fold_symmetry_90_210_330 <IntegerVector>

  the chi number at which to apply two fold symmetry across the 0/180 axis
  

  -use_terminal_residues <Boolean>

  Use separate ACE and NME residues as terminal capping groups, rather than patches
  Default: false
  

  -k_medoids <Boolean>

  Use k-medoids instead of k-means clustering
  Default: false
  

• match

  -match <Boolean>

  match option group
  

  -lig_name <String>

  Name of the ligand to be matched. This should be the same as the NAME field of the ligand's parameter file (the .params file)
  

  -bump_tolerance <Real>

  The permitted level of spherical overlap betweeen any two atoms. Used to detect collisions between the upstream atoms and the background, the upstream atoms and the downstream atoms, and the downstream atoms and the background
  Default: 0.0
  

  -active_site_definition_by_residue <File>

  File describing the active site of the scaffold as a set of resid/radius pairs
  

  -active_site_definition_by_gridlig <File>

  File containing 1s and Os describing the volume of space for the active site. .gridlig file format from Rosetta++
  

  -required_active_site_atom_names <File>

  File listing the downstream-residue-atom names which must reside in the defined active site. Requires either the flag active_site_definition_by_residue or the flag active_site_definition_by_gridlig to be specified.
  

  -grid_boundary <File>

  File describing the volume in space in which the third orientation atom must lie
  Default: ""
  

  -geometric_constraint_file <File>

  File describing the geometry of the downstream object relative to the upstream object
  

  -scaffold_active_site_residues <File>

  File with the residue indices on the scaffold that should be considered as potential launch points for the scaffold's active site. File format described in MatcherTask.cc in the details section of the initialize_scaffold_active_site_residue_list_from_command_line() method.
  Default: ""
  

  -scaffold_active_site_residues_for_geomcsts <File>

  File which lists the residue indices on the scaffold to consider as potential launch points for the scaffold's active site for each geometric constraint; each constraint may have a separate set of residue ids. File format described in MatcherTask.cc in the details section of the initialize_scaffold_active_site_residue_list_from_command_line() method.
  Default: ""
  

  -euclid_bin_size <Real>

  The bin width for the 3-dimensional coordinate hasher, in Angstroms
  Default: 1.0
  

  -euler_bin_size <Real>

  The bin width for the euler angle hasher, in degrees
  Default: 10.0
  

  -consolidate_matches <Boolean>

  Instead of outputting all matches, group matches and then write only the top -match::output_matches_per_group from each group.
  Default: false
  

  -output_matches_per_group <Integer>

  The number of matches to output per group. Requires the -match::consolidate_matches flag is active.
  Default: 10
  

  -orientation_atoms <StringVector>

  The three atoms, by name, on the downstream partner to use to describe its 6 dimensional coordinate; its position and orientation. Only usable when the downstream partner is a single residue. Exactly 3 atom names must be given. If these atoms are unspecified, the matcher will use the residues neighbor atom and two atoms bonded to the neighbor atom to define the orientation. The euclidean coordinate of the third orientation atom is used as the first the dimensions of the downstream residues 6D coordinate; the other three dimensions are the three euler angles described by creating a coordinate frame at orientation atom 3, with the z axis along the vector from orientation atom 2 to orientation atom 3, and the y axis lying in the plane with orientation atoms 1,2&3.
  

  -output_format <String>

  The format in which the matches are output
  Default: "CloudPDB"
  

  -match_grouper <String>

  The parameters that matches are grouped according to by the MatchConsolidator or the CloudPDBWriter
  Default: "SameSequenceAndDSPositionGrouper"
  

  -grouper_downstream_rmsd <Real>

  Maximum allowed rmsd between two orientations of the downstream pose to be considered part of the same group
  Default: 1.5
  

  -output_matchres_only <Boolean>

  Whether to output the matched residues only or the whole pose for every match
  Default: false
  

  -geom_csts_downstream_output <IntegerVector>

  For which of the geometric constraints the downstream residue/ligand will be output
  Default: ['1']
  

  -filter_colliding_upstream_residues <Boolean>

  Filter the output matches if the hits induce a collision between the upstream residues
  Default: true
  

  -upstream_residue_collision_tolerance <Real>

  The amount of atom overlap allowed between upstream residues in a match. If this is unspecified on the command line, then the value in the bump_tolerance option is used
  Default: 0.0
  

  -upstream_residue_collision_score_cutoff <Real>

  The score cutoff for upstream residue pairs to use in the collision filter. Activating this cutoff uses the etable atr/rep/sol terms to evaluate residue-pair interactions instead of hard-sphere overlap detection
  Default: 10.0
  

  -upstream_residue_collision_Wfa_atr <Real>

  The fa_atr weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
  Default: 0.8
  

  -upstream_residue_collision_Wfa_rep <Real>

  The fa_rep weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
  Default: 0.44
  

  -upstream_residue_collision_Wfa_sol <Real>

  The fa_sol weight to use in the upstream-collision filter; use in tandem with upstream_residue_collision_score_cutoff
  Default: 0.0
  

  -filter_upstream_downstream_collisions <Boolean>

  Filter the output matches if the hits induce a collision between the upstream residues and the downstream pose
  Default: true
  

  -updown_collision_tolerance <Real>

  The amount of atom overlap allowed between upstream and downstream atoms in a match. If this is unspecified on the command line, then the value in the bump_tolerance option is used
  Default: 0.0
  

  -updown_residue_collision_score_cutoff <Real>

  The score cutoff for upstream/downstream residue pairs to use in the collision filter. Activating this cutoff uses the etable atr/rep/sol terms to evaluate residue-pair interactions instead of hard-sphere overlap detection
  Default: 10.0
  

  -updown_residue_collision_Wfa_atr <Real>

  The fa_atr weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
  Default: 0.8
  

  -updown_residue_collision_Wfa_rep <Real>

  The fa_rep weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
  Default: 0.44
  

  -updown_residue_collision_Wfa_sol <Real>

  The fa_sol weight to use in the upstream-downstream-collision filter; use in tandem with updown_residue_collision_score_cutoff
  Default: 0.0
  

  -define_match_by_single_downstream_positioning <Boolean>

  Enumerate combinations of matches where a single positioning of the downstream partner as well as the conformations of the upstream residues defines the match; it is significantly faster to enumerate unique matches when they are defined this way instead of enumerating the (combinatorially many) matches when a match is defined by n-geometric-constraint locations of the downstream partner. This faster technique for outputting matches is automatically chosen when the flag -match::output_format is PDB.
  

  -ligand_rotamer_index <Integer>

  Match with a particular conformation of the ligand; the index represents which conformation in the multi-model .pdb file specified in the ligand's .params file by the PDB_ROTAMERS field. The index of the first conformation in that file is 1; valid indices range from 1 to the number of entries in the multi-model .pdb file. If this command-line flag is not used, then the conformation of the ligand described by the ICOOR_INTERNAL lines of the ligand's .params file is used instead.
  

  -enumerate_ligand_rotamers <Boolean>

  Match with all ligand rotamers specified in the multi-model .pdb file specified in the ligand's .params file by the PDB_ROTAMERS field. This flag may not be used in combination with the match::ligand_rotamer_index flag. Geometry of the ligand rotamers in the .pdb file will be idealized to the .params file bond angles and lengths.
  Default: true
  

  -only_enumerate_non_match_redundant_ligand_rotamers <Boolean>

  Only defined if enumerate_ligand_rotamers is true this option causes the matcher to determine which rotamers in the ligand rotamer library are redundant in terms of matching, meaning the atoms they're matched through are superimposable. after having subdivided the ligand rotamer library into match-redundant subgroups, the matcher will then only place the first nonclashing rotamer from each subgroup.
  Default: true
  

  -dynamic_grid_refinement <Boolean>

  When too many hits land in the same 'connected component', requiring the enumeration of twoo many matches, refine the grid size to be smaller so that fewer matches have to be enumerated. This process works on individual connected components and is not applied to all regions of 6D. This is significantly more efficient than enumerating all matches, while allowing the grid size to remain large and the rotamer and external geometry to remain dense. (A connected component refers to
  

  -build_round1_hits_twice <Boolean>

  Memory saving strategy that avoids paying for the storage of all the round-1 hits and instead records only what 6D voxels those hits fall in to. Then the second round of matching proceeds storing only the hits that fall into the same voxels that the hits from the first round fell into. Then the matcher goes back and generates the first-round hits again, but only keeps the ones that land into the same voxels that hits from round 2 fell into. To be used, round 2 must also use the classic match algorithm (and must not use secondary matching).
  Default: false
  

• matdes

  -matdes <Boolean>

  matdes option group
  

  -num_subs_building_block <Integer>

  The number of subunits in the oligomeric building block
  Default: 1
  

  -num_subs_total <Integer>

  The number of subunits in the target assembly
  Default: 1
  

  -pdbID <String>

  The PDB ID
  Default: "0xxx"
  

  -prefix <String>

  Prefix appended to output PDB files. Perhaps useful to describe the architecture, e.g., 532_3_...
  Default: "pre_"
  

  -radial_disp <RealVector>

  Specify the radial displacement from the center of a closed point group assembly. Use with -in::olig_search::dump_pdb
  

  -angle <RealVector>

  Specify the angle by which a building block is rotated in a symmetrical assembly. Use with -in::olig_search::dump_pdb
  

  -tag <String>

  Four digit ID tag attached to a design model during design
  

• matdes:dock

  -dock <Boolean>

  dock option group
  

  -neg_r <Real>

  Specify whether radial displacement is positive or negative. 1 for negative, 0 for positive.
  Default: 0
  

  -dump_pdb <Boolean>

  Dump a pdb of a particular docked configuration
  Default: false
  

  -dump_chainA_only <Boolean>

  Only output chain A (the asymmetric unit) of the symmetrical assembly. Use with -in::olig_search::dump_pdb
  Default: false
  

• matdes:design

  -design <Boolean>

  design option group
  

  -contact_dist <Real>

  CA-CA distance for defining interface residues
  Default: 10.0
  

  -grid_size_angle <Real>

  The width of angle space to start design/minimize runs from, centered on the starting angle
  Default: 1.0
  

  -grid_size_radius <Real>

  The width of radius space to start design/minimize runs from, centered on the starting radius
  Default: 1.0
  

  -grid_nsamp_angle <Integer>

  The number of samples the rigid body grid is divided into in angle space
  Default: 9
  

  -grid_nsamp_radius <Integer>

  The number of samples the rigid body grid is divided into in radius space
  Default: 9
  

  -fav_nat_bonus <Real>

  Bonus to be awarded to native residues
  Default: 0.0
  

• matdes:mutalyze

  -mutalyze <Boolean>

  mutalyze option group
  

  -calc_rot_boltz <Boolean>

  Specify whether to calculate RotamerBoltzmann probabilities or not
  Default: 0
  

  -ala_scan <Boolean>

  Specify whether to calculate ddGs for alanine-scanning mutants at the designed interface
  Default: 1
  

  -revert_scan <Boolean>

  Specify whether to calculate ddGs for reversion mutants at the designed interface
  Default: 1
  

  -min_rb <Boolean>

  Specify whether to minimize the rigid body DOFs
  Default: 1
  

• mc

  -mc <Boolean>

  mc option group
  

  -log_scores_in_MC <Boolean>

  Score each decoy during a simulation and output it to log; slows down run!
  Default: false
  

  -hierarchical_pool <String>

  specify prefix in order to look for hierarchical pool
  

  -read_structures_into_pool <File>

  specify the silent-structs to create a hierarchy for lazy users
  

  -convergence_check_frequency <Integer>

  how often check for convergences in MC object?
  Default: 100
  

  -known_structures <File>

  specify a filename of a silent-file containing known structures
  Default: "known_structs.in"
  

  -max_rmsd_against_known_structures <Real>

  stop sampling if rmsd to a known-structure is lower than X
  Default: 1.5
  

  -excluded_residues_from_rmsd <IntegerVector>

  residues that are not used for RMSD computation in pool
  

  -heat_convergence_check <Integer>

  jump out of current abinitio run if X unsuccesful mc-trials reached
  Default: 0
  

• mean_field

  -mean_field <Boolean>

  mean_field option group
  

  -bb_list <FileVector>

  Specifies list of pdb files in backbone ensemble
  

  -dump_transfac <File>

  filename prefix for dumping the predicted specificity profile in transfac format
  Default: ""
  

  -spec_profile <File>

  specify filename of specificity profile (PWM) (transfac format). Used as gold standard to compare to mean-field predicted result.
  Default: ""
  

  -bb_boltz_probs <File>

  specify filename of backbone Boltzmann probabilities. Can be used in conjunction with bb_list as Boltz probs of backbones in bb_list.
  Default: ""
  

  -rot_norm_weight <Real>

  weight rot_norm term
  Default: 0.0
  

  -bb_average_weight <Real>

  bb_average_weight term
  Default: 0.0
  

  -rf_peptide <File>

  specify filename of resfile used for identifying peptide residues (or residues designated for sequence tolerance analysis)
  Default: ""
  

  -include_all_aa <Boolean>

  upweight probabilities of all amino acids by adding 50 to each value
  Default: false
  

  -ga_pack_detect_interface <Boolean>

  automatically detect protein-peptide interface for calculation of fitness function
  Default: false
  

  -biased_dist_all_gen <Boolean>

  use biased distribution (as specified in spec_profile) for all generations of GA
  Default: false
  

• mh

  -mh <Boolean>

  mh option group
  

  -motif_out_file <String>

  file to dump ResPairMotifs to
  Default: "motifs"
  

  -harvest_motifs <FileVector>

  files to harvest ResPairMotifs from
  Default: "SPECIFY_ME_DUMMY"
  

  -print_motifs <FileVector>

  files to print ResPairMotifs from
  Default: "SPECIFY_ME_DUMMY"
  

  -remove_duplicates <FileVector>

  files to remove dup ResPairMotifs from
  Default: "SPECIFY_ME_DUMMY"
  

  -dump_motif_pdbs <FileVector>

  files to extract ResPairMotifs clusters from
  Default: "SPECIFY_ME_DUMMY"
  

  -merge_motifs <FileVector>

  files to merge ResPairMotifs from
  Default: "SPECIFY_ME_DUMMY"
  

  -merge_scores <FileVector>

  files to merge scores from
  Default: "SPECIFY_ME_DUMMY"
  

  -merge_motifs_one_per_bin <Boolean>

  keep only one motif per hash bin (for sepcified grid)
  Default: false
  

  -gen_reverse_motifs_on_load <Boolean>

  
  Default: false
  

  -dump_input_pdb <FileVector>

  files to dump biount interpretation from
  Default: "SPECIFY_ME_DUMMY"
  

  -score_pdbs <FileVector>

  files to score with input counts file
  Default: "SPECIFY_ME_DUMMY"
  

  -sequence_recovery <FileVector>

  pdb files to score
  Default: "SPECIFY_ME_DUMMY"
  

  -explicit_motif_score <FileVector>

  pdb files to score
  Default: "SPECIFY_ME_DUMMY"
  

  -harvest_scores <FileVector>

  get counts from ResPairMotif files and dump to binary counts file
  Default: ""
  

  -print_scores <File>

  print a binary counts file
  Default: ""
  

  -dump_matching_motifs <FileVector>

  pdb files to score
  Default: "SPECIFY_ME_DUMMY"
  

  -score_across_chains_only <Boolean>

  ignore intra-chain motifs
  Default: false
  

  -normalize_score_ncontact <Boolean>

  normalize by total num contacts
  Default: true
  

  -harvest_motifs_min_hh_ends <Integer>

  restrict to middle of hilix contacts
  Default: 0
  

  -ignore_io_errors <Boolean>

  
  Default: false
  

  -motif_match_radius <Real>

  width of euler angle bin
  Default: 9e9
  

  -merge_similar_motifs <RealVector>

  give 3 hash params
  

• mh:score

  -score <Boolean>

  score option group
  

  -background_weight <Real>

  weight on cb contacts, kinda
  Default: 0.0
  

  -ca_cb_clash_weight <Real>

  weight on cb clashes, kinda
  Default: 1.0
  

  -noloops <Boolean>

  ignore loop ss in scored structs
  Default: false
  

  -nosheets <Boolean>

  ignore strand ss in scored structs
  Default: false
  

  -nohelix <Boolean>

  ignore helix ss in scored structs
  Default: false
  

  -spread_ss_element <Boolean>

  
  Default: false
  

  -min_cover_fraction <Real>

  
  Default: 0.0
  

  -strand_pair_weight <Real>

  
  Default: 1.0
  

  -anti_polar_weight <Real>

  
  Default: 1.0
  

  -min_contact_pairs <Real>

  
  Default: 1.0
  

  -max_contact_pairs <Real>

  
  Default: 9e9
  

  -max_cb_dis <Real>

  
  Default: 9.0
  

  -coverage_pow <Real>

  
  Default: 0.0
  

  -use_ss1 <Boolean>

  
  Default: true
  

  -use_ss2 <Boolean>

  
  Default: true
  

  -use_aa1 <Boolean>

  
  Default: false
  

  -use_aa2 <Boolean>

  
  Default: false
  

  -use_log <Boolean>

  
  Default: true
  

• mh:path

  -path <Boolean>

  path option group
  

  -biounit <StringVector>

  path to search for biounits in the ab/1abc.pdb1.gz format
  Default: utility::vector1<std::string>()
  

  -biounit_ideal <StringVector>

  idealized biounit coords, missing PDBInfo metadatab
  Default: utility::vector1<std::string>()
  

  -pdb <StringVector>

  path to search for pdbs in the ab/1abc.pdb.gz format
  Default: utility::vector1<std::string>()
  

  -motifs <StringVector>

  concrete motifs in .rpm.bin.gz format
  Default: utility::vector1<std::string>()
  

  -motifs_SC_SC <StringVector>

  concrete SC_SC motifs, try to replace with path::motifs
  Default: utility::vector1<std::string>()
  

  -motifs_SC_BB <StringVector>

  concrete SC_BB motifs, try to replace with path::motifs
  Default: utility::vector1<std::string>()
  

  -motifs_BB_BB <StringVector>

  concrete BB_BB motifs, try to replace with path::motifs
  Default: utility::vector1<std::string>()
  

  -motifs_BB_PH <StringVector>

  concrete BB_PH motifs, try to replace with path::motifs
  Default: utility::vector1<std::string>()
  

  -motifs_BB_PO <StringVector>

  concrete BB_PO motifs, try to replace with path::motifs
  Default: utility::vector1<std::string>()
  

  -motifs_PH_PO <StringVector>

  concrete PH_PO motifs, try to replace with path::motifs
  Default: utility::vector1<std::string>()
  

  -scores <StringVector>

  motif hash data for scoring, mixed, may not use
  

  -scores_SC_SC <StringVector>

  motif hash data for scoring SC_SC
  

  -scores_SC_BB <StringVector>

  motif hash data for scoring SC_BB
  

  -scores_BB_BB <StringVector>

  motif hash data for scoring
  

  -scores_BB_PH <StringVector>

  motif hash data for scoring BB_PH
  

  -scores_BB_PO <StringVector>

  motif hash data for scoring BB_PO
  

  -scores_PH_PO <StringVector>

  motif hash data for scoring strand pairings
  

  -scores_frags <StringVector>

  motif hash data for scoring strand pairings
  

• mh:harvest

  -harvest <Boolean>

  harvest option group
  

  -hash_cart_resl <Real>

  width of cartesian bin
  Default: 0.8
  

  -hash_angle_resl <Real>

  width of euler angle bin
  Default: 15.0
  

  -smoothing_factor <Real>

  smoothing radius exp(-d/resl**2 * factor)
  Default: 1.0
  

  -idealize <Boolean>

  
  Default: false
  

  -dump <Boolean>

  
  Default: false
  

  -min_bin_val <Real>

  
  Default: 0.0
  

  -sep_aa <Boolean>

  
  Default: false
  

  -sep_aa1 <Boolean>

  
  Default: false
  

  -sep_aa2 <Boolean>

  
  Default: false
  

  -sep_ss <Boolean>

  
  Default: false
  

  -sep_dssp <Boolean>

  
  Default: false
  

  -sep_lj <RealVector>

  
  Default: utility::vector1<double>()
  

  -sep_hb <RealVector>

  
  Default: utility::vector1<double>()
  

  -sep_nbrs <RealVector>

  
  Default: utility::vector1<double>()
  

  -sep_bfac <RealVector>

  
  Default: utility::vector1<double>()
  

  -sep_dist <RealVector>

  
  Default: utility::vector1<double>()
  

  -weight_by_energy <Boolean>

  
  Default: true
  

  -max_rmsd <Real>

  skip structure if refined rms to input is higher than this
  Default: 0.5
  

  -max_res <Integer>

  max res in biounit (or whatever) for harvest
  Default: 1000
  

  -agg_with_max <Boolean>

  
  Default: false
  

  -multiplier <Real>

  
  Default: 1.0
  

• mh:match

  -match <Boolean>

  match option group
  

  -interface_only <Boolean>

  
  Default: true
  

  -ss <Boolean>

  
  Default: true
  

  -ss1 <Boolean>

  
  Default: true
  

  -ss2 <Boolean>

  
  Default: true
  

  -aa <Boolean>

  
  Default: false
  

  -aa1 <Boolean>

  
  Default: false
  

  -aa2 <Boolean>

  
  Default: false
  

• mh:dump

  -dump <Boolean>

  dump option group
  

  -limit_per_pair <Integer>

  
  Default: 999999
  

  -max_per_res <Integer>

  
  Default: 30
  

  -max_ca_dis <Real>

  
  Default: 12.0
  

  -max_rms <Real>

  
  Default: 0.5
  

  -resfile_min_pair_score <Real>

  
  Default: 0.00
  

  -resfile_min_tot_score <Real>

  
  Default: 0.00
  

  -resfile_dump <Boolean>

  
  Default: false
  

  -symmetric_motifs <Boolean>

  
  Default: false
  

• mh:filter

  -filter <Boolean>

  filter option group
  

  -filter_harvest <Boolean>

  filter while harvesting
  Default: false
  

  -filter_io <Boolean>

  filter while reading filter
  Default: true
  

  -pdb <String>

  4/5 letter pdb code
  

  -lig <String>

  3 letter lig code
  

  -motif_type <String>

  bb pb sc pp
  

  -restype1 <String>

  allowed res types for res1
  Default: "ACDEFGHIKLMNPQRSTVWY"
  

  -restype2 <String>

  allowed res types for res2
  Default: "ACDEFGHIKLMNPQRSTVWY"
  

  -restype <String>

  allowed res types
  Default: "ACDEFGHIKLMNPQRSTVWY"
  

  -restype_one <String>

  allowed res types need at least one
  Default: "ACDEFGHIKLMNPQRSTVWY"
  

  -not_restype <String>

  disallowed res types
  Default: "ACGP"
  

  -not_restype_one <String>

  disallowed res types at least one not
  Default: "ACGP"
  

  -seqsep <Integer>

  min filter seqsep
  Default: 0
  

  -max_seqsep <Integer>

  min filter seqsep
  Default: 99999
  

  -no_hb_bb <Boolean>

  no bb hbonded
  Default: false
  

  -mindist2 <Real>

  min CA-CA dist sq
  Default: 0.0
  

  -maxdist2 <Real>

  max CA-CA dist sq
  Default: 999999.0
  

  -ss1 <String>

  filter ss1
  Default: ""
  

  -ss2 <String>

  filter ss2
  Default: ""
  

  -dssp1 <String>

  filter dssp1
  Default: ""
  

  -dssp2 <String>

  filter dssp2
  Default: ""
  

  -aa1 <String>

  filter aa1
  Default: ""
  

  -aa2 <String>

  filter aa2
  Default: ""
  

  -sasa <Real>

  filter max sasa
  Default: 999.0
  

  -faatr <Real>

  filter max faatr (default 999.0 = no filtering
  Default: 999.0
  

  -hb_sc <Real>

  filter max hb_sc (default 999.0 = no filtering
  Default: 999.0
  

  -hb_bb_sc <Real>

  filter max hb_bb_sc (default 999.0 = no filtering
  Default: 999.0
  

  -hb_bb <Real>

  filter max hb_bb (default 999.0 = no filtering
  Default: 999.0
  

  -occupancy <Real>

  filter min occupancy (default 0.0 = no filtering
  Default: 0.0
  

  -coorderr <Real>

  filter max bfac coorderr = sqrt(B/8*pi**2)) (default 999.0 = no filtering
  Default: 999.0
  

  -uniformfrag <Boolean>

  is frag and all same ss in frag
  Default: false
  

  -faatr_or_hbbb <Real>

  filter require atr or hb (bb allowed) below thresh
  Default: 999.0
  

  -faatr_or_hb <Real>

  filter require atr or hb below thresh
  Default: 999.0
  

  -noloops <Boolean>

  
  Default: false
  

  -oneloop <Boolean>

  
  Default: false
  

  -nodisulf <Boolean>

  
  Default: false
  

  -score <Real>

  filter on ResPairMotir::score()
  Default: 999.0
  

• magnesium

  -magnesium <Boolean>

  magnesium option group
  

  -scan <Boolean>

  default mode: scan Mg(2+) through PDB
  Default: true
  

  -mg_res <IntegerVector>

  supply PDB residue numbers of Mg(2+) to look at [leave blank to scan a new Mg(2+)]
  

  -minimize_during_scoring <Boolean>

  minimize mg(2+) during scoring/hydration of each position
  Default: true
  

  -ligand_res <ResidueChainVector>

  in scan, look at positions near these residues (PDB numbering/chains)
  

  -pose_ligand_res <IntegerVector>

  in scan, look at positions near these residues, pose numbering (1,2,..)
  

  -lores_scan <Boolean>

  do not try hydration or minimization during scan
  Default: false
  

  -xyz_step <Real>

  increment in Angstroms for xyz scan
  Default: 0.50
  

  -score_cut <Real>

  score cut for silent output (5.0 for hires; -8.0 for lores)
  Default: 5.0
  

  -score_cut_PDB <Real>

  score cut for PDB output from scanning (deprecated)
  Default: 0.0
  

  -integration_test <Boolean>

  Stop after first mg position found – for testing
  Default: false
  

  -tether_to_closest_res <Boolean>

  stay near closest ligand res; helps force unique grid sampling in different cluster jobs.
  Default: false
  

  -fixup <Boolean>

  test mode: align the 6 octahedral virtual 'orbitals' for specified mg_res
  Default: false
  

  -pack_water_hydrogens <Boolean>

  test mode: strip out non-mg waters, align mg frames, pack mg waters for specified mg_res
  Default: false
  

  -hydrate <Boolean>

  test mode: strip out waters and hydrate mg(2+) for specified mg_res
  Default: false
  

  -monte_carlo <Boolean>

  test mode: monte carlo sampling of Mg(2+) and surrounding waters
  Default: false
  

  -scored_hydrogen_sampling <Boolean>

  in -pack_water_hydrogens test mode, when packing water hydrogens, use a complete scorefunction to rank (slow)
  Default: false
  

  -all_hydration_frames <Boolean>

  in -hydration test mode, Sample all hydration frames (slow)
  Default: false
  

  -leave_other_waters <Boolean>

  in -hydration test mode, do not remove all waters
  Default: false
  

  -minimize <Boolean>

  minimize Mg(2+) after hydration or hydrogen-packing
  Default: false
  

  -minimize_mg_coord_constraint_distance <Real>

  harmonic tether to Mg(2+) during minimize
  Default: 0.2
  

• magnesium:montecarlo

  -montecarlo <Boolean>

  montecarlo option group
  

  -temperature <Real>

  temperature for Monte Carlo
  Default: 1.0
  

  -cycles <Integer>

  Monte Carlo cycles
  Default: 100000
  

  -dump <Boolean>

  dump PDBs from Mg monte carlo
  Default: false
  

  -add_delete_frequency <Real>

  add_delete_frequency for Monte Carlo
  Default: 0.1
  

• motifs

  -motifs <Boolean>

  motifs option group
  

  -close_enough <Real>

  4-atom rmsd cutoff beyond which you don't bother trying an inverse rotamer
  Default: 1.0
  

  -max_depth <Integer>

  Maximum recursion depth - i.e., maximum number of motifs to incorporate
  Default: 1
  

  -keep_motif_xtal_location <Boolean>

  used to dna_motif_collector - controls whether motifs are moved away from original PDB location (comparison is easier if they are moved, so that's default)
  Default: false
  

  -pack_score_cutoff <Real>

  used in dna_motif_collector - fa_atr + fa_rep energy threshold for a two-residue interaction to determine if it is a motif
  Default: -0.5
  

  -hb_score_cutoff <Real>

  used in dna_motif_collector - hbond_sc energy threshold for a two-residue interaction to determine if it is a motif
  Default: -0.3
  

  -water_score_cutoff <Real>

  used in dna_motif_collector - h2o_hbond energy threshold for a two-residue interaction to determine if it is a motif
  Default: -0.3
  

  -pack_min_threshold <Real>

  Used for motif extraction - packing scores below this value will cause a motif to be discarded
  Default: -9999.0
  

  -pack_max_threshold <Real>

  Used for motif extraction - packing scores above this value will cause a motif to be discarded
  Default: 9999.0
  

  -hbond_min_threshold <Real>

  Used for motif extraction - hbond scores below this value will cause a motif to be discarded
  Default: -9999.0
  

  -hbond_max_threshold <Real>

  Used for motif extraction - hbond scores above this value will cause a motif to be discarded
  Default: 9999.0
  

  -elec_min_threshold <Real>

  Used for motif extraction - fa_elec scores below this value will cause a motif to be discarded
  Default: -9999.0
  

  -elec_max_threshold <Real>

  Used for motif extraction - fa_elec scores above this value will cause a motif to be discarded
  Default: 9999.0
  

  -duplicate_dist_cutoff <Real>

  Value for determining whether a motif is different from others already in a library
  Default: 1.0
  

  -duplicate_angle_cutoff <Real>

  Value for determining whether a motif is different from others already in a library
  Default: 0.4
  

  -motif_output_directory <String>

  used in dna_motif_collector - path for the directory where all the collected motifs are dumped as 2-residue pdbs
  

  -eliminate_weak_motifs <Boolean>

  used to dna_motif_collector - controls whether only the top 1-2 motifs are counted for every protein position in a protein-DNA interface
  Default: true
  

  -duplicate_motif_cutoff <Real>

  used in dna_motif_collector - RMSD cutoff for an identical base placed via a motif to see if that motif already exists in a motif library
  Default: 0.2
  

  -preminimize_motif_pdbs <Boolean>

  used to dna_motif_collector - controls whether the input PDB structure sidechains and bb are minimized before motifs are collected
  Default: false
  

  -preminimize_motif_pdbs_sconly <Boolean>

  used to dna_motif_collector - controls whether the input PDB structure sidechains are minimized before motifs are collected
  Default: false
  

  -place_adduct_waters <Boolean>

  used to dna_motif_collector - whether or not adduct waters are placed before motifs are collected, there will be no water interaction calculated if this is false
  Default: true
  

  -list_motifs <FileVector>

  File(s) containing list(s) of PDB files to process
  

  -motif_filename <String>

  File containing motifs
  

  -file_prefix <String>

  File containing motifs
  Default: "motif"
  

  -build_residue_file <String>

  File containing the target positions for building and incorporating motifs
  

  -motif_flexible_loop_file <String>

  File containing the flexible loop definition
  

  -residue_trim_file <String>

  File a list of residues to trim to Ala before motif incorporation.
  

  -BPData <String>

  File containing BuildPosition specific motifs and/or rotamers
  

  -list_dnaconformers <FileVector>

  File(s) containing list(s) of PDB files to process
  

  -target_dna_defs <StringVector>

  
  Default: ""
  

  -motif_build_defs <StringVector>

  
  Default: ""
  

  -motif_build_positions <IntegerVector>

  
  

  -r1 <Real>

  RMSD cutoff between motif anchor position and motif target position for allowing a particular motif rotamer to continue on to expand with DNA conformers
  Range: 0-
  Default: 4.5
  

  -r2 <Real>

  RMSD cutoff between motif anchor position and motif target position for accepting the motif
  Range: 0-
  Default: 1.1
  

  -z1 <Real>

  DNA motif specific: cutoff between motif target DNA position and standardized base for allowing a particular motif to continue on to expand with DNA conformers
  Range: 0-
  Default: 0.75
  

  -z2 <Real>

  DNA motif specific: cutoff between motif target DNA position and DNA conformer placed according to motif for accepting the pair of residues
  Range: 0-
  Default: 0.95
  

  -dtest <Real>

  DNA motif specific: cutoff between motif target DNA position and DNA conformer placed according to motif for accepting the pair of residues
  Range: 0-
  Default: 5.5
  

  -rotlevel <Integer>

  level of rotamer sampling for motif search
  Range: 1-
  Default: 5
  

  -num_repacks <Integer>

  number of cycles of dropping special_rot weight and design
  Range: 0-
  Default: 5
  

  -minimize <Boolean>

  whether or not to minimize the motifs toward the xtal structure DNA
  Default: true
  

  -minimize_dna <Boolean>

  whether or not to minimize DNA after every round of design with special_rot weight dropping
  Default: true
  

  -run_motifs <Boolean>

  whether or not to use motifs in DnaPackerMotif
  Default: true
  

  -expand_motifs <Boolean>

  whether or not to use expand (use all types) motifs in DnaPackerMotif
  Default: true
  

  -aromatic_motifs <Boolean>

  whether or not to use expand (use aromatic only types) motifs in DnaPackerMotif
  Default: true
  

  -dump_motifs <Boolean>

  whether or not to output pdbs with the best rotamer/conformer for each motifs
  Default: true
  

  -quick_and_dirty <Boolean>

  quick motif run to get a list of all possible motifs before doing a real run
  Default: true
  

  -special_rotweight <Real>

  starting weight for the weight on motif rotamers
  Default: -40.0
  

  -output_file <String>

  name of output file for all the best motifs and rotamers or for the dna_motif_collector it is the file where all the motifs are dumped
  

  -data_file <String>

  name of output file for any data about how many rotamers and motifs pass what tests, etc
  

  -target_aa <String>

  three letter code for the target amino acid for finding motifs
  Default: "LEU"
  

  -flex_sugar <Boolean>

  whether or not to add the flexible sugar, not using PB way of adding options
  Default: true
  

  -clear_bprots <Boolean>

  whether or not to clear the rotamers that were read in from a previous run and restart with only the motifs that were read in and the specified rotlevel
  Default: true
  

  -rots2add <Integer>

  number of rotamers to add to design from the MotifSearch for each amino acid type
  Range: 1-
  Default: 100
  

  -restrict_to_wt <Boolean>

  restrict the motif search to finding motifs of the same amino acid as the starting pose, for homology modeling
  Default: true
  

  -rerun_motifsearch <Boolean>

  setting the MotifSearch to run again, using the rotamers in the build position, most likely to change stringency or amino acid type on a second run
  Default: true
  

  -no_rotamer_bump <Boolean>

  skip the bump check when making the rotamers that will be tested for motif interactions, makes code much slower, but it is advised to increase the max_rotbump_energy to at least 10.0 instead of the default of 5.0 if bump_check is being used
  Default: false
  

  -ligand_motif_sphere <Real>

  option to specify radius of motif search around ligand
  Default: 6.0
  

• ms

  -ms <Boolean>

  ms option group
  

  -pop_from_ss <Integer>

  generate starting sequence population based on single-state design results
  Default: 0
  

  -pop_size <Integer>

  genetic algorithm population size
  Default: 100
  

  -generations <Integer>

  number of genetic algorithm generations
  Default: 20
  

  -num_packs <Integer>

  number of repack trials per sequence/state combination
  Default: 1
  

  -numresults <Integer>

  number of top-fitness results to save for explicit reference at the end of multistate design
  Default: 1
  

  -anchor_offset <Real>

  energy offset from the energy of single-state design toward the target state – used to generate an affinity anchor for fitness calculations
  Default: 5.0
  

  -Boltz_temp <Real>

  thermodynamic temperature to use for specificity calculations
  Default: 0.6
  

  -mutate_rate <Real>

  rate of mutation per position
  Default: 0.5
  

  -fraction_by_recombination <Real>

  fraction of the population that should be generated by recombination during the evolution stage
  Default: 0.5
  

• ms:checkpoint

  -checkpoint <Boolean>

  checkpoint option group
  

  -prefix <String>

  prefix to add to the beginning of checkpoint file names
  Default: ""
  

  -interval <Integer>

  frequency with which the entity checkpoint is written
  Default: 0
  

  -gz <Boolean>

  compress checkpoing files with gzip
  Default: false
  

  -rename <Boolean>

  rename checkpoint files after genetic algorithm completes
  Default: false
  

• mutate

  -mutate <Boolean>

  mutate option group
  

  -mutation <String>

  Single mutation: Format: One-letter code / residue number / one-letter code. Example: A163F
  

• nonlocal

  -nonlocal <Boolean>

  nonlocal option group
  

  -chunks <File>

  Decsribes how the structure is partitioned into chunks. Each residue must be present in 1 and only 1 chunk. Loop file format.
  

  -randomize_missing <Boolean>

  Randomize the coordinates of missing loops. This occurs often in broken-chain folding from a sequence alignment and template pdb. Default value is false to preserve existing behavior in ThreadingJobInputter
  Default: false
  

• optE

  -optE <Boolean>

  optE option group
  

  -load_from_silent <String>

  load from silent instead of pdb - uses path of requested pdb to find silent file, each PDB needs to have all of its structures in its own folder (ie: 1agy/pdb_set.silent) - only works in optimize_decoy_discrimination
  Default: "pdb_set.silent"
  

  -data_in <String>

  file from which to read in optE data
  Default: "optE.data"
  

  -data_out <String>

  file to which to write optE data
  Default: "optE.data.out"
  

  -weights <String>

  a conventional weightfile that optE will use to determine which weights will be counted. All non-zero weights in the file will contribute to rotamer energies and be fit; use the -optE::fix option to fix any of these weights. Weight values will also be used as starting values for optimization.
  

  -fix <StringVector>

  weights to be fixed (must also appear in the weightfile given by the -optE::weights option)
  

  -free <File>

  IterativeOptEDriver flag: specify a file to read score types that are free – optionally include a starting weight for each score type
  

  -fixed <File>

  IterativeOptEDriver flag: specify a file to read score types and weights for score types that are on but fixed
  

  -parse_tagfile <File>

  a file in utility::tag format that optE may parse to customize its operation
  

  -constant_logic_taskops_file <File>

  a file in utility::tag format that optE uses to build a task that will not change with the context of the pose after design
  

  -optE_soft_rep <Boolean>

  Instruct the IterativeOptEDriver to use the soft-repulsion etable
  

  -no_hb_env_dependence <Boolean>

  Disable environmental dependent weighting of hydrogen bond terms
  

  -no_hb_env_dependence_DNA <Boolean>

  Disable environmental dependent weighting of hydrogen bonds involving DNA
  

  -optE_no_protein_fa_elec <Boolean>

  Instruct the IterativeOptEDriver to use the soft-repulsion etable
  Default: false
  

  -include_intra_res_protein <Boolean>

  Instruct the IterativeOptEDriver to turn on intra-residue interactions (needed for BetaNov15 score function)
  Default: false
  

  -centroid_rot <Boolean>

  Use CENTROID_ROT vdw radii
  Default: false
  

  -centroid_rot_min <Boolean>

  Use CENTROID_ROT_MIN vdw radii
  Default: false
  

  -design_first <Boolean>

  Do not optimize the weights in the context of the native structure, but rather, start by designing the protein with the input weight set. Requires that all score types listed in -optEfree have specificed weights.
  

  -n_design_cycles <Integer>

  The number of outer-loop design cycles to complete; default of 10 after which convergence has usually occurred
  Default: 10
  

  -recover_nat_rot <Boolean>

  With the iterative optE driver, repack to recover the native rotamers
  

  -component_weights <File>

  With the iterative optE driver, weight the individual components according to the input file – default weight of 1 for all components. Weight file consists of component-name/weight pairs on separate lines: e.g. prob_native_structure 100.0
  

  -optimize_nat_aa <Boolean>

  With the iterative optE driver, optimize weights to maximize the probability of the native rotamer
  

  -optimize_nat_rot <Boolean>

  With the iterative optE driver, optimize weights to maximize the probability of the native rotamer in the native context
  

  -optimize_ligand_rot <File>

  With the iterative optE driver, optimize weights to maximize the probability of the native rotamer around the ligand
  

  -optimize_pssm <Boolean>

  With the iterative optE driver, optimize weights to maximize the match between a BLAST generated pssm probabillity distribution
  

  -optimize_dGbinding <File>

  With the iterative optE driver, optimize weights to minimize squared error between the predicted dG of binding and the experimental dG; provide a file listing 1. bound PDB structure, 2. unbound PDB structure, and 3. measured dG
  

  -optimize_ddG_bind_correlation <File>

  With the iterative optE driver, optimize weights to minimize squared error between the predicted ddG of binding for a mutation to the experimental ddG; provide a file listing 1. list file containing wt complexes, 2. list file containing mut complexes, 3. list file containing wt unbounds structures, 4. list file containing mut unbounds structures, and 5. measured ddG of binding
  

  -optimize_ddGmutation <File>

  With the iterative optE driver, optimize weights to minimize the predicted ddG of mutation and the measured ddG; provide a file listing 1. repacked wt pdb list, 2. repacked mut pdb list, and 3. measured ddG triples
  

  -optimize_ddGmutation_straight_mean <Boolean>

  With the iterative optE driver, predict the the ddGmut to be the difference between the straight mean (1/n Sum(E_i)) of the WT and MUT structures provided. Requires the -optimize_ddGmutation flag be set.
  

  -optimize_ddGmutation_boltzman_average <Boolean>

  With the iterative optE driver, predict the the ddGmut to be the difference between the boltzman average energies ( Sum( E_i * e**-E_i/kT)/Sum( e**-E_i/kT) ) of the WT and MUT structures provided. Requires the -optimize_ddGmutation flag be set.
  

  -exclude_badrep_ddGs <Real>

  With the iterative optE driver, consider only ddG data where the unweighted repulsive energy delta mut-wt < given value
  

  -pretend_no_ddG_repulsion <Boolean>

  With the iterative optE driver, set all repulsive scores to zero when looking for ddG correlations
  

  -optimize_decoy_discrimination <File>

  With the iterative optE driver, optimize weights to maximize the partition between relaxed natives and low-scoring decoys. File is a list of file-list pairs and a single pdb file < native_pdb_list, decoy_pdb_list, crystal_native_pdb >.
  

  -normalize_decoy_score_spread <String>

  In decoy discrimination optimization, normalize both the native and decoy energies generated by a set of weights by sigma_curr /sigma_start where sigma_start is computed as the standard deviation of the decoy energies given an input weight set
  

  -ramp_nativeness <Boolean>

  In decoy discrimination optimization, give structures in the range between max_rms_from_native and min_decoy_rms_to_native a nativeness score (which ramps linearly from 1 to 0 in that range) and include scores from structures in the numerator of the partition.
  

  -n_top_natives_to_optimize <Integer>

  For use with the -optimize_decoy_discrimination flag. Objective function considers top N natives in partition function
  Default: 1
  

  -approximate_decoy_entropy <Real>

  Alpha expansion of conformation space size as a function of nres: size ~ alpha ^ nres; entropy ~ nres ln alpha.
  

  -repack_and_minimize_decoys <Boolean>

  Generate new structures in each round of iterative optE by repacking and minimizing the input decoys & natives using the weights obtained in the last round
  

  -repack_and_minimize_input_structures <Boolean>

  Minimizing the input decoys & natives using the starting weights – allows structures a chance to see the energy function before decoy discrimination begins without the memory overhead of the repack_and_minimize_decoys flag
  

  -output_top_n_new_decoys <Integer>

  For use with repack_and_minimize_decoys flag: Write out the top N decoys generated each round in this iterative refinement
  Default: 0
  

  -optimize_ligand_discrimination <File>

  With the iterative optE driver, optimize weights to maximize the partition between relaxed natives and low-scoring decoys. File is a list of file-list pairs and a single pdb file < native_pdb_list, decoy_pdb_list, crystal_native_pdb >.
  

  -no_design <Boolean>

  Don't bother loading pdbs and doing design; just optimize weights for decoy-discrim and or native rotamer recovery
  

  -sqrt_pssm <Boolean>

  Turn the pssm probability vectors into unit vectors so that dot product is a true similarity measure
  

  -min_decoy_rms_to_native <Real>

  For use with the optimize_decoy_discrimination flag: exclude decoys that are within a certain RMS of the native structure
  

  -max_rms_from_native <Real>

  For use with the optimize_decoy_discrimination flag: exclude natives that are more than a certain RMS of the crystal structure. max_rms_from_native of 1.5, min_decoy_rms_from_native 2.0 would throw out structures in the range of 1.5 and 2.0 RMS from consideration
  

  -optimize_starting_free_weights <Boolean>

  With the iterative optE driver, try many different starting points for the minimization
  Default: false
  

  -wrap_dof_optimization <File>

  Create new dofs and setup arithmetic dependencies for free dofs.
  

  -randomly_perturb_starting_free_weights <Real>

  With the iterative optE driver, perturb the weights by +/- <input value>=""> for those weights listed as free
  

  -inv_kT_natrot <Real>

  1 / kT for the pNativeRotamer fitness function
  Default: 1
  

  -inv_kT_nataa <Real>

  1 / kT for the pNatAA and PSSM fitness function
  Default: 1
  

  -inv_kT_natstruct <Real>

  1 / kT for the pNativeStructure fitness function
  Default: 1
  

  -mpi_weight_minimization <Boolean>

  Distribute OptEMultifunc func/dfunc evaluations across nodes
  

  -dont_use_reference_energies <Boolean>

  Do not use reference energies anywhere during the protocol.
  Default: false
  

  -number_of_swarm_particles <Integer>

  The number of particles to use during particle swarm weight optimization.
  Default: 100
  

  -number_of_swarm_cycles <Integer>

  The number of cycles to run the swarm minimizer for.
  Default: 20
  

  -constrain_weights <File>

  When minimizing the fitness objective function, also include weight constraints in the objective function
  

  -fit_reference_energies_to_aa_profile_recovery <Boolean>

  In the inner-loop sequence recovery/weight tweaking stage, accept/reject weight sets based on both the sequence recovery rate, and the mutual information between the expected and observed amino acid frequency distributions
  

  -starting_refEs <File>

  IterativeOptEDriver flag: specify a weights file to read reference energies from; do not optimize reference energies in the first round of weight fitting
  

  -repeat_swarm_optimization_until_fitness_improves <Boolean>

  After the first time though the particle swarm optimization phase, if the end fitness is not better than the start fitness, recreate the swarm around the start dofs and repeat the swarm optimization.
  Default: false
  

  -design_with_minpack <Boolean>

  Use the min-packer to design during the sequence recovery stages.
  Default: false
  

  -design_with_offrotpack <Boolean>

  Use the off-rotamer-packer to design during the sequence recovery stages.
  Default: false
  

  -limit_bad_scores <Boolean>

  Quit after 100,000 inf or NaN errors in optE objective function
  

  -no_design_pdb_output <Boolean>

  Do not write out the designed pdbs to the workdir_ directories over the course of the optE run
  

• optE:rescore

  -rescore <Boolean>

  rescore option group
  

  -weights <File>

  Weight set to use when rescoring optE partition functions
  

  -context_round <Integer>

  Integer of the context PDBs generated during design to use to measure the pNatAA
  

  -outlog <File>

  File to which the OptEPosition data should be written
  

  -measure_sequence_recovery <Boolean>

  When rescoring a weight set, run design with that weight set and measure the sequence recovery.
  Default: false
  

• packstat

  -packstat <Boolean>

  packstat option group
  

  -include_water <Boolean>

  Revert to old style etables
  Default: false
  

  -oversample <Integer>

  Precision of SASA measurements
  Default: 0
  

  -packstat_pdb <Boolean>

  Output a pdb with packing visualizations
  Default: false
  

  -surface_accessibility <Boolean>

  Compute extra cavity burial information
  Default: false
  

  -residue_scores <Boolean>

  Output the score for each resdiue
  Default: false
  

  -cavity_burial_probe_radius <Real>

  Radius probe to consider a cavity buried
  Default: 1.4
  

  -raw_stats <Boolean>

  Output the raw stats per-residue (for training, etc...)
  Default: false
  

  -threads <Integer>

  Number of threads to use (0 for no threading)
  Default: 0
  

  -cluster_min_volume <Real>

  voids smaller than this will not be shown.
  Default: 30
  

  -min_surface_accessibility <Real>

  voids must be at least this exposed
  Default: -1.0
  

  -min_cluster_overlap <Real>

  void-balls must overlap by this much to be clustered
  Default: 0.1
  

  -min_cav_ball_radius <Real>

  radius of smallest void-ball to consider
  Default: 0.7
  

• patterson

  -patterson <Boolean>

  patterson option group
  

  -weight <Real>

  wt of patterson correlation
  Default: 0.0
  

  -sc_scaling <Real>

  Scale sidechain density by this amount (default = same as mainchain density)
  Default: 1.0
  

  -radius_cutoffs <RealVector>

  patterson-space radius cuttoffs
  

  -resolution_cutoffs <RealVector>

  reciprocal space F^2 cuttoffs
  

  -Bsol <Real>

  solvent B
  Default: 300.0
  

  -Fsol <Real>

  solvent fraction
  Default: 0.95
  

  -model_B <Real>

  B factor computing patterson CC
  Default: 0.0
  

  -rmsd <Real>

  Expected RMS error for sigma-A calculation
  Default: 2.0
  

  -no_ecalc <Boolean>

  Do not normalize p_o with ecalc
  Default: false
  

  -nshells <Integer>

  Number of resolution shells for patterson normalization
  Default: 50
  

  -use_spline_interpolation <Boolean>

  use spline interpolation for derivative evaluation? (default trilinear)
  Default: false
  

  -use_on_repack <Boolean>

  SLOW - use patterson correlation on repacks (default no)
  Default: false
  

  -dont_use_symm_in_pcalc <Boolean>

  perform Pcalc in P1 (default no)
  Default: false
  

• pb_potential

  -pb_potential <Boolean>

  pb_potential option group
  

  -charged_chains <IntegerVector>

  Chain numbers that carries charge in the PB calculation
  Default: 1
  

  -sidechain_only <Boolean>

  Only calculate interactions to sidechain.
  Default: true
  

  -revamp_near_chain <IntegerVector>

  Scale down PB interactions if near the given chain. Use chain numbers as input.
  

  -apbs_path <String>

  Path to the APBS (Adaptive Poisson-Boltzmann Solver) executable
  

  -potential_cap <Real>

  Cap for PB potential input
  Default: 20.0
  

  -tolerance <Real>

  Tolerance in A. When a charged atom moves byond this tolerance, the PDE is resolved.
  Default: 1.0
  

  -apbs_debug <Integer>

  APBS debug level [0-6]
  Default: 2
  

  -calcenergy <Boolean>

  Calculate energy?
  Default: false
  

• PCS

  -PCS <Boolean>

  PCS option group
  

  -write_extra <File>

  Write into the File PCS calc, PCS exp, PCS dev, tensor informations, AT EACH ENERGY EVALUATION. More suited for rescoring
  

  -normalization_id <Integer>

  Normalize individual data set. The integer identify the normalization method to be used
  

• PCSTS1

  -PCSTS1 <Boolean>

  PCSTS1 option group
  

  -write_extra <File>

  Write into the File PCS calc, PCS exp, PCS dev, tensor imformation, AT EACH ENERGY EVALUATION. More suited for rescoring
  

  -normalization_id <Integer>

  Normalize individual data set. The integer identify the normalization method to be used
  

• PCSTS2

  -PCSTS2 <Boolean>

  PCSTS2 option group
  

  -write_extra <File>

  Write into the File PCS calc, PCS exp, PCS dev, tensor imformation, AT EACH ENERGY EVALUATION. More suited for rescoring
  

  -normalization_id <Integer>

  Normalize individual data set. The integer identify the normalization method to be used
  

• PCSTS3

  -PCSTS3 <Boolean>

  PCSTS3 option group
  

  -write_extra <File>

  Write into the File PCS calc, PCS exp, PCS dev, tensor imformation, AT EACH ENERGY EVALUATION. More suited for rescoring
  

  -normalization_id <Integer>

  Normalize individual data set. The integer identify the normalization method to be used
  

• PCSTS4

  -PCSTS4 <Boolean>

  PCSTS4 option group
  

  -write_extra <File>

  Write into the File PCS calc, PCS exp, PCS dev, tensor imformation, AT EACH ENERGY EVALUATION. More suited for rescoring
  

  -normalization_id <Integer>

  Normalize individual data set. The integer identify the normalization method to be used
  

• pepspec

  -pepspec <Boolean>

  pepspec option group
  

  -soft_wts <String>

  No description
  Default: "soft_rep.wts"
  

  -cen_wts <String>

  No description
  Default: "cen_ghost.wts"
  

  -binding_score <Boolean>

  No description
  Default: true
  

  -no_cen <Boolean>

  No description
  Default: true
  

  -no_cen_rottrials <Boolean>

  No description
  Default: true
  

  -run_sequential <Boolean>

  No description
  Default: false
  

  -pep_anchor <Integer>

  No description
  

  -pep_chain <String>

  No description
  Default: " "
  

  -n_peptides <Integer>

  No description
  Default: 8
  

  -n_build_loop <Integer>

  No description
  Default: 1000
  

  -n_cgrelax_loop <Integer>

  No description
  Default: 1
  

  -n_dock_loop <Integer>

  No description
  Default: 4
  

  -interface_cutoff <Real>

  No description
  Default: 5.0
  

  -use_input_bb <Boolean>

  No description
  Default: false
  

  -remove_input_bb <Boolean>

  No description
  Default: false
  

  -homol_csts <String>

  No description
  Default: "prep.csts"
  

  -p_homol_csts <Real>

  No description
  Default: 1.0
  

  -gen_pep_bb_sequential <Boolean>

  No description
  Default: false
  

  -input_seq <String>

  No description
  

  -ss_type <String>

  No description
  

  -upweight_interface <Boolean>

  No description
  Default: false
  

  -calc_sasa <Boolean>

  No description
  Default: false
  

  -diversify_pep_seqs <Boolean>

  No description
  Default: true
  

  -diversify_lvl <Integer>

  No description
  Default: 10
  

  -dump_cg_bb <Boolean>

  No description
  Default: false
  

  -save_low_pdbs <Boolean>

  No description
  Default: true
  

  -save_all_pdbs <Boolean>

  No description
  Default: false
  

  -no_design <Boolean>

  No description
  Default: false
  

  -pdb_list <String>

  No description
  

  -ref_pdb_list <String>

  No description
  

  -add_buffer_res <Boolean>

  No description
  Default: false
  

  -cg_res_type <String>

  No description
  Default: "ALA"
  

  -native_pep_anchor <Integer>

  No description
  

  -native_pep_chain <String>

  No description
  Default: ""
  

  -native_align <Boolean>

  No description
  Default: false
  

  -rmsd_analysis <Boolean>

  No description
  Default: false
  

  -anchor_type <String>

  No description
  Default: "ALA"
  

  -no_prepack_prot <Boolean>

  No description
  Default: false
  

  -prep_use_ref_rotamers <Boolean>

  No description
  Default: false
  

  -n_prepend <Integer>

  No description
  Default: 0
  

  -n_append <Integer>

  No description
  Default: 0
  

  -clash_cutoff <Real>

  No description
  Default: 5
  

  -n_anchor_dock_std_devs <Real>

  No description
  Default: 1.0
  

  -prep_trans_std_dev <Real>

  No description
  Default: 0.5
  

  -prep_rot_std_dev <Real>

  No description
  Default: 10.0
  

  -seq_align <Boolean>

  No description
  Default: false
  

  -prep_align_prot_to <String>

  No description
  

• pH

  -pH <Boolean>

  pH option group
  

  -pH_mode <Boolean>

  Allow protonated/deprotonated versions of the residues based on pH
  Default: false
  

  -keep_input_protonation_state <Boolean>

  Read in residue protonation states from input pdb?
  Default: false
  

  -value_pH <Real>

  pH value input for the pHEnergy score
  Default: 7.0
  

• pH:calc_pka

  -calc_pka <Boolean>

  calc_pka option group
  

  -pka_all <Boolean>

  Calculate pKa values for all protonatable protein residues in the PDB?
  Default: false
  

  -pka_for_resnos <RealVector>

  Residue no whose pKa value is to be determined
  Default: 0
  

  -pka_for_chainno <String>

  Chain no of the residue whose pKa is to be determined
  Default: "A"
  

  -pH_neighbor_pack <Boolean>

  Pack the neighbors while calculating pKa?
  Default: false
  

  -pka_rad <Real>

  Radius of repack
  Default: 5.0
  

  -pH_prepack <Boolean>

  Prepack structure before calculating pKa values?
  Default: false
  

  -pH_relax <Boolean>

  Relax structure before calculating pKa values?
  Default: false
  

  -rotamer_prot_stats <Boolean>

  Get rotamer protonation statistics when titrating?
  Default: false
  

• pH

  -pH_unbound <FileVector>

  Name(s) of unbound receptor and ligand PDB file(s)
  

  -output_raw_scores <Boolean>

  Return raw scores contributing to interface score?
  

  -pre_process <Boolean>

  Refine rigid body orientation?
  

  -cognate_partners <String>

  Chain IDs for the cognate complex
  Default: "_"
  

  -cognate_pdb <File>

  File containing the cognate Antigen-Antibody complex
  

• pocket_grid

  -pocket_grid <Boolean>

  pocket_grid option group
  

  -pocket_grid_size <Real>

  grid spacing in Angstroms
  Default: 0
  

  -pocket_grid_size_x <Real>

  grid spacing in Angstroms
  Default: 10
  

  -pocket_grid_size_y <Real>

  grid spacing in Angstroms
  Default: 10
  

  -pocket_grid_size_z <Real>

  grid spacing in Angstroms
  Default: 10
  

  -pocket_grid_spacing <Real>

  grid spacing in Angstroms
  Default: 0.5
  

  -pocket_max_spacing <Real>

  Maximum residue-residue distance to be considered a pocket
  Default: 8
  

  -pocket_min_size <Real>

  Minimum pocket size to score, in cubic Angstroms
  Default: 10
  

  -pocket_max_size <Real>

  Maximum pocket size to report, in cubic Angstroms, 0 for no limit
  Default: 0
  

  -pocket_probe_radius <Real>

  radius of surface probe molecule
  Default: 1.0
  

  -central_relax_pdb_num <String>

  Residue number:(optional)Chain around which to do Pocket Constraint
  Default: "-1"
  

  -pocket_ntrials <Integer>

  Number of trials to use for backrub
  Default: 100000
  

  -pocket_num_angles <Integer>

  Number of different pose angles to measure pocket score at
  Default: 1
  

  -pocket_side <Boolean>

  Include only side chain residues for target surface
  Default: false
  

  -pocket_dump_pdbs <Boolean>

  Generate PDB files
  Default: false
  

  -pocket_dump_exemplars <Boolean>

  Generate exemplar PDB files
  Default: false
  

  -pocket_filter_by_exemplar <Boolean>

  Restrict the pocket to the exemplars
  Default: false
  

  -pocket_limit_exemplar_color <Boolean>

  Include surface donors/acceptors only when they are within range of the main pocket
  Default: true
  

  -pocket_limit_small_exemplars <Boolean>

  Require exemplar to have at least 5 hydrophobic elements to output to exemplar file
  Default: true
  

  -pocket_dump_rama <Boolean>

  Generate Ramachandran maps for each pocket cluster
  Default: false
  

  -pocket_restrict_size <Boolean>

  Pockets that are too large return score of 0
  Default: false
  

  -pocket_ignore_buried <Boolean>

  Ignore pockets that are not solvent exposed
  Default: true
  

  -pocket_only_buried <Boolean>

  Identify only pockets buried in the protein core (automatically sets -pocket_ignored_buried false)
  Default: false
  

  -pocket_psp <Boolean>

  Mark Pocket-Solvent-Pocket events as well
  Default: true
  

  -pocket_sps <Boolean>

  Unmark Solvent-Pocket-Solvent events
  Default: false
  

  -pocket_search13 <Boolean>

  Search in 13 directions (all faces and edges of a cube) versus faces and diagonal
  Default: false
  

  -pocket_surface_score <Real>

  Score given to pocket surface
  Default: 0
  

  -pocket_surface_dist <Real>

  Distance to consider pocket surface
  Default: 2.5
  

  -pocket_buried_score <Real>

  Score given to deeply buried pocket points
  Default: 5.0
  

  -pocket_buried_dist <Real>

  Distance to consider pocket buried
  Default: 2.0
  

  -pocket_exemplar_vdw_pen <Real>

  Temporary max penalty for vdW class in exemplar discovery
  Default: 300.0
  

  -pocket_debug_output <Boolean>

  Print any and all debuggind output related to pockets
  Default: false
  

  -dump_pocketGrid <Boolean>

  print the pocket grid points into a PDB file
  Default: false
  

  -dump_Grid <Boolean>

  print the grid points into a PDB file
  Default: false
  

  -extend_eggshell <Boolean>

  Extend the eggshell points
  Default: false
  

  -extend_eggshell_dist <Real>

  Distance to extend eggshell
  Default: 1
  

  -extra_eggshell_dist <Real>

  Distance to extend extra eggshell points
  Default: 4
  

  -eggshell_dist <Real>

  Distance to extend eggshell points from ligand atoms
  Default: 4
  

  -reduce_rays <Boolean>

  reduce no. of rays by rounding and removing duplicate xyz coordinates
  Default: true
  

  -pocket_static_grid <Boolean>

  No autoexpanding grid
  Default: false
  

  -dump_espGrid <Boolean>

  print the electrostaticpotential grid into a PDB file
  Default: false
  

  -dump_connollySurface <Boolean>

  print the connolly surface points into a PDB file
  Default: false
  

  -esp_buffer_dist <Real>

  buffer dist added to Vdw radius atom while assigining electrostatic potential values
  Default: 0.5
  

  -round_pocketGrid_center <Boolean>

  round_pocketGrid_center
  Default: true
  

• gen_pharmacophore

  -gen_pharmacophore <Boolean>

  gen_pharmacophore option group
  

  -clash_distance_cutoff <Real>

  clash distance cutoff to include ideal hydrogen bonding atoms
  Default: 1.0
  

  -ring_sasa_cutoff <Integer>

  ring_sasa_cutoff to include in pharmacophore
  Default: 25
  

  -min_num_ring <Integer>

  minimimum number of rings to be in a cluster
  Default: 1
  

  -ring_ring_dist_cutoff <Real>

  ring - ringatom distance to include in the pharmacophore clusters
  Default: 5.0
  

  -ring_atm_dist_cutoff <Real>

  ring - hbond atom distance to include in the pharmacophore clusters
  Default: 5.0
  

• fingerprint

  -fingerprint <Boolean>

  fingerprint option group
  

  -print_eggshell <Boolean>

  print the eggshell points into a PDB file
  Default: false
  

  -atom_radius_scale <Real>

  Scale to shrink the radius of atom
  Default: 0.9
  

  -atom_radius_buffer <Real>

  Value to subtract from all atomic radii, to match PocketGrid buffer thickness
  Default: 1.0
  

  -packing_weight <Real>

  Add weight to rho large deviation
  Default: 1
  

  -dist_cut_off <Real>

  set cut_off distance to add packing weight
  Default: 5
  

  -include_extrashell_to_set_origin <Boolean>

  include extrashell points to set origin
  Default: false
  

  -include_hydrogens <Boolean>

  include hydrogen atoms for fingerprint
  Default: false
  

  -multiple_origin <Boolean>

  set multiple origin points for ray casting
  Default: false
  

  -use_DARC_gpu <Boolean>

  use GPU when computing DARC score
  Default: false
  

  -square_score <Boolean>

  square the terms in DARC scoring function
  Default: false
  

  -darc_components <Boolean>

  get the score for individual components in DARC scoring function
  Default: false
  

  -set_origin <Integer>

  option to set orgin: 0 to choose origin based on R(rugedness) value, 1 for protein_center, 2 for eggshell_bottom, 3 for vector from eggshell_plane closest to protein_center, 4 for vector from eggshell_plane distant to protein_center, 5 for choosing a residue center as origin(use the flag -origin_res_num for choosing the residue number)
  Default: 0
  

  -origin_res_num <String>

  Residue number:(optional)Chain to be used as origin for ray-casting
  Default: "1"
  

  -add_esp <Boolean>

  add electrostatic calculations
  Default: false
  

  -darc_shape_only <Boolean>

  darc with shape only
  Default: false
  

  -darc_elsts_only <Boolean>

  darc with electrostatics only
  Default: false
  

  -esp_weight <Real>

  add weight for electrostatic energy
  Default: 0.117
  

  -esp_protein_wt <Real>

  add weight for electrostatic energy inside protein
  Default: 0
  

  -esp_surface_wt <Real>

  add weight for electrostatic energy on protein surface
  Default: 0
  

  -delphi_grid <Boolean>

  input electrostatic potential grid if from DELPHI, default is ZAP grid
  Default: false
  

  -cap_e_potential <Real>

  max/min value to cap electrostatic potential
  Default: 10.0
  

  -return_zero_darc_score <Boolean>

  return 0 as darc score
  Default: false
  

  -set_surface_esp_to_zero <Boolean>

  set surface electrostatic potential to zero
  Default: false
  

  -set_protein_esp_to_zero <Boolean>

  set protein electrostatic potential to zero
  Default: false
  

  -inp_lig <String>

  inp_lig
  Default: "inp_lig.pdb"
  

  -ref_lig <String>

  ref_lig
  Default: "ref_lig.pdb"
  

• ProQ

  -ProQ <Boolean>

  ProQ option group
  

  -svmmodel <Integer>

  SVM model to use (in cross-validation, default is to use all [1-5])
  Default: 1
  

  -basename <String>

  basename location for sequence specific inputfile)
  Default: ""
  

  -membrane <Boolean>

  use membrane version (ProQM)
  Default: false
  

  -prof_bug <Boolean>

  reproduce the profile bug in ProQres
  Default: false
  

  -output_feature_vector <Boolean>

  outputs the feature vector
  Default: false
  

  -output_local_prediction <Boolean>

  outputs the local predicted values
  Default: false
  

  -prefix <String>

  prefix for outputfiles)
  Default: ""
  

  -use_gzip <Boolean>

  gzip output files
  Default: false
  

  -normalize <Real>

  Normalizing factor (usually target sequence length)
  Default: 1.0
  

• qsar

  -qsar <Boolean>

  qsar option group
  

  -weights <String>

  select qsar weight set to use
  Default: "talaris2013"
  

  -grid_dir <String>

  Directory to store grids in
  

  -max_grid_cache_size <Integer>

  delete old grids if grid cache exceeds specified size
  

• rbe

  -rbe <Boolean>

  rbe option group
  

  -server_url <String>

  serverurl for rosetta backend
  

  -server_port <String>

  port for rosetta backend
  Default: "80"
  

  -poll_frequency <Real>

  No description
  Default: 1.0
  

• RBSegmentRelax

  -RBSegmentRelax <Boolean>

  RBSegmentRelax option group
  

  -input_pdb <File>

  input pdb file
  Default: "--"
  

  -rb_file <File>

  input rb segment file
  Default: "--"
  

  -nrbmoves <Integer>

  number of rigid-body moves
  Default: 100
  

  -nrboutercycles <Integer>

  number of rigid-body moves
  Default: 5
  

  -rb_scorefxn <String>

  number of rigid-body moves
  Default: "score5"
  

  -skip_fragment_moves <Boolean>

  omit fragment insertions (in SS elements)
  Default: false
  

  -skip_seqshift_moves <Boolean>

  omit sequence shifting moves
  Default: false
  

  -skip_rb_moves <Boolean>

  omit rigid-body moves
  Default: false
  

  -helical_movement_params <RealVector>

  helical-axis-rotation, helical-axis-translation, off-axis-rotation, off-axis-translation
  Default: utility::vector1<float>(4,0.0)
  

  -strand_movement_params <RealVector>

  strand-in-plane-rotation, strand-in-plane-translation, out-of-plane-rotation, out-of-plane-translationn
  Default: utility::vector1<float>(4,0.0)
  

  -default_movement_params <RealVector>

  default-rotation, default-translation
  Default: utility::vector1<float>(2,0.0)
  

  -cst_seqwidth <Integer>

  sequence width on constraints
  Default: 0
  

• hydrate

  -hydrate <Boolean>

  hydrate option group
  

  -hyfile <File>

  This file defines which residues to hydrate; add waters de novo around their polar atoms.
  

  -hydrate_all <Boolean>

  Add de novo water molecules to the entire structure, not compatible with design.
  Default: false
  

  -ignore_fa_sol_at_positions <IntegerVector>

  Set all implicit solvation contributions to zero when involving the position numbers in the given IntegerVector.
  Default: []
  

  -attempt_all_polar <Boolean>

  Attempt to hydrate all polar atoms regardless of them having room or not.
  Default: false
  

  -partial_hydrate_dew <Real>

  During the first round of packing when using double edge water (dew) molecules, only this fraction of de novo waters will be considered.
  Default: 0.75
  

  -water_energy_threshold <Real>

  Water molecules with energy above this threshold will be removed after packing.
  Default: 5.0
  

  -water_rotamers_cap <Integer>

  Limits the maximum number of water rotamers.
  Default: 500
  

  -water_packing_radius <Real>

  Defines the radius a water molecule is allowed to explore during packing
  Default: 1.0
  

  -water_angular_resolution <Real>

  Defines the angular resolution for water rotamers. As a corollary, it also defines the number of rotamers for each water molecule ((2*space_res+1)^3 * 2 * 2*ang_res^2).
  Default: 3
  

  -water_space_resolution <Real>

  Defines the spacial resolution for water rotamers. As a corollary, it also defines the number of rotamers for each water molecule ((2*space_res+1)^3 * 2 * 2*ang_res^2).
  Default: 2
  

  -hbond_threshold <Real>

  Hydrogen bond threshold. New water rotamers must make hbond of at least this value.
  Default: -0.1
  

  -hbond_entropy_threshold <Real>

  Threshold for water hbonds to contribute to entropy.
  Default: -0.5
  

  -water_desolvation <Real>

  Desolvation energy of a water molecule. Energy difference between a molecule in bulk water and near a protein. This value will be scaled by the scoring function weight for wat_desolv
  Default: 4.8
  

  -pack_nloop <Integer>

  How many times to repack
  Default: 25
  

  -pre_bump_check <Boolean>

  Do bump check before store them in memory
  Default: true
  

  -bias_design_search_to_native <Boolean>

  It gives an artificially large negative energy to any native rotamer during packing. It was implemented to test the use of design waters.
  Default: false
  

  -show_derivatives_check <Boolean>

  Show derivatives check when minimizing in the hydrate protocol.
  Default: false
  

  -keep_non_buried_waters <Boolean>

  Keep non buried waters in the final structure (not recommended).
  Default: false
  

  -display_water_hb_network <Boolean>

  Shows the water hydrogen bonds connections.
  Default: true
  

  -show_pre_post_filter_water_rotamers <Boolean>

  Shows the exigen location of the post and pre filtered water rotamers.
  Default: false
  

  -show_pre_filtered_water_rotamers_count <Boolean>

  Shows the total number of pre-filtered water rotamers; Helps assessing the memory requirements.
  Default: false
  

  -show_residues_near_water <Boolean>

  Print out the residues that are near hydratable water after water packing and placement.
  Default: false
  

  -only_remove_non_buried_waters <Boolean>

  Remove non-buried waters from input, then exit.
  Default: false
  

  -just_score <Boolean>

  Just score the input structures with the hybrid solvation protocol.
  Default: false
  

  -show_rotamer_count <Boolean>

  Output the rotamer counts for each water and amino acid, then exit.
  Default: false
  

  -protein_flexibility <String>

  Defines the protein flexibility during the run
  Default: "not"
  

  -near_water_threshold <Real>

  Threshold for res to be considered flexible when using the near_water option in -hydrate:protein_flexibility
  Default: 4.0
  

  -minimize_bb_where_packing <Boolean>

  Allow backbone to move when minimizing.
  Default: false
  

  -dont_hydrate_hb_engaged_bb_O <Boolean>

  Avoid hydrating hydrogen bond engaged backbone oxygens, even if it is just one hb. The purpose is to avoid disrupting atable structures (helices and sheets).
  Default: true
  

  -short_residence_time_mode <Boolean>

  A faster mode to capture short residence time water molecules. Not good for energy predictions, and the results are better analyzed as an ensamble rather than a single structure.
  Default: false
  

  -min_backbone_file <File>

  This file defines whether the backbone is allowed to move for a specific residue.
  

  -single_away_rotamer <Boolean>

  Use single away water rotamer. The sampling gets biased towards keeping more water present.
  Default: false
  

  -force_enforce_all_waters <Boolean>

  Keep water molecules enforced throughout hybrid solvation protocol.
  Default: false
  

• rdc

  -rdc <Boolean>

  rdc option group
  

  -correct_NH_length <Boolean>

  fix N-H bond-vector to 1.04 as measured in ottiger&bax 98
  Default: true
  

  -reduced_couplings <Boolean>

  gives more equal weights to different bond-vectors
  Default: false
  

  -weights <File>

  specify weights for individual residues ( works for all couplings at this reside)
  

  -iterate_weights <Real>

  do a wRDC computation, i.e., iterate tensor calculation until weights are ~exp ( -dev2/sigma )
  Default: 1
  

  -segment_file <File>

  Definition of rigid segments for alignment tensor optimization
  

  -segment_scoring_mode <String>

  Type of treatment of alignment tensor-based scoring : pairwise or fixed_axis_z (e.g. for homo-dimers)
  

  -total_weight <Real>

  Weight for RDC scores of individual al. tensors
  Default: 1.0
  

  -tensor_weight <Real>

  Weight for pairwise scoring of al. tensors
  Default: 1.0
  

  -print_rdc_values <File>

  print computed vs experimental RDC values
  

  -iterate_tol <Real>

  tolerance for tensor iterations
  Default: 0.01
  

  -iterate_reset <Boolean>

  reset weights to 1.0 when optimizing for new structure
  Default: false
  

  -dump_weight_trajectory <File>

  if yes, write weights to file for each scoring event
  

  -fix_normAzz <RealVector>

  divide by this axial tensor component
  

  -fit_method <String>

  No description
  Default: "nls"
  

  -fixDa <RealVector>

  No description
  

  -fixR <RealVector>

  No description
  

  -nlsrepeat <Integer>

  No description
  Default: 5
  

• relax

  -relax <Boolean>

  relax option group
  

  -fast <Boolean>

  Do a preset, small cycle number FastRelax
  

  -thorough <Boolean>

  Do a preset, large cycle number FastRelax
  

  -centroid_mode <Boolean>

  Use centroid relax protocol
  Default: false
  

  -default_repeats <Integer>

  Default number of repeats done by FastRelax. Has no effect if a custom script is used!
  Default: 5
  

  -dualspace <Boolean>

  Do 3 FastRelax cycles of internal coordinate relax followed by two cycles of Cartesian relax - cart_bonded energy term is required, pro_close energy term should be turned off, and use of -relax::minimize_bond_angles is recommended. Use of the -nonideal flag switches all these and sets up correct min cycles, minimizer type, etc.
  

  -cyclic_peptide <Boolean>

  Set up N-to-C constraints in a cyclic peptide
  

• relax:range

  -range <Boolean>

  range option group
  

  -set_tm_helical <Boolean>

  Set helical secondary structure in TM region
  Default: false
  

  -kT <Real>

  Advanced option: kT
  Default: 1.0
  

  -angle_max <Real>

  Maximum dihedral angle deviation for Small and ShearMover inside RangeRelax
  Default: 0.1
  

  -nmoves <String>

  Number of Small and Shear moves inside RangeRelax, can be 'nres' for all residues or an integer
  Default: "nres"
  

  -spherical_wave <Boolean>

  Relax in a spherical wave pattern starting at the center residue outwards.
  Default: false
  

  -repack_again <Boolean>

  Do an additional round of repacking all residues after the RangeRelax
  Default: false
  

  -cycles <Integer>

  Maximum number of cycles for repacking and minimization. Default 3
  Default: 3
  

  -min_cycles <Integer>

  Maximum number of cycles within the Minimizer. Default 2000
  Default: 2000
  

  -idealize <Boolean>

  Idealize decoy after run. Default: true
  Default: true
  

  -skip_relax <Boolean>

  Skip relax step. Default: false
  Default: false
  

• relax

  -ramady <Boolean>

  Run ramady code which aleviates stuck bad ramachandran energies
  Default: false
  

  -ramady_rms_limit <Real>

  (ramady-only) Reject rama changes which perturb structure by more than this
  Default: 0.5
  

  -ramady_cutoff <Real>

  (ramady-only) Cutoff at which a rama is considered bad
  Default: 2.0
  

  -ramady_max_rebuild <Integer>

  (ramady-only) The maximum number of bad ramas to fix per repack-min cycle
  Default: 1
  

  -ramady_force <Boolean>

  (ramady-only) Force rebuilding of bad ramas (normal skip-rate = 10%)
  Default: false
  

  -script <File>

  Relax script file
  Default: ""
  

  -script_max_accept <Integer>

  Limit number of best accepts
  Default: 10000000
  

  -superimpose_to_native <Boolean>

  Superimpose input structure to native
  Default: false
  

  -superimpose_to_file <File>

  Superimpose input structure to file
  Default: "false"
  

  -constrain_relax_to_native_coords <Boolean>

  For relax and fastrelax, tether backbone coordinates of the pdbs being relaxed to the coordinates in the xtal native
  Default: false
  

  -constrain_relax_to_start_coords <Boolean>

  For relax and fastrelax, tether backbone coordinates of the pdbs being relaxed to the coordinates in the xtal native
  Default: false
  

  -coord_constrain_sidechains <Boolean>

  For relax and fastrelax, also tether sidechain heavy atom coordinates (requires either -constrain_relax_to_native_coords or -constrain_relax_to_start_coords)
  Default: false
  

  -sc_cst_maxdist <Real>

  Use distance constraints between pairs of input side-chains atoms which are closer than the given upper distance cutoff (0 => no sc-sc restraints)
  Default: 0.0
  

  -limit_aroma_chi2 <Boolean>

  limit chi2 rotamer of PHE,TYR, and HIS around 90
  Default: false
  

  -respect_resfile <Boolean>

  Tell FastRelax to respect the input resfile. Used mainly for doing design within FastRelax.
  Default: false
  

  -use_explicit_water <Boolean>

  Consider explicit waters (part of the hybrid solvation protocol) during relax
  Default: false
  

  -bb_move <Boolean>

  allow backbone to move during relax
  Default: true
  

  -chi_move <Boolean>

  allow sidechain to move during relax
  Default: true
  

  -jump_move <Boolean>

  allow jump to move during relax
  Default: false
  

  -dna_move <Boolean>

  allow dna to move during relax + allow DNA-DNA interactions. Best if used with orbitals scorefunction. DNA stays together with great molprobity results. Not recommended for general use at this time.
  Default: false
  

  -fix_omega <Boolean>

  Fix omega angles during relax
  Default: false
  

  -minimize_bond_lengths <Boolean>

  Free bond length DOFs during relax for all atoms
  Default: false
  

  -minimize_bond_angles <Boolean>

  Free bond angle DOFs during relax for all atoms
  Default: false
  

  -minimize_bondlength_subset <Integer>

  Minimize only a subset of bondlengths 0 Default all bondlengths 1 backbone only 2 sidechain only 3 CA only (Ca-C,Ca-N and Ca-Cb)
  Default: 0
  

  -minimize_bondangle_subset <Integer>

  Minimize only a subset of bondlengths 0 Default all bondangles 1 backbone only 2 sidechain only 3 tau only 4 Ca-Cb only
  Default: 0
  

  -min_type <String>

  minimizer to use during relax.
  Default: "lbfgs_armijo_nonmonotone"
  

  -cartesian <Boolean>

  Use Cartesian minimizer
  Default: false
  

  -chainbreak_weight <Real>

  chainbreak weight
  Default: 0.0
  

  -linear_chainbreak_weight <Real>

  linear chainbreak weight
  Default: 0.0
  

  -overlap_chainbreak_weight <Real>

  overlap chainbreak weight
  Default: 0.0
  

  -classic <Boolean>

  Do very old classic relax ! This is a poor protocol - don't use it !
  

  -sequence_file <File>

  Relax script file
  Default: ""
  

  -quick <Boolean>

  Do a preset, small cycle number FastRelax
  

  -sequence <Boolean>

  Do a preset, small cycle number FastRelax
  

  -minirelax_repeats <Integer>

  
  Default: 2
  

  -minirelax_sdev <Real>

  tether on coordinate constraints for minirelax
  Default: 0.5
  

  -wobblemoves <Boolean>

  Do Wobble moves ?
  Default: false
  

  -constrain_relax_segments <File>

  loop definition file
  Default: ""
  

  -coord_cst_width <Real>

  Width on coordinate constraints from constrain_relax_ options
  Default: 0.0
  

  -coord_cst_stdev <Real>

  Stdev on coordinate constraints from constrain_relax_* options
  Default: 0.5
  

  -ramp_constraints <Boolean>

  Ramp constraints during phase1 of relax from full to zero
  Default: false
  

  -energycut <Real>

  Rottrial energycut (per residue!)
  Default: 0.01
  

  -mini <Boolean>

  perform a relax that is only a minimization and repack.
  Default: false
  

  -stage1_ramp_cycles <Integer>

  Ramp cyclesin stage 1
  Default: 8
  

  -stage1_ramp_inner_cycles <Integer>

  Inner cycles means how many small shear moves + rottrials
  Default: 1
  

  -stage2_repack_period <Integer>

  Full repack after how many cycles in stage 2
  Default: 100
  

  -stage2_cycles <Integer>

  How many stage 2 cycles ? (by default its -1 means Nresidues*4 )
  Default: -1
  

  -min_tolerance <Real>

  Minimizer tolerance
  Default: 0.00025
  

  -stage3_cycles <Integer>

  How many stage 3 cycles ? (by default its -1 means Nresidues )
  Default: -1
  

  -cycle_ratio <Real>

  Post-multiplier for cycle numbers
  Default: 1.0
  

  -filter_stage2_beginning <Real>

  FArelax score filter
  Default: 99999999.00
  

  -filter_stage2_quarter <Real>

  FArelax score filter
  Default: 99999999.00
  

  -filter_stage2_half <Real>

  FArelax score filter
  Default: 99999999.00
  

  -filter_stage2_end <Real>

  FArelax score filter
  Default: 99999999.00
  

• relax:centroid

  -centroid <Boolean>

  centroid option group
  

  -weights <String>

  Weights to use for centroid minimization
  Default: "score4_smooth_cen_relax"
  

  -ramp_vdw <Boolean>

  Ramp up the VDW weight
  Default: true
  

  -ramp_rama <Boolean>

  Ramp up the rama/rama2b weight
  Default: false
  

  -parameters <String>

  Database file for ramp/min parameter
  Default: "sampling/cen_relax/default_relax_parameters.txt"
  

  -do_final_repack <Boolean>

  Repack sidechains in movemap after protocol if given a fullatom structure
  Default: false
  

  -increase_vdw_radii <Boolean>

  Increase BB vdw radii
  Default: false
  

• remodel

  -remodel <Boolean>

  remodel option group
  

  -blueprint <File>

  blueprint file name
  

  -cstfile <File>

  description
  

  -cst_fa_only <Boolean>

  false
  

  -cstfilter <Integer>

  filter cst energy
  Default: 10
  

  -cen_sfxn <String>

  centroid score function to be used for building
  Default: "remodel_cen"
  

  -check_scored_centroid <Boolean>

  dump centroid structures after build
  Default: false
  

  -num_trajectory <Integer>

  Number of remodel trajectories.
  Default: 10
  

  -save_top <Integer>

  the number of final low scoring pdbs to keep.
  Default: 5
  

  -swap_refine_confirm_protocols <Boolean>

  swapping the protocols used refinement and confirmation
  Default: false
  

  -bypass_fragments <Boolean>

  only works on input PDB, so no extensions or deletions are honored in the blueprint. Blueprint (H,L,E,D) becomes allow_move definitionsi.
  

  -use_same_length_fragments <Boolean>

  harvest fragments that matches the length to rebuild
  Default: true
  

  -no_jumps <Boolean>

  will setup simple foldtree and fold through it during centroid build.
  Default: false
  

  -reroot_tree <Integer>

  rerooting the tree for the build.
  Default: 1
  

  -use_blueprint_sequence <Boolean>

  picks fragments based on both secondary structure and the second column (sequence) in blueprint file
  

  -quick_and_dirty <Boolean>

  only do fragment insertion
  

  -checkpoint <Boolean>

  this writes out the best pdbs collected so far after each design step.
  

  -use_pose_relax <Boolean>

  an alternative to the default minimization step, but use constraints in a similar way.
  

  -use_cart_relax <Boolean>

  an alternative to the default minimization step, but use constraints in a similar way.
  

  -free_relax <Boolean>

  running pose_relax with no constraints.
  Default: false
  

  -generic_aa <String>

  the type of AA for centroid building
  Default: "V"
  

  -cluster_radius <Real>

  cluster radius for accumulator, default to auto set value
  Default: -1.0
  

  -use_clusters <Boolean>

  use clustering in accumulator
  Default: false
  

  -run_confirmation <Boolean>

  use KIC rms confirmation
  Default: false
  

  -cluster_on_entire_pose <Boolean>

  cluster use all pose, not just loops
  Default: false
  

  -dr_cycles <Integer>

  number of design-refine cycles to use
  Default: 3
  

  -two_chain_tree <Integer>

  label the start of the second chain
  

  -repeat_structure <Integer>

  build identical repeats this many times
  Default: 1
  

  -lh_ex_limit <Integer>

  loophasing neighboring bin expansion limit
  Default: 5
  

  -lh_filter_string <StringVector>

  loophash ABEGO filter target fragment type. list sequentially for each loop
  

  -lh_cbreak_selection <Integer>

  loophash with cbreak dominant weight
  Default: 10
  

  -lh_closure_filter <Boolean>

  filter for close rms when bypass_closure is used
  Default: false
  

  -cen_minimize <Boolean>

  centroid minimization after fragment building
  Default: false
  

  -core_cutoff <Integer>

  number of neighbors required to consider core in auto design
  Default: 18
  

  -boundary_cutoff <Integer>

  number of neighbors required to consider boundary in auto design
  Default: 15
  

  -coreAA <String>

  amino acid set for core
  Default: ""
  

  -boundaryAA <String>

  amino acid set for boundary
  Default: ""
  

  -surfaceAA <String>

  amino acid set for surface
  Default: ""
  

  -design_around_ligand <Boolean>

  apply manual design mode around the ligand
  Default: false
  

  -move_ligand <Boolean>

  apply ligand handler to move ligand
  Default: false
  

  -resclass_by_sasa <Boolean>

  switch to use sasa for residue classification
  Default: false
  

  -helical_rise <Real>

  helical parameter: rise
  Default: 0.0
  

  -helical_radius <Real>

  helical parameter: radius
  Default: 0.0
  

  -helical_omega <Real>

  helical parameter: omega
  Default: 0.0
  

  -filter_rise <RealVector>

  filter value range for helical params rise
  

  -filter_radius <RealVector>

  filter value range for helical params radius
  

  -filter_omega <RealVector>

  filter value range for helical params omega
  

  -COM_sd <Real>

  center of mass coordinate constraint sd value
  Default: 1.0
  

  -COM_tolerance <Real>

  center of mass coordinate constraint tolerance value
  Default: 0.0
  

  -vdw <Real>

  set vdw weight
  Default: 1.0
  

  -rama <Real>

  set rama weight
  Default: 0.1
  

  -cbeta <Real>

  set cbeta weight
  Default: 0.0
  

  -cenpack <Real>

  set cenpack weight
  Default: 0.0
  

  -rg_local <Real>

  set rg_local weight
  Default: 0.0
  

  -hb_lrbb <Real>

  set hbond_lrbb weight
  Default: 0.0
  

  -hb_srbb <Real>

  set hbond_srbb weight
  Default: 0.0
  

  -rg <Real>

  set rg weight
  

  -rsigma <Real>

  set rsigma weight
  Default: 0.0
  

  -ss_pair <Real>

  set sspair weight
  Default: 0.0
  

  -build_disulf <Boolean>

  build disulfides
  Default: false
  

  -match_rt_limit <Real>

  match RT score cutoff
  Default: 0.4
  

  -disulf_landing_range <IntegerVector>

  residue range for disulf landing sites
  

  -rank_by_bsasa <Boolean>

  rank results by bsasa.
  

• remodel:staged_sampling

  -staged_sampling <Boolean>

  sampling first with 9mers then 3mers. Staged energies. For rebuilding entire structure not loop closure
  Default: false
  

  -loop_9mer_score_file <String>

  stage1_score
  

  -loop_3mer_score_file <String>

  stage2_score
  

  -all_9mer_score_file <String>

  stage3_score
  

  -all_3mer_score_file <String>

  stage4_score
  

  -loop_9mer_cycles <Integer>

  stage1_cycles
  

  -loop_3mer_cycles <Integer>

  stage2_cycles
  

  -all_9mer_cycles <Integer>

  stage3_cycles
  

  -all_3mer_cycles <Integer>

  stage4_cycles
  

  -fa_mode <Boolean>

  does the fragment assembly stage in fa
  Default: false
  

  -fa_relax_moves <Boolean>

  Adds a stage of fa relax
  Default: false
  

  -loop_btw_parametric_components <Boolean>

  Sets up a mode where a loop can be inserted into a parametric repeat
  Default: false
  

  -pre_centroid <Boolean>

  initialize fa mode with 200 cycles of centroid
  Default: false
  

  -sample_over_loops <Boolean>

  sample residues defined as loops in the blueprint
  Default: false
  

  -small_moves <Boolean>

  add a stage of small moves
  Default: false
  

  -starting_sequence <String>

  AA sequence to start
  Default: ""
  

  -starting_pdb <File>

  pdb to start
  Default: ""
  

  -starting_non_canonical <String>

  position,non canonical to be added
  Default: ""
  

  -start_w_ideal_helices <Boolean>

  begins with all helices set to -63.8 phi and -41.1 for psi.
  Default: false
  

  -sym_move <Boolean>

  Adds a symmetry move to the abinitio stage
  Default: false
  

  -residues_to_sample <File>

  residues to allow sampling (format:1,3,5)
  Default: ""
  

  -require_frags_match_blueprint <Boolean>

  makes sure the frags match the definition in the blueprint
  Default: true
  

• remodel:domainFusion

  -domainFusion <Boolean>

  domainFusion option group
  

  -insert_segment_from_pdb <File>

  segment pdb file to be inserted [insert pdb file name].
  Default: ""
  

  -insert_segment2_from_pdb <File>

  segment2 pdb file to be inserted [insert pdb file name].
  Default: ""
  

• remodel:design

  -design <Boolean>

  design option group
  

  -no_design <Boolean>

  skips all design steps. WARNING: will only output centroid level structures and dump all fragment tries.
  

  -design_all <Boolean>

  force AUTO design procedure (layered) to perform design on all positions.
  

  -allow_rare_aro_chi <Boolean>

  allow all aromatic rotamers, not issuing AroChi2 filter
  Default: false
  

  -skip_partial <Boolean>

  skip design stage that operate only on burial positions
  Default: false
  

  -design_neighbors <Boolean>

  design neighbors.
  Default: false
  

  -find_neighbors <Boolean>

  find neighbors for design/repack
  Default: false
  

  -include_current <Boolean>

  include current rotamers
  Default: true
  

• remodel:RemodelLoopMover

  -RemodelLoopMover <Boolean>

  RemodelLoopMover option group
  

  -max_linear_chainbreak <Real>

  linear chainbreak is <= this value, loop is considered closed (default 0.07)
  Default: 0.07
  

  -randomize_loops <Boolean>

  randomize loops prior to running main protocol (default true)
  Default: true
  

  -use_loop_hash <Boolean>

  centroid build with loop hash (default false)
  Default: false
  

  -set_segment <File>

  directly set segment phi-psi-omega from file
  Default: ""
  

  -allowed_closure_attempts <Integer>

  the allowed number of overall closure attempts (default 1)
  Default: 1
  

  -loophash_cycles <Integer>

  the number of loophash closure cycles to perform (default 8)
  Default: 8
  

  -simultaneous_cycles <Integer>

  the number of simultaneous closure cycles to perform (default 2)
  Default: 2
  

  -independent_cycles <Integer>

  the number of independent closure cycles to perform (default 8)
  Default: 8
  

  -boost_closure_cycles <Integer>

  the maximum number of possible lockdown closure cycles to perform (default 30)
  Default: 30
  

  -threshold_for_boost_closure <Real>

  numerical chainbreak threshold for entering boost_closure_stage
  Default: 1.0
  

  -force_cutting_index <Integer>

  force a cutpoint shift index of blueprint assignment
  Default: 1
  

  -force_cutting_N <Boolean>

  force a cutpoint at N-term side of blueprint assignment
  Default: false
  

  -bypass_closure <Boolean>

  turning off CCD closure in the mover for tethered docking purpose
  Default: false
  

  -cyclic_peptide <Boolean>

  circularize structure joining N and C-term.
  Default: false
  

  -temperature <Real>

  temperature for monte carlo ( default 2.0)
  Default: 2.0
  

• resample

  -resample <Boolean>

  resample option group
  

  -silent <File>

  a silent file for decoys to restart sampling from
  Default: ""
  

  -tag <String>

  which decoy to select from silent file
  Default: ""
  

  -stage1 <Boolean>

  if true restart after stage1, otherwise after stage2
  Default: false
  

  -stage2 <Boolean>

  if true restart after stage1, otherwise after stage2
  Default: false
  

  -jumps <Boolean>

  if true restart after stage1, otherwise after stage2
  Default: false
  

  -min_max_start_seq_sep <RealVector>

  range of (random) start values for seq-separation
  Default: 0
  

• rescore

  -rescore <Boolean>

  rescore option group
  

  -assign_ss <Boolean>

  Invoke DSSP to assign secondary structure.
  Default: false
  

  -skip <Boolean>

  Dont actually call scoring function (i.e. get evaluators only)
  

  -verbose <Boolean>

  Full break down of weights, raw scores and weighted scores ?
  

• rna

  -rna <Boolean>

  rna option group
  

  -corrected_geo <Boolean>

  Use PHENIX-based RNA sugar close energy and params files
  Default: true
  

  -vary_geometry <Boolean>

  Let bond lengths and angles vary from ideal in minimizer
  Default: false
  

  -data_file <String>

  RDAT or legacy-format file with RNA chemical mapping data
  Default: ""
  

  -cut_at_rna_chainbreak <Boolean>

  If O3' to P distance is > 2.5 Angstroms, assume cutpoint.
  Default: false
  

  -evaluate_base_pairs <Boolean>

  In final scoring, compute number of Watson-Crick, non-Watson-Crick pairs; compare to native if available.
  

• rna:denovo

  -denovo <Boolean>

  denovo option group
  

  -cycles <Integer>

  Default number of Monte Carlo cycles
  Default: 0
  

  -rna_protein_docking_freq <Real>

  RNA/protein docking frequency (between 0 (no docking) and 1 (all docking))
  Default: 0.4
  

  -rounds <Integer>

  Number of rounds to split cycles into during fragment assembly
  Default: 10
  

  -temperature <Real>

  temperature
  Default: 2.0
  

  -minimize_rna <Boolean>

  Minimize RNA after fragment assembly
  Default: false
  

  -sequence <StringVector>

  RNA sequence to model (better to supply in -fasta)
  

  -secstruct <String>

  RNA sec struct to model (better to supply in -secstruct_file)
  Default: ""
  

  -secstruct_general <String>

  RNA sec struct to model with possible noncanonical pairs
  Default: ""
  

  -secstruct_file <String>

  RNA sec struct to model in dot-parens notation
  Default: ""
  

  -secstruct_general_file <String>

  RNA sec struct (+non-canonical pairs) to model in dot-parens notation
  Default: ""
  

  -secstruct_legacy <String>

  RNA sec struct in old 1D notation: H,helix; L,loop; X,unknown; N,bulge
  Default: ""
  

  -lores_scorefxn <String>

  Low resolution scorefunction weights file
  Default: "farna/rna_lores.wts"
  

  -set_lores_weights <StringVector>

  Modification to lores scorefxnweights via the command line. Applied in ScoreFunctionFactory::create_score_function inside the function apply_user_defined_reweighting_. Format is a list of paired strings: -set_lores_weights <score_type1> <setting1> <score_type2> <setting2> ...
  Default: []
  

  -symm_hack_arity <Integer>

  For hacky symmetry that forces matching fragment insertions, what's the n-repeats?
  Default: 1
  

  -params_file <String>

  Input file for pairings [deprecated!]
  Default: "default.prm"
  

  -filter_lores_base_pairs <Boolean>

  Filter for models that satisfy structure parameters
  Default: true
  

  -filter_lores_base_pairs_early <Boolean>

  Filter for models that satisfy structure parameters at round 2 of 10
  Default: true
  

  -filter_chain_closure <Boolean>

  Filter for models that have closed chains after lores before minimize
  Default: true
  

  -filter_chain_closure_halfway <Boolean>

  Filter for models that have closed chains after lores before minimize at round 5 of 10
  Default: true
  

  -filter_chain_closure_distance <Real>

  Mean distance across 3 chainbreak atoms to filter models that have closed chains after lores
  Default: 6.0
  

  -relax_rna <Boolean>

  Relax RNA after fragment assembly
  Default: false
  

  -simple_relax <Boolean>

  Relax by minimizing after any fragment insertion
  Default: false
  

  -ignore_secstruct <Boolean>

  Ignore sec struct in input file
  Default: false
  

  -jump_change_frequency <Real>

  jump change frequency
  Default: 0.1
  

  -close_loops <Boolean>

  close loops after de novo protocol and again after minimization
  Default: true
  

  -close_loops_after_each_move <Boolean>

  close loops during frag insertion and jump mover – can be expensive
  Default: false
  

  -heat <Boolean>

  Heat (random frag insertions)
  Default: false
  

  -staged_constraints <Boolean>

  Apply constraints in stages depending on sequence separation
  Default: false
  

  -jump_library_file <String>

  Input file for jumps
  Default: "1jj2_RNA_jump_library.dat"
  

  -vall_torsions <String>

  Torsions file containing information on fragments from RNA models
  Default: "RICHARDSON_RNA09.torsions"
  

  -use_1jj2_torsions <Boolean>

  Use original (ribosome) fragments, 1JJ2
  Default: false
  

  -fuzz_fragments <Real>

  When picking fragments, fuzz fragments with multiple samples with Gaussians of this standard deviation
  Default: 0
  

  -rna_lores_chainbreak_weight <Real>

  chainbreak weight for lo res sampling
  Default: 0.0
  

  -rna_lores_linear_chainbreak_weight <Real>

  linear chainbreak weight for lo res sampling
  Default: 0.0
  

  -fixed_stems <Boolean>

  Seed each stem with a Watson-Crick base pair instead of having the strands find each other
  Default: false
  

  -allow_bulge <Boolean>

  Automatically virtualize residues that are not energetically stable
  Default: false
  

  -allowed_bulge_res <IntegerVector>

  Use with allow_bulge, allowable pos for virtualization
  Default: []
  

  -allow_consecutive_bulges <Boolean>

  allow_consecutive_bulges
  Default: false
  

  -move_first_rigid_body <Boolean>

  first_rigid_body is usually kept frozen, but might be useful to sample it.
  Default: false
  

  -root_at_first_rigid_body <Boolean>

  places coordinate system away from the usual last virtual residue and puts it on the first rigid body. useful if this rigidbody needs to be fixed, but other bodies need to move as if this one is moving. Use with -move_first_rigid_body.
  Default: false
  

  -dock_each_chunk <Boolean>

  Dock each chunk, set fold tree up so that there are jumps from root virtual residue to all chunks, very useful for optimizing positions in density, use with -new_fold_tree_initializer
  Default: true
  

  -dock_each_chunk_per_chain <Boolean>

  Dock each chunk, including multiple chunks from the same chain, set fold tree up so that there are jumps from root virtual residue to all chunks, very useful for optimizing positions in density, use with -dock_each_chunk and -new_fold_tree_initializer, may also want to use with -initial_structures
  Default: false
  

  -center_jumps_in_single_stranded <Boolean>

  For RNA chains that don't have any base pairs, set up jumps in the center rather than at the first residue in the chain, use with -new_fold_tree_initializer and -dock_each_chunk
  Default: false
  

  -initial_structures <FileVector>

  Initial structure for fragment assembly, useful for initializing rigid body orientations for docking especially with density
  Default: ""
  

  -helical_substructs <FileVector>

  Files provided with -s or -in:file:silent that represent helices, use with dock_each_chunk_per_chain and -new_fold_tree_initializer, includes moves that rotate and translate these helices along their helical axis
  Default: ""
  

  -suppress_bp_constraint <Real>

  Factor by which to lower base pair constraint weight.
  Default: 1.0
  

  -output_filters <Boolean>

  output lores scores at early stage (round 2 of 10) and at end – could be useable for early termination of unpromising early starts
  Default: false
  

  -autofilter <Boolean>

  Automatically skip output/minimize if lores score is worse than 20th percentile, updated on the fly.
  Default: true
  

  -no_filters <Boolean>

  Turn off filters in FARFAR. (umbrella flag) -autofilter false -filter_lores_base_pairs false -filter_lores_base_pairs_early false -filter_chain_closure false -filter_chain_closure_halfway false -filter_chain_closure_distance false
  Default: false
  

  -output_res_num <ResidueChainVector>

  Numbering (and chain) of residues in output PDB or silent file
  Default: []
  

  -offset <Integer>

  Numbering offset for output PDB or silent file (better to use -output_res_num))
  Default: 0
  

  -input_silent_res <ResidueChainVector>

  Input residues for silent files
  Default: []
  

  -virtual_anchor <ResidueChainVector>

  In rigid body movements, which residues in each body are rotation centers
  Default: []
  

  -obligate_pair <ResidueChainVector>

  Residue pairs that must form a base pair (possibly non canonical)
  Default: []
  

  -obligate_pair_explicit <StringVector>

  Residue pairs that must form a base pair, with specification of base edges (W/H/S/X) and orientation (A/P/X or C/T/X)
  Default: []
  

  -chain_connection <StringVector>

  Give SET1 ... and SET2 ... to define segments forming at least one base pair
  Default: []
  

  -remove_pair <ResidueChainVector>

  Residue pairs to remove from secondary structure
  Default: []
  

  -remove_obligate_pair <ResidueChainVector>

  Residue pairs to remove from obligate pair list
  Default: []
  

  -refine_silent_file <String>

  Name of the silent file to be refined.
  Default: ""
  

  -refine_silent_tags <StringVector>

  Tags of structures from the silent file to be refined.
  

  -refine_silent_number_of_poses <Integer>

  Number of low scoring poses to refine from the refine_silent_file
  Default: 0
  

  -get_fold_tree_from_silent_file <String>

  Use the fold tree specified in a silent file
  Default: ""
  

  -fold_tree_from_silent_file_tag <StringVector>

  Tag of the structure in the get_fold_tree_from_silent_file to use
  

  -refine_native_get_good_FT <Boolean>

  Get a reasonable fold tree when refining native - especially important if some stuff shold stay fixed
  Default: false
  

  -refine_native <Boolean>

  Refine starting from the native pose
  Default: false
  

  -override_refine_pose_rounds <Boolean>

  Override rounds/other run parameters that get set if refining pose
  Default: false
  

  -bps_moves <Boolean>

  Base pair step moves
  Default: false
  

  -disallow_bps_at_extra_min_res <Boolean>

  Disallow base pair step moves inside input domains, even extra_min_res
  Default: false
  

  -allow_fragment_moves_in_bps <Boolean>

  Allow fragment/jump moves in regions claimed by base pair steps
  Default: false
  

  -frag_size <Integer>

  Force specific fragment size rather than staged from 3 to 2 to 1
  Default: 0
  

  -VDW_rep_screen_include_sidechains <Boolean>

  Include side chains in the VDW rep screen, use with -VDW_rep_screen_info
  Default: true
  

  -gradual_constraints <Boolean>

  Gradually turn on the atom_pair_constraints and coordinate_constraints?
  Default: true
  

  -ramp_rnp_vdw <Boolean>

  Gradually turn on rnp_vdw?
  Default: false
  

  -grid_vdw_weight <Real>

  Weight for the grid vdw score term
  Default: 1.0
  

  -tag <String>

  tag for naming silent file; legacy of rna_denovo_setup.py
  Default: ""
  

  -working_native <String>

  Native to use if we only know a fragment
  Default: "false"
  

  -use_legacy_setup <Boolean>

  Use old de novo setup without residue/chain mapping
  Default: false
  

  -cst_gap <Boolean>

  Setup up atompair constraints to keep chain ends close if they are known to be part of the same chain in full model pose
  Default: false
  

  -convert_protein_CEN <Boolean>

  Convert protein residues to centroid mode during low-res fragment assembly
  Default: true
  

  -rna_protein_docking <Boolean>

  Do RNA/protein docking?
  Default: false
  

  -small_docking_moves <Boolean>

  Use small translation and rotation perturbation magnitudes
  Default: false
  

  -docking_move_size <Real>

  Size of docking moves, between 0.0 and 1.0, 1.0 is normal docking move sizes, 0.0 is smallest docking moves
  Default: 1.0
  

  -rna_protein_docking_legacy <Boolean>

  Do RNA/protein docking, legacy style?
  Default: false
  

  -rnp_high_res_relax <Boolean>

  Do additional high res relaxation/refinement stage for RNPs
  Default: true
  

  -rnp_high_res_cycles <Integer>

  Number of RNP high res refinement cycles to do
  Default: 10
  

  -rnp_pack_first <Boolean>

  Pack protein sidechains first in RNP high res mover
  Default: false
  

  -rnp_min_first <Boolean>

  Minimize the structure before RNP high res mover is applied
  Default: false
  

  -rnp_ramp_rep <Boolean>

  Ramp fa_rep in RNP high res mover
  Default: false
  

  -new_fold_tree_initializer <Boolean>

  Use the new fold tree initializer framework
  Default: false
  

  -randomize_init_rnp <Boolean>

  Randomize the initial rigid body position and orientation of the RNA relative to proteins
  Default: true
  

  -dock_into_density <Boolean>

  Do rigid body transforms to dock the pose into the density?
  Default: false
  

  -dock_into_density_legacy <Boolean>

  Do rigid body transforms to dock the pose into the density legacy style?
  Default: false
  

  -exclude_fragments <IntegerVector>

  Exclude these fragments from vall
  Default: []
  

  -exclusion_match_type <String>

  How tightly should we match fragments? Either sequence-independent (MATCH_ALL), purine vs. pyrimidine (MATCH_YR), or exact (MATCH_EXACT)
  Default: "MATCH_EXACT"
  

  -fragment_homology_rmsd <Real>

  Distance in RMSD below which a fragment is considered homologous to the native
  Default: 1.0
  

  -exclude_native_fragments <Boolean>

  Exclude fragments from -in:file:native
  Default: false
  

  -exclude_fragment_files <StringVector>

  Files from which to exclude fragments
  Default: []
  

  -dump_stems <Boolean>

  Dump initial stem assignment
  Default: false
  

• rna:denovo:out

  -out <Boolean>

  out option group
  

  -output_lores_silent_file <Boolean>

  output lores stuff
  Default: false
  

  -dump <Boolean>

  Dump pdb
  Default: false
  

  -binary_output <Boolean>

  force output to binary rna silentstruct
  Default: false
  

  -output_score_file <String>

  output running score to this file [specify 'none' if no score output; .SCORES.txt in default]
  Default: ""
  

  -output_score_frequency <Integer>

  output running score with this frequency [0 means no running output]
  Default: 0
  

  -output_jump_res <ResidueChainVector>

  output jump information for these two residues
  

  -output_jump_o3p_to_o5p <Boolean>

  compute jump from o3' to o5' (instead of base centroid coordinate systems)
  Default: false
  

  -output_jump_chainbreak <Boolean>

  compute jump from lower chainbreak triad to upper chainbreak triad; perfect overlapwill be (Vector(0.0), identity matrix).
  Default: false
  

  -output_rotation_vector <Boolean>

  output rotation information as rotation vector (in degrees), not euler angles
  Default: false
  

  -output_jump_reference_RT <String>

  output jump information relative to this rigid body transformation [if empty provided, code will error out but give reference RT for -native or -align_pdb]
  Default: ""
  

  -target_xyz <RealVector>

  Target coordinates for harmonic penalty, o5' relative to o3' stub
  Default: []
  

  -save_jump_histogram <Boolean>

  Save jump information into a 6D histogram
  Default: false
  

  -output_histogram_file <String>

  output histogram to this file [specify 'none' if no score output; .HISTOGRAM.txt is default]
  Default: ""
  

  -jump_histogram_boxsize <Real>

  Boxsize (max +/-x,y,z), Angstroms
  Default: 40.0
  

  -jump_histogram_binwidth <Real>

  Bin-width for x,y,z,, Angstroms
  Default: 4.0
  

  -jump_histogram_binwidth_rotvector <Real>

  Bin-width for rotation vector (degrees)
  Default: 36.0
  

• rna:denovo:db

  -db <Boolean>

  db option group
  

  -jump_database <Boolean>

  Generate a database of jumps extracted from base pairings from a big RNA file
  Default: false
  

  -bps_database <Boolean>

  Generate a database of base pair steps extracted from a big RNA file
  Default: false
  

• rna:denovo:minimize

  -minimize <Boolean>

  minimize option group
  

  -minimize_rounds <Integer>

  The number of rounds of minimization.
  Default: 2
  

  -skip_coord_constraints <Boolean>

  Skip first stage of minimize with coordinate constraints
  Default: false
  

  -skip_o2prime_trials <Boolean>

  No O2* packing in minimizer
  Default: false
  

  -deriv_check <Boolean>

  In rna_minimize, check derivatives numerically
  Default: false
  

  -minimizer_use_coordinate_constraints <Boolean>

  Use coordinate constraints for first round of minimizer
  Default: true
  

  -min_type <String>

  Minimizer type
  Default: "lbfgs_armijo_nonmonotone"
  

  -minimize_bps <Boolean>

  Minimize base pair steps (from Rosetta library)
  Default: true
  

  -minimize_all_protein <Boolean>

  Minimize protein residues?
  Default: false
  

  -minimize_protein_sc <Boolean>

  Minimize protein sidechains?
  Default: false
  

  -protein_packing <Boolean>

  Pack protein residues?
  Default: false
  

  -protein_pack_all <Boolean>

  Pack all protein residues?
  Default: false
  

  -protein_packing_distance <Real>

  Pack protein residues within this distance of RNA
  Default: 10.0
  

  -extra_minimize_res <ResidueChainVector>

  Extra residues during minimize step
  Default: []
  

  -extra_minimize_chi_res <ResidueChainVector>

  Extra side-chain chis to move during minimize step
  Default: []
  

• rna:erraser

  -erraser <Boolean>

  erraser option group
  

  -rna_prot_erraser <Boolean>

  Allows rna_prot_erraser residue type set, featuring both RNA and protein (for ERRASER purposes). You must also use -rna:corrected_geo.
  Default: false
  

  -constrain_P <Boolean>

  constrain phosphate
  Default: false
  

  -fixed_res <ResidueChainVector>

  optional: residues to be held fixed in minimizer
  Default: []
  

  -ready_set_only <Boolean>

  load in and output directly for reformatting the pdb
  Default: false
  

  -skip_minimize <Boolean>

  output the pdb without minimization
  Default: false
  

  -attempt_pyrimidine_flip <Boolean>

  try to flip pyrimidine by 180 degrees and pick the better energy conformer
  Default: false
  

• rotamerdump

  -rotamerdump <Boolean>

  rotamerdump option group
  

  -xyz <Boolean>

  when using the RotamerDump application, output the xyz coords of every rotamer
  Default: false
  

  -one_body <Boolean>

  when using the RotamerDump application, output the one_body energies of every rotamer
  Default: false
  

  -two_body <Boolean>

  when using the RotamerDump application, output the two_body energies of every rotamer
  Default: false
  

  -annealer <Boolean>

  Run the annealer and output the rotamers it chose
  Default: false
  

• sample_around

  -sample_around <Boolean>

  sample_around option group
  

  -alpha_increment <Real>

  if sampling jump, rotation increment, in degrees
  Default: 40.0
  

  -cosbeta_increment <Real>

  if sampling jump, cosbeta increment, no units
  Default: 0.25
  

  -gamma_increment <Real>

  if sampling jump, rotation increment, in degrees
  Default: 40.0
  

• sicdock

  -sicdock <Boolean>

  sicdock option group
  

  -clash_dis <Real>

  max acceptable clash dis
  Default: 3.5
  

  -contact_dis <Real>

  max acceptable contact dis
  Default: 12.0
  

  -hash_2D_vs_3D <Real>

  grid spacing top 2D hash
  Default: 1.3
  

• legacy_sewing

  -legacy_sewing <Boolean>

  legacy_sewing option group
  

  -model_file_name <File>

  Filename for model file (creation or reading)
  

  -score_file_name <File>

  Filename for scores file (creation or reading)
  

  -new_model_file_name <File>

  Filename for new model file to be written
  

  -remove_any_dssp <String>

  If a given model has any segments with this DSSP, remove it
  Default: ""
  

  -remove_all_dssp <String>

  If a given model has all non-loop segments with this DSSP, remove it
  Default: ""
  

  -min_helix_length <Integer>

  Helices less than supplied length will be removed from model file
  Default: 0
  

  -max_helix_length <Integer>

  Helices greater than supplied length will be removed from model file
  Default: 1000
  

  -min_loop_length <Integer>

  Loops less than supplied length will be removed from model file
  Default: 0
  

  -max_loop_length <Integer>

  Loops greater than supplied length will be removed from model file
  Default: 1000
  

  -min_strand_length <Integer>

  Strands less than supplied length will be removed from model file
  Default: 0
  

  -max_strand_length <Integer>

  Strands greater than supplied length will be removed from model file
  Default: 1000
  

  -leave_models_by_ss_num <Boolean>

  Only models with certain number of secondary structures remain
  Default: false
  

  -model_should_have_this_num_of_ss <Integer>

  Only models with this number of secondary structures remain
  

  -model_should_have_at_least_1_E_at_terminal_segment <Boolean>

  model_should_have_at_least_one_E_at_terminal_segment
  Default: false
  

  -model_should_have_at_least_1_E <Boolean>

  model_should_have_at_least_one_E
  Default: false
  

  -model_should_have_at_least_1_H <Boolean>

  model_should_have_at_least_one_H
  Default: false
  

  -leave_models_with_E_terminal_ss <Boolean>

  leave only models_with_E_terminal_ss
  Default: false
  

  -leave_models_with_H_terminal_ss <Boolean>

  leave only models_with_H_terminal_ss
  Default: false
  

  -leave_antiparallel_way_H_bonded_models_by_terminal_strands <Boolean>

  leave only anti-pa H_bonded_models by_terminal_strands
  Default: false
  

  -leave_parallel_way_H_bonded_models_by_terminal_strands <Boolean>

  leave only pa H_bonded_models by_terminal_strands
  Default: false
  

  -leave_certain_model_ids <Boolean>

  Only models with selected ids are left
  Default: false
  

  -leave_these_model_ids <String>

  Only models with selected ids are left
  

  -box_length <Integer>

  Neighborhood lookup box size, 3 for 27 boxes, 4 for 64 boxes etc
  Default: 3
  

  -mode <String>

  The mode sewing_hasher should run.
  Default: "hash"
  

  -disregard_num_segment_matches <Boolean>

  if true, disregard num_segment_matches
  

  -do_not_remove_connection_inconsistencies <Boolean>

  if true, do not remove_connection_inconsistencies
  

  -score_between_opposite_terminal_segments <Boolean>

  if true, score_between_opposite_terminal_segments like 1-5 or 5-1
  

  -num_models_to_dump <Integer>

  Used for ModelDumper. How many random models should be dumped?
  

  -models_to_dump <IntegerVector>

  Used for ModelDumper for specifying model ids you want to dump
  

  -min_hash_score <Integer>

  Minimum number of overlapping atoms per segment
  Default: 10
  

  -max_clash_score <Integer>

  Maximum number of atoms found in the same bin, but not from superimposed fragments
  Default: 0
  

  -num_segments_to_match <Integer>

  Number of segments required to have min_hash_score atom matches
  Default: 1
  

  -match_segments <IntegerVector>

  Segment scored by the hasher
  

  -max_models <Integer>

  Maximum models to hash, for testing purposes only
  

  -starting_model <Integer>

  Starting model for hashing
  

  -num_procs <Integer>

  Number of processors to split up hashing with
  

  -rank <Integer>

  The processor rank for this process
  

  -hash_tag_only_terminal_Es <Boolean>

  hash_tag_only_terminal_Es
  Default: false
  

  -assembly_type <String>

  Type of Assembly class to generate
  Default: "continuous"
  

  -num_edges_to_follow <Integer>

  Maximum number of edges on graph to follow
  

  -base_native_bonus <Real>

  Weighting term for packing native rotamers
  

  -neighbor_cutoff <Integer>

  Cutoff for favoring natives in SEWING refinement. Any residues with fewer neighbors is not favored
  

  -dump_pdbs <Boolean>

  Dump intermediate PDBs
  Default: false
  

  -skip_refinement <Boolean>

  Should you refine the final assembly
  Default: false
  

  -skip_filters <Boolean>

  Should the Assembly be filtered before refinment
  Default: false
  

  -min_motif_score <Real>

  Minimum allowable motif score
  Default: 20
  

  -may_add_already_added_model <Boolean>

  may_add_already_added_model
  Default: false
  

  -offset_bump_dsq <Real>

  offset to bump_dsq
  Default: 0
  

  -num_repeats <Integer>

  Number of repeats to print in final structures
  Default: 3
  

  -repeat <Boolean>

  Should the AssemblyConstraintsMover treat this as a repeat?
  Default: false
  

  -pose_segment_starts <IntegerVector>

  Segment begin indices
  

  -pose_segment_ends <IntegerVector>

  Segment end indices
  

  -keep_source_segments <Boolean>

  Keep the source segments rather than the target segments. For use with append
  Default: false
  

  -partner_pdb <File>

  A PDB that is not part of the Assembly, but will be used for clash checking
  

  -keep_model_residues <IntegerVector>

  A list of residues from the input pose that will not be designed (but are repacked)
  

  -min_lh_fragments <Integer>

  Minimium number of LoopHash fragments necessary for each designed loop
  Default: 10
  

  -skip_loop_generation <Boolean>

  Should you skip generation of loops
  Default: false
  

  -max_ss_num <Integer>

  max_ss_num so either 3 (smotif) or 5 (5-ss_models)
  Default: 5
  

  -dump_every_model <Boolean>

  dump_every_model
  Default: false
  

• SSrbrelax

  -SSrbrelax <Boolean>

  SSrbrelax option group
  

  -rb_file <File>

  rb definition file
  Default: "rb_file"
  

  -rb_param_file <File>

  rb param file
  Default: "rb_param_file"
  

  -frag_sizes <IntegerVector>

  lengths of fragments to be used in loop modeling
  Default: ['9', '3', '1']
  

  -frag_files <FileVector>

  fragment libraries files
  Default: ['"FragFile9"', '"FragFile3"', '"FragFile1"']
  

• stepwise

  -stepwise <Boolean>

  stepwise option group
  

  -s1 <StringVector>

  input file(s)
  

  -s2 <StringVector>

  input file(s)
  

  -silent1 <StringVector>

  input file
  

  -silent2 <StringVector>

  input file
  

  -tags1 <StringVector>

  input tag(s)
  

  -tags2 <StringVector>

  input tag(s)
  

  -slice_res1 <IntegerVector>

  Residues to slice out of starting file
  Default: []
  

  -slice_res2 <IntegerVector>

  Residues to slice out of starting file
  Default: []
  

  -input_res1 <IntegerVector>

  Residues already present in starting file
  Default: []
  

  -input_res2 <IntegerVector>

  Residues already present in starting file2
  Default: []
  

  -backbone_only1 <Boolean>

  just copy protein backbone DOFS, useful for homology modeling
  

  -backbone_only2 <Boolean>

  just copy protein backbone DOFS, useful for homology modeling
  

  -fixed_res <IntegerVector>

  Do not move these residues during minimization.
  Default: []
  

  -test_encapsulation <Boolean>

  Test ability StepWiseRNA Modeler to figure out what it needs from just the pose - no JobParameters
  Default: false
  

  -choose_random <Boolean>

  ask swa residue sampler for a random solution
  Default: false
  

  -num_random_samples <Integer>

  In choose_random/monte-carlo mode, number of samples from swa residue sampler before minimizing best
  Default: 20
  

  -max_tries_multiplier_for_ccd <Integer>

  In choose_random/monte-carlo mode, when CCD closure needs to occur, multiple # tries by this factor
  Default: 10
  

  -num_pose_minimize <Integer>

  optional: set_num_pose_minimize by Minimizer
  Default: 0
  

  -atr_rep_screen <Boolean>

  In sampling, screen for contacts (but no clash) between partitions before packing
  Default: true
  

  -atr_rep_screen_for_docking <Boolean>

  In just docking moves, screen for contacts (but no clash) between partitions before packing
  Default: false
  

  -align_pdb <String>

  PDB to align to. Default will be -native, or no alignment
  Default: ""
  

  -new_align_pdb <String>

  PDB to align to with the new RNA_AlignmentEnergy.
  Default: ""
  

  -enumerate <Boolean>

  For SWM. Force enumeration (SWA-like) instead of random
  Default: false
  

  -preminimize <Boolean>

  For SWM. Just prepack and minimize
  Default: false
  

  -skip_preminimize <Boolean>

  Skip preminimize before stepwise monte carlo
  Default: false
  

  -minimize_waters <Boolean>

  When hydrating magnesiums, minimize any waters that appear
  Default: false
  

  -test_all_moves <Boolean>

  Try all moves from starting pose, recursing through additions
  Default: false
  

  -new_move_selector <Boolean>

  For SWM. Use new move selector which does keep track of proposal probabilities.
  Default: true
  

  -dump <Boolean>

  Dump intermediate silent & PDB files
  Default: false
  

  -VERBOSE <Boolean>

  VERBOSE
  Default: false
  

  -use_green_packer <Boolean>

  use packer instead of rotamer trials for side-chain packing and O2' optimization
  Default: false
  

  -rmsd_screen <Real>

  keep sampled residues within this rmsd from the native pose
  Default: 0.0
  

  -skip_minimize <Boolean>

  Skip minimize, e.g. in prepack step
  Default: false
  

  -virtualize_packable_moieties_in_screening_pose <Boolean>

  Virtualize 2'-OH, terminal phosphates in stepwise contact screening, before actual packing
  Default: false
  

  -minimizer_mode <String>

  Minimize using thermal sampler (THERMAL_SAMPLER) or traditionally (TRADITIONAL_MINIMIZER, or really anything else)
  Default: "TRADITIONAL_MINIMIZER"
  

  -sampler_silent_file <String>

  In StepWiseConnectionSampler, where to output all poses that pass filters
  Default: ""
  

  -superimpose_over_all <Boolean>

  In final superimposition, do not keep any domains fixed, superimpose over everything
  Default: true
  

  -alignment_anchor_res <ResidueChainVector>

  Single residue that resides in the single input domain that should be superimposed prior to RMSD calculation
  

  -move <StringVector>

  For SWM. Format: 'ADD 5 BOND_TO_PREVIOUS 4'
  Default: []
  

  -min_type <String>

  Minimizer type
  Default: "lbfgs_armijo_nonmonotone"
  

  -min_tolerance <Real>

  Minimizer tolerance
  Default: 0.000025
  

  -output_minimized_pose_list <Boolean>

  Use legacy output that puts out all minimized poses; set to true in legacy SWA
  Default: false
  

  -virtualize_free_moieties_in_native <Boolean>

  Virtualize bulges, terminal phosphates, and 2' hydroxyls detected to be non-interacting ('free') in native pose. I.e., do not calculate RMSD over those atoms.
  Default: true
  

  -output_cluster_size <Boolean>

  Output cluster_size in StepWiseClusterer as an extra score in the pose
  Default: false
  

  -lores <Boolean>

  Use coarse-grained energy function to sample; no minimize.
  Default: false
  

  -verbose_sampler <Boolean>

  verbose output from StepWiseConnectionSampler sample-and-screen.
  Default: false
  

  -pack_protein_side_chains <Boolean>

  allow neighboring protein side chains to be packed.
  Default: true
  

  -definitely_virtualize <IntegerVector>

  definitely virtualize these residues (by seqpos)
  Default: []
  

  -force_moving_res_for_erraser <Boolean>

  For ERRASER resample moves, ENSURE that the appropriate residue is moving
  Default: false
  

• stepwise:monte_carlo

  -monte_carlo <Boolean>

  monte_carlo option group
  

  -verbose_scores <Boolean>

  Show all score components
  Default: false
  

  -skip_deletions <Boolean>

  no delete moves – just for testing
  Default: false
  

  -allow_internal_hinge_moves <Boolean>

  Allow moves in which internal suites are sampled (hinge-like motions)
  Default: true
  

  -allow_internal_local_moves <Boolean>

  Allow moves in which internal cutpoints are created to allow ERRASER rebuilds
  Default: true
  

  -allow_skip_bulge <Boolean>

  Allow moves in which an intervening residue is skipped and the next one is modeled as floating base
  Default: false
  

  -skip_bulge_frequency <Real>

  Compared to 'normal' add moves, how often to skip a bulge and do addition.
  Default: 0.0
  

  -from_scratch_frequency <Real>

  Allow modeling of 'free' dinucleotides that are not part of input poses
  Default: 0.1
  

  -allow_split_off <Boolean>

  Allow chunks that do not contain fixed domains to split off after nucleating on fixed domains.
  Default: true
  

  -cycles <Integer>

  Number of Monte Carlo cycles
  Default: 50
  

  -temperature <Real>

  Monte Carlo temperature
  Default: 1.0
  

  -add_proposal_density_factor <Real>

  Increase/decrease the proposal_density_ratio for add moves by this factor
  Default: 1.0
  

  -add_delete_frequency <Real>

  Frequency of add/delete vs. resampling
  Default: 0.5
  

  -docking_frequency <Real>

  Frequency of docking vs. folding moves
  Default: 0.2
  

  -submotif_frequency <Real>

  Frequency of submotif additions
  Default: 0.2
  

  -intermolecular_frequency <Real>

  Same as -docking_frequency, to be deprecated soon
  Default: 0.2
  

  -minimize_single_res_frequency <Real>

  Frequency with which to minimize the residue that just got rebuilt, instead of all
  Default: 0.0
  

  -allow_variable_bond_geometry <Boolean>

  In 10% of moves, let bond angles & distance change
  Default: true
  

  -switch_focus_frequency <Real>

  Frequency with which to switch the sub-pose that is being modeled
  Default: 0.5
  

  -just_min_after_mutation_frequency <Real>

  After a mutation, how often to just minimize (without further sampling the mutated residue)
  Default: 0.5
  

  -local_redock_only <Boolean>

  In ResampleMover, docking partners can change anywhere across connected chains. Force the new partners to be close to the old ones.
  Default: true
  

  -make_movie <Boolean>

  create silent files in movie/ with all steps and accepted steps
  Default: false
  

  -recover_low <Boolean>

  Output lowest energy model in monte carlo, not the last frame
  Default: true
  

  -use_precomputed_library <Boolean>

  In from_scratch moves, do not sample dinucleotides explicitly, but instead use library saved to disk.
  Default: true
  

  -allow_submotif_split <Boolean>

  for submotif moves, allow submotifs to be split. (inconsistent with detailed balance.)
  Default: false
  

  -force_submotif_without_intervening_bulge <Boolean>

  for submotif moves, only add base pairs that have an attachment point and a cutpoint closed, with no intervening bulge
  Default: false
  

  -use_first_jump_for_submotif <Boolean>

  for submotif moves, only use first jump from jump library – does not change stepwise -lores (which resamples jump) except in balance of move selection.
  Default: false
  

  -exclude_submotifs <StringVector>

  submotifs in database/sampling/rna/submotif/submotifs.txt to exclude
  Default: []
  

  -vary_loop_length_frequency <Real>

  In design, allow loops ('n') to shorten from loop lengths defined in FASTA files.
  Default: 0.0
  

  -designing_with_noncanonicals <Boolean>

  Are we designing with noncanonicals, meaning 'n' has to read from a set of possible symbols (instead of 4 canonical NAs)?
  Default: false
  

  -checkpointing_frequency <Integer>

  How often should we output checkpoint files?
  Default: 100
  

  -continue_until_none_missing <Boolean>

  If there are missing residues when we've reached n-cycles, just keep going! Suggested with checkpointing.
  Default: false
  

  -full_model_constraints <FileVector>

  One or more files containing constraints to be applied in a 'full-model' setting, i.e., only in the Modeler and only once residues exist.
  Default: []
  

• stepwise:monte_carlo:csa

  -csa <Boolean>

  csa option group
  

  -csa_bank_size <Integer>

  Do conformational space annealing (population monte carlo) with this number of models in the bank
  Default: 0
  

  -csa_rmsd <Real>

  RMSD cutoff for calling two poses different in conformational space annealing (population monte carlo)
  Default: 1.0
  

  -csa_output_rounds <Boolean>

  output silent files at intermediate stages (at integral multiples of bank_size)
  Default: false
  

  -annealing <Boolean>

  Actually anneal the RMSD from the half the average distance between first-bank models to one-fifth that distance
  Default: false
  

• stepwise:polar_hydrogens

  -polar_hydrogens <Boolean>

  polar_hydrogens option group
  

  -vary_polar_hydrogen_geometry <Boolean>

  Optimize hydrogens that form hydrogen bonds
  Default: false
  

  -bond_angle_sd_polar_hydrogen <Real>

  Standard deviation for bond_geometry angle term with -vary_polar_hydrogen_geometry flag, in degrees
  Default: 60.0
  

  -bond_torsion_sd_polar_hydrogen <Real>

  Standard deviation for bond_geometry torsion term with -vary_polar_hydrogen_geometry flag, in degrees
  Default: 30.0
  

  -fix_lengths <Boolean>

  with -vary_geometry, disallow bond length change
  Default: false
  

  -fix_angles <Boolean>

  with -vary_geometry, disallow bond angle change
  Default: false
  

  -fix_torsions <Boolean>

  with -vary_geometry, disallow bond torsion change beyond standard movemap
  Default: false
  

  -disallow_pack_polar_hydrogens <Boolean>

  with -vary_polar_hydrogen_geometry, disallow polar hydrogen packing step before minimizing
  Default: false
  

  -disallow_vary_geometry_proton_chi <Boolean>

  no packing/minimizing of 2'-OH or other hydrogens controlled by chi torsion
  Default: false
  

• stepwise:rna

  -rna <Boolean>

  rna option group
  

  -sampler_num_pose_kept <Integer>

  set_num_pose_kept by ResidueSampler )
  Default: 108
  

  -native_edensity_score_cutoff <Real>

  native_edensity_score_cutoff
  Default: -1.0
  

  -o2prime_legacy_mode <Boolean>

  complete virtualization of O2' hydrogen during sampling, and then complete restoration and packing
  Default: false
  

  -allow_virtual_o2prime_hydrogens <Boolean>

  allow O2' hydrogen to be virtualized during packing.
  Default: false
  

  -sampler_perform_phosphate_pack <Boolean>

  perform terminal phosphate packing inside StepWiseRNA_ResidueSampler
  Default: false
  

  -force_phosphate_instantiation <Boolean>

  Require terminal phosphates to be instantiated.
  Default: false
  

  -distinguish_pucker <Boolean>

  distinguish pucker when cluster:both in sampler and clusterer
  Default: true
  

  -finer_sampling_at_chain_closure <Boolean>

  Sampler: finer_sampling_at_chain_closure
  Default: false
  

  -PBP_clustering_at_chain_closure <Boolean>

  Sampler: PBP_clustering_at_chain_closure
  Default: false
  

  -sample_all_chi <Boolean>

  Sample all chi angles (use for blind learning of chi potential)
  Default: false
  

  -sampler_allow_syn_pyrimidine <Boolean>

  sampler_allow_syn_pyrimidine
  Default: false
  

  -sampler_extra_chi_rotamer <Boolean>

  Sampler: extra_syn_chi_rotamer
  Default: false
  

  -sampler_extra_beta_rotamer <Boolean>

  Sampler: extra_beta_rotamer
  Default: false
  

  -sampler_extra_epsilon_rotamer <Boolean>

  Sampler: extra_epsilon_rotamer
  Default: true
  

  -force_centroid_interaction <Boolean>

  Require base stack or pair even for single residue loop closed (which could also be bulges!)
  Default: false
  

  -virtual_sugar_legacy_mode <Boolean>

  In virtual sugar sampling, use legacy protocol to match Parin's original workflow
  Default: false
  

  -VDW_rep_optimize_memory_usage <Boolean>

  RNA_VDW_BinChecker, do not store vector of occupied xyz bins.
  Default: false
  

  -erraser <Boolean>

  Use KIC sampling
  Default: false
  

  -centroid_screen <Boolean>

  centroid_screen
  Default: true
  

  -VDW_atr_rep_screen <Boolean>

  classic VDW_atr_rep_screen
  Default: true
  

  -minimize_and_score_native_pose <Boolean>

  minimize_and_score_native_pose
  Default: false
  

  -rm_virt_phosphate <Boolean>

  Remove virtual phosphate patches during minimization
  Default: false
  

  -VDW_rep_screen_info <StringVector>

  VDW_rep_screen_info to create VDW_rep_screen_bin ( useful when building loop from large poses )
  Default: []
  

  -VDW_rep_alignment_RMSD_CUTOFF <Real>

  use with VDW_rep_screen_info
  Default: 0.001
  

  -VDW_rep_delete_matching_res <StringVector>

  delete residues in VDW_rep_pose that exist in the working_pose
  Default: []
  

  -VDW_rep_screen_physical_pose_clash_dist_cutoff <Real>

  The distance cutoff for VDW_rep_screen_with_physical_pose
  Default: 1.2
  

  -integration_test <Boolean>

  integration_test
  Default: false
  

  -allow_bulge_at_chainbreak <Boolean>

  Allow sampler to replace chainbreak res with virtual_rna_variant if it looks have bad fa_atr score.
  Default: true
  

  -parin_favorite_output <Boolean>

  parin_favorite_output
  Default: true
  

  -reinitialize_CCD_torsions <Boolean>

  Sampler: reinitialize_CCD_torsions: Reinitialize_CCD_torsion to zero before every CCD chain closure
  Default: false
  

  -sample_both_sugar_base_rotamer <Boolean>

  Sampler: Super hacky for SQUARE_RNA
  Default: false
  

  -sampler_include_torsion_value_in_tag <Boolean>

  Sampler:include_torsion_value_in_tag
  Default: true
  

  -sampler_assert_no_virt_sugar_sampling <Boolean>

  sampler_assert_no_virt_sugar_sampling
  Default: false
  

  -sampler_try_sugar_instantiation <Boolean>

  for floating base sampling, try to instantiate sugar if it looks promising
  Default: false
  

  -do_not_sample_multiple_virtual_sugar <Boolean>

  Sampler: do_not_sample_multiple_virtual_sugar
  Default: false
  

  -sample_ONLY_multiple_virtual_sugar <Boolean>

  Sampler: sample_ONLY_multiple_virtual_sugar
  Default: false
  

  -allow_base_pair_only_centroid_screen <Boolean>

  allow_base_pair_only_centroid_screen
  Default: false
  

  -minimizer_rename_tag <Boolean>

  Reorder and rename the tag by the energy_score
  Default: true
  

  -minimize_res <IntegerVector>

  alternative to fixed_res
  Default: []
  

  -alignment_res <StringVector>

  align_res_list
  Default: []
  

  -native_alignment_res <IntegerVector>

  optional: native_alignment_res
  Default: []
  

  -rmsd_res <IntegerVector>

  residues that will be use to calculate rmsd ( for clustering as well as RMSD to native_pdb if specified )
  Default: []
  

  -missing_res <IntegerVector>

  Residues missing in starting pose_1, alternative to input_res
  Default: []
  

  -missing_res2 <IntegerVector>

  Residues missing in starting pose_2, alternative to input_res2
  Default: []
  

  -job_queue_ID <Integer>

  swa_rna_sample()/combine_long_loop mode: Specify the tag pair in filter_output_filename to be read in and imported ( start from 0! )
  Default: 0
  

  -minimize_and_score_sugar <Boolean>

  minimize and sugar torsion + angle? and include the rna_sugar_close_score_term
  Default: true
  

  -global_sample_res_list <IntegerVector>

  A list of all the nucleotide to be build/sample over the entire dag.
  Default: []
  

  -filter_output_filename <File>

  CombineLongLoopFilterer: filter_output_filename
  Default: "filter_struct.txt"
  

  -combine_long_loop_mode <Boolean>

  Sampler: combine_long_loop_mode
  Default: false
  

  -combine_helical_silent_file <Boolean>

  CombineLongLoopFilterer: combine_helical_silent_file
  Default: false
  

  -output_extra_RMSDs <Boolean>

  output_extra_RMSDs
  Default: false
  

  -protonated_H1_adenosine_list <IntegerVector>

  optional: protonate_H1_adenosine_list
  Default: []
  

  -native_virtual_res <IntegerVector>

  optional: native_virtual_res
  Default: []
  

  -simple_append_map <Boolean>

  simple_append_map
  Default: false
  

  -allow_fixed_res_at_moving_res <Boolean>

  mainly just to get Hermann Duplex modeling to work
  Default: false
  

  -force_user_defined_jumps <Boolean>

  Trust and use user defined jumps
  Default: false
  

  -jump_point_pairs <StringVector>

  optional: extra jump_points specified by the user for setting up the fold_tree
  Default: []
  

  -add_virt_root <Boolean>

  add_virt_root
  Default: false
  

  -floating_base <Boolean>

  floating_base
  Default: false
  

  -floating_base_anchor_res <Integer>

  If we want floating base to be connected via a jump to an anchor res (with no intervening virtual residues), specify the anchor.
  Default: 0
  

  -allow_chain_boundary_jump_partner_right_at_fixed_BP <Boolean>

  mainly just to get Hermann nano - square RNA modeling to work
  Default: false
  

  -rebuild_bulge_mode <Boolean>

  rebuild_bulge_mode
  Default: false
  

  -virtual_sugar_keep_base_fixed <Boolean>

  When instantiating virtual sugar, keep base fixed – do not spend a lot of time to minimize!
  Default: true
  

  -virtual_sugar_do_minimize <Boolean>

  When instantiating virtual sugar, minimize (as in original SWA code) – takes extra time!
  Default: true
  

  -sampler_max_centroid_distance <Real>

  max centroid distance of moving base to reference in floating base sampler
  Default: 0.0
  

  -filter_user_alignment_res <Boolean>

  filter_user_alignment_res
  Default: true
  

  -tether_jump <Boolean>

  In rigid body moves, keep moving residue close to (jump-connected) reference residue (8.0 A) and force centroid interaction between them
  Default: true
  

  -turn_off_rna_chem_map_during_optimize <Boolean>

  When using rna_chem_map, only score with this after minimizing (takes too long to compute during optimizing).
  Default: true
  

• stepwise:protein

  -protein <Boolean>

  protein option group
  

  -global_optimize <Boolean>

  In clustering, packing, minimizing, use all residues.
  Default: false
  

  -disable_sampling_of_loop_takeoff <Boolean>

  For KIC protein loop closure, disallow sampling of psi at N-terminus and phi at C-terminus takeoff residues
  Default: false
  

  -sample_beta <Boolean>

  sample beta strand pairing – later need to specify parallel/antiparallel
  Default: false
  

  -ghost_loops <Boolean>

  Virtualize loops in centroid screening
  Default: false
  

  -centroid_screen <Boolean>

  Centroid Screen
  Default: false
  

  -centroid_score_diff_cut <Real>

  If doing -centroid_screen, only keep poses whose energies are within this energy of reference..
  Default: 20.0
  

  -centroid_weights <String>

  weights for centroid filter
  Default: "score3.wts"
  

  -score_diff_cut <Real>

  score difference cut for clustering
  Default: 10.0
  

  -filter_native_big_bins <Boolean>

  Figure out various terms for score12
  Default: false
  

  -cluster_by_all_atom_rmsd <Boolean>

  cluster by all atom rmsd
  Default: false
  

  -centroid_output <Boolean>

  output centroid structure during screening
  Default: false
  

  -n_sample <Integer>

  number of samples per torsion angle
  Default: 18
  

  -nstruct_centroid <Integer>

  Number of decoys to output from centroid screening
  Default: 0
  

  -ccd_close <Boolean>

  Close loops with CCD
  Default: false
  

  -bridge_res <IntegerVector>

  instead of enumerative sampling of backbone torsions, combine silent files that contains pieces of loops
  Default: []
  

  -cart_min <Boolean>

  Use cartesian minimizer
  Default: false
  

  -move_jumps_between_chains <Boolean>

  Move all jumps
  Default: false
  

  -use_packer_instead_of_rotamer_trials <Boolean>

  Use packer instead of rotamer trials in residue sampling
  Default: false
  

  -expand_loop_takeoff <Boolean>

  expand -sample_res loop to include connection to previous/next residues
  Default: false
  

  -skip_coord_constraints <Boolean>

  Skip first stage of minimize with coordinate constraints
  Default: false
  

  -allow_virtual_side_chains <Boolean>

  In packing, allow virtual side chains
  Default: true
  

  -protein_prepack <Boolean>

  In packing, prepack separate partitions
  Default: true
  

  -disulfide_file <String>

  File with pairs of numbers for desired disulfides.
  Default: ""
  

• full_model

  -full_model <Boolean>

  full_model option group
  

  -global_seq_file <String>

  File with global sequence and modeled sequence.
  Default: ""
  

  -cutpoint_open <ResidueChainVector>

  open cutpoints in full model
  Default: []
  

  -cutpoint_closed <ResidueChainVector>

  closed cutpoints in full model
  Default: []
  

  -cyclize <ResidueChainVector>

  cyclize points in full model
  Default: []
  

  -twoprime <ResidueChainVector>

  twoprime branch points in full model
  Default: []
  

  -fiveprime_cap <ResidueChainVector>

  fiveprime capped residues and their corresponding 7MGs
  Default: []
  

  -other_poses <StringVector>

  list of PDB files containing other poses
  

  -jump_res <ResidueChainVector>

  optional: residues for defining jumps – please supply in pairs
  Default: []
  

  -disulfide_res <ResidueChainVector>

  optional: residues for defining disulfides – please supply in pairs
  Default: []
  

  -extra_min_res <ResidueChainVector>

  specify residues other than those being built that should be minimized
  Default: []
  

  -extra_min_jump_res <ResidueChainVector>

  specify jump-connected pairs other than those being built that should be minimized
  Default: []
  

  -root_res <ResidueChainVector>

  optional: desired root res (used in SWM move testing)
  Default: []
  

  -virtual_sugar_res <ResidueChainVector>

  optional: starting virtual sugars (used in SWM move testing)
  Default: []
  

  -virtual_res <ResidueChainVector>

  optional: residues for defining virtual residues
  Default: []
  

  -sample_res <ResidueChainVector>

  residues to build (for SWA, the first element is the actual sample res while the other are the bulge residues)
  Default: []
  

  -calc_rms_res <ResidueChainVector>

  residues over which to calculate rms for SWA. Not in wide use anymore.
  Default: []
  

  -working_res <ResidueChainVector>

  residues that are being built [by default will be set from sample_res and any input pdbs]
  Default: []
  

  -motif_mode <Boolean>

  in fixed PDB parts, minimize residues right next to loops & disallow pair/stacking in most distal residues
  Default: false
  

  -allow_jump_in_numbering <Boolean>

  useful for design. if residue numbers jump from i to i+1 do not assume cutpoint.
  Default: false
  

• full_model:rna

  -rna <Boolean>

  rna option group
  

  -terminal_res <ResidueChainVector>

  optional: residues that are not allowed to stack during sampling
  Default: []
  

  -block_stack_above_res <ResidueChainVector>

  optional: residues on which other residues cannot stack above (uses repulsion atoms)
  Default: []
  

  -block_stack_below_res <ResidueChainVector>

  optional: residues on which other residues cannot stack below (uses repulsion atoms)
  Default: []
  

  -force_syn_chi_res_list <ResidueChainVector>

  optional: sample only syn chi for the res in sampler.
  Default: []
  

  -force_anti_chi_res_list <ResidueChainVector>

  optional: sample only anti chi for the res in sampler.
  Default: []
  

  -force_north_sugar_list <ResidueChainVector>

  optional: sample only north sugar for the res in sampler.
  Default: []
  

  -force_south_sugar_list <ResidueChainVector>

  optional: sample only south sugar for the res in sampler.
  Default: []
  

  -bulge_res <ResidueChainVector>

  optional: residues to be turned into a bulge variant
  Default: []
  

  -sample_sugar_res <ResidueChainVector>

  optional: residues in fixed input pose whose sugars can still move
  Default: []
  

• recces

  -seq1 <String>

  sequence 1 to model, 5' to 3'
  Default: ""
  

  -seq2 <String>

  sequence 2 to model, 5' to 3'
  Default: ""
  

  -n_cycle <Integer>

  Number of cycles for random sampling Markov chain Monte Carlo
  Default: 10000
  

  -a_form_range <Real>

  Range of sampling near A-form for duplexes in RECCES (turner)
  Default: 60.0
  

  -dump_pdb <Boolean>

  Dump pdb files
  Default: false
  

  -dump_silent <Boolean>

  Dump structures to a silent file
  Default: false
  

  -out_torsions <Boolean>

  Print out torsion angles
  Default: false
  

  -temps <RealVector>

  Simulated tempering temperatures
  Default: []
  

  -st_weights <RealVector>

  Simulated tempering weights
  Default: []
  

  -save_score_terms <Boolean>

  Save scores and individual score terms of all sampled conformers
  Default: false
  

  -out_prefix <String>

  prefix for the out file
  Default: "recces"
  

  -dump_freq <Integer>

  Frequency to dump pdb or silent files
  Default: 500
  

  -n_intermediate_dump <Integer>

  Number of intermediate conformations to be dumped
  Default: 0
  

  -output_min_pose <Boolean>

  Make last pose the minimum score pose ('recover low')
  Default: true
  

  -accept_no_op_moves <Boolean>

  override behavior where no_ops (e.g. for moving jump out of range) are not accepts
  Default: false
  

  -histogram_min <Real>

  Minimum energy for histogram
  Default: -100.05
  

  -histogram_max <Real>

  Maximum energy for histogram
  Default: +800.05
  

  -histogram_spacing <Real>

  Spacing for histogram
  Default: 0.1
  

• recces:base_pair

  -base_pair <Boolean>

  base_pair option group
  

  -rmsd_cutoff <Real>

  base pair RMSD cutoff for jump sampling
  Default: 2.0
  

  -translation_mag <Real>

  magnitude of random translation moves
  Default: 0.01
  

  -rotation_mag <Real>

  magnitude of random rotation moves (in degrees)
  Default: 1.0
  

  -recces <Boolean>

  turn on RECCES in rb_entropy pilot app
  Default: false
  

  -block_stack <Boolean>

  put block_stack atoms on test base pair
  Default: false
  

  -sample_jump <Boolean>

  force base pair jump to be sampled when pose is setup vi -seq1, -seq2 (legacy turner mode)
  Default: false
  

• recces:thermal_sampling

  -thermal_sampling <Boolean>

  thermal_sampling option group
  

  -sample_residues <IntegerVector>

  residues to sample
  Default: []
  

  -free_residues <IntegerVector>

  residues that are 'free,' affects stdev of chi sampler
  Default: []
  

  -loop_residues <IntegerVector>

  residues that are in loops and merit total BB sampling
  Default: []
  

  -angle_range_bb <Real>

  range bb torsions are allowed to move
  Default: 20
  

  -angle_range_free_bb <Real>

  range free bb torsions are allowed to move
  Default: 180
  

  -angle_range_chi <Real>

  range chi torsions are allowed to move
  Default: 20
  

  -angle_range_free_chi <Real>

  range free chi torsions are allowed to move
  Default: 180
  

  -chi_stdev <Real>

  standard deviation for chi sampler
  Default: 20
  

  -bb_stdev <Real>

  standard deviation for backbone sampler
  Default: 1
  

  -standard_bb_stdev <Real>

  standard deviation for standard backbone sampler
  Default: 1
  

  -setup_base_pair_constraints <Boolean>

  Identify Watson/Crick pairs in input pose and put in constraints.
  Default: false
  

• strand_assembly

  -strand_assembly <Boolean>

  strand_assembly option group
  

  -min_num_strands_to_deal <Integer>

  Minimum number of strands to handle beta-sandwich
  

  -max_num_strands_to_deal <Integer>

  Maximum number of strands to handle beta-sandwich
  

  -extract_native_only <Boolean>

  if true, extract native full strands only
  

  -min_res_in_strand <Integer>

  minimum number of residues in a strand, for edge strand definition & analysis
  

  -max_res_in_strand <Integer>

  Maximum number of residues in a strand, for edge strand definition & analysis
  

  -min_O_N_dis <Real>

  Minimum distance between backbone oxygen and backbone nitrogen
  

  -max_O_N_dis <Real>

  Maximum distance between backbone oxygen and backbone nitrogen
  

  -min_sheet_dis <Real>

  Minimum distance between sheets (CA and CA)
  

  -max_sheet_dis <Real>

  Maximum distance between sheets (CA and CA)
  

  -min_sheet_torsion <Real>

  Minimum torsion between sheets (CA and CA) with respect to terminal residues
  

  -max_sheet_torsion <Real>

  Maximum torsion between sheets (CA and CA) with respect to terminal residues
  

  -min_sheet_angle <Real>

  Minimum angle between sheets (CA and CA)
  

  -max_sheet_angle <Real>

  Maximum angle between sheets (CA and CA)
  

  -min_shortest_dis_sidechain_inter_sheet <Real>

  minimum distance between sidechains between sheets (pairs of strands)
  

• TailSegment

  -TailSegment <Boolean>

  TailSegment option group
  

  -refine_cycles <Integer>

  refinement phase runs for <input> cycles
  Default: 100
  

  -refine_repack_cycles <Integer>

  refinement phase runs repack every <input> cycles
  Default: 10
  

• templates

  -templates <Boolean>

  templates option group
  

  -config <File>

  read a list of templates and alignments
  Default: "templates.dat"
  

  -fix_aligned_residues <Boolean>

  pick only from template fragments and then keep these residues fixed
  Default: false
  

  -fix_frag_file <File>

  fragments from this file are picked once in beginning and then kept fixed
  Default: ""
  

  -fix_margin <Integer>

  keep n residues at edges of fixed fragments moveable
  Default: 1
  

  -min_nr_large_frags <Integer>

  how many large fragments should be present
  Default: 100000
  

  -min_nr_small_frags <Integer>

  how many small fragments should be present
  Default: 100000
  

  -no_pick_fragments <Boolean>

  no further fragment picking from templates
  Default: false
  

  -nr_large_copies <Integer>

  make N copies of each picked template fragment – a hacky way to weight them
  Default: 4
  

  -nr_small_copies <Integer>

  make N copies of each picked template fragment – a hacky way to weight them
  Default: 20
  

  -pairings <Boolean>

  use pairings from templates
  Default: false
  

  -pick_multiple_sizes <Boolean>

  pick 9mers, 18mers and 27mers
  Default: false
  

  -strand_constraint <Boolean>

  use the template-based strand-constraints
  Default: false
  

  -vary_frag_size <Boolean>

  pick fragments as long as aligned regions
  Default: false
  

  -no_culling <Boolean>

  dont throw out constraints that are violated by other templates
  Default: false
  

  -helix_pairings <File>

  file with list of pairings that are enforced (pick jumps from templates with H)
  Default: ""
  

  -prefix <File>

  path for config directory – applied to all filenames in template_config_file
  Default: ""
  

  -change_movemap <Integer>

  stage in which movemap is switched to allow all bb-residues to move, valid stages: 3..4 (HACK)
  Default: 3
  

  -force_native_topology <Boolean>

  force the native toplogy (geometries from templates)
  Default: false
  

  -topology_rank_cutoff <Real>

  select jumps from all topologies with a higher relative score than if 1.0 take top 5
  Default: 1.0
  

  -min_frag_size <Integer>

  smallest fragment picked from aligned template regions
  Default: 6
  

  -max_shrink <Integer>

  pick fragments up to max_shrink smaller than aligned regions
  Default: 0
  

  -shrink_step <Integer>

  shrink_step 5 , eg., 27mer 22mer 17mer
  Default: 5
  

  -shrink_pos_step <Integer>

  distance between start pos in shrinked fragments
  Default: 5
  

  -min_padding <Integer>

  minimum space between fragment and gap
  Default: 0
  

  -min_align_pos <Integer>

  ignore aligned residues before this position
  Default: 0
  

  -max_align_pos <Integer>

  ignore aligned residues after this position
  Default: -1
  

• templates:cst

  -cst <Boolean>

  cst option group
  

  -topN <Integer>

  topN ranking models are used for constraints ( culling and source )
  Default: 0
  

  -wTopol <Real>

  weight for beta-pairing topology score in ranking
  Default: 0.5
  

  -wExtern <Real>

  weight for external score ( column in template_config_file, e.g, svn-score
  Default: 0.5
  

• templates:fragsteal

  -fragsteal <Boolean>

  fragsteal option group
  

  -topN <Integer>

  topN ranking models are used for fragment stealing
  Default: 0
  

  -wTopol <Real>

  weight for beta-pairing topology score in ranking
  Default: 0.5
  

  -wExtern <Real>

  weight for external score ( column in template_config_file, e.g, svn-score
  Default: 0.5
  

• unfolded_state

  -unfolded_state <Boolean>

  unfolded_state option group
  

  -unfolded_energies_file <File>

  path to an alternative unfolded state energies file
  

  -split_unfolded_energies_file <File>

  path to an alternative split unfolded state energies file
  

  -split_unfolded_energies_atom_type <String>

  name of the atom type specfied in the file defeined by the split_unfolded_energies_file option
  

• wum

  -wum <Boolean>

  wum option group
  

  -n_slaves_per_master <Integer>

  A value between 32 and 128 is usually recommended
  Default: 64
  

  -n_masters <Integer>

  Manual override for -n_slaves_per_master. How many master nodes should be spawned ? 1 by default. generall 1 for eery 256-512 cores is recommended depending on master workload
  Default: 1
  

  -memory_limit <Integer>

  Memory limit for queues (in kB)
  Default: 0
  

  -extra_scorefxn <String>

  Extra score function for post-batchrelax-rescoring
  

  -extra_scorefxn_ref_structure <File>

  Extra score function for post-batchrelax-rescoring reference structure for superimposition (for scorefunctions that depend on absolute coordinates such as electron denisty)
  

  -extra_scorefxn_relax <Integer>

  After doing batch relax and adding any extra_scorefunction terms do another N fast relax rounds (defaut=0)
  Default: 0
  

  -trim_proportion <Real>

  No description
  Default: 0.0
  

• blivens

  -blivens <Boolean>

  blivens option group
  

• blivens:disulfide_scorer

  -disulfide_scorer <Boolean>

  disulfide_scorer option group
  

  -nds_prob <Real>

  The probability of scoring a non-disulfide pair
  Default: 0.0
  

  -cys_prob <Real>

  The probability of outputing a pair of non-disulf cysteines. Default to nds_prob
  Default: -1.0
  

• blivens

  -score_type <String>

  The scoring type to use, eg for a filter.
  Default: "total_score"
  

• cmiles

  -cmiles <Boolean>

  cmiles option group
  

• cmiles:kcluster

  -kcluster <Boolean>

  kcluster option group
  

  -num_clusters <Integer>

  Number of clusters to use during k clustering
  

• cmiles:jumping

  -jumping <Boolean>

  jumping option group
  

  -resi <Integer>

  Residue i
  

  -resj <Integer>

  Residue j
  

• crossmatch

  -crossmatch <Boolean>

  crossmatch option group
  

  -clash_dis <Real>

  
  Default: 3.0
  

• dwkulp

  -dwkulp <Boolean>

  dwkulp option group
  

  -forcePolyAAfragments <String>

  a single amino acid that will be used for fragment picking,default is blank which means taking actual sequence from pose
  Default: ""
  

• evolution

  -evolution <Boolean>

  evolution option group
  

  -parentlist <FileVector>

  File(s) containing list(s) of Parent PDB files to process
  

  -childlist <FileVector>

  File(s) containing list(s) of Parent PDB files to process
  

  -action <String>

  One of the following: diversify, intensify
  Default: "diversify"
  

  -rms_threshold <Real>

  RMS Clustering threshold
  Default: 3.5
  

  -rms_topmargin <Real>

  RMS Clustering threshold
  Default: 5.0
  

  -targetdir <String>

  Write target new parent polulation to this directory !
  Default: "./"
  

  -padding_score_filter <Real>

  RMS Clustering threshold
  Default: 5.0
  

  -padding_stage2_filter <Real>

  RMS Clustering threshold
  Default: 15.0
  

• james

  -james <Boolean>

  james option group
  

  -min_seqsep <Integer>

  No description
  Default: 0
  

  -atom_names <StringVector>

  No description
  Default: utility::vector1<std::string>()
  

  -dist_thresholds <RealVector>

  No description
  Default: utility::vector1<float>(1, 1.0)
  

  -torsion_thresholds <RealVector>

  No description
  Default: utility::vector1<float>(1, 30.0)
  

  -debug <Boolean>

  No description
  Default: false
  

  -real <Real>

  Option for keeping things real.
  Default: 7.0
  

  -n_designs <Integer>

  total number of designs that James should make.
  Default: 1
  

  -thread_unaligned <Boolean>

  basic_threading without performing an alignment
  Default: false
  

• krassk

  -krassk <Boolean>

  krassk option group
  

  -tail_mode <Boolean>

  No description
  Default: false
  

  -tail_mode_name <Integer>

  No description
  Default: 1
  

  -tail_output_file_name <String>

  No description
  Default: "tail_output"
  

• loodo

  -loodo <Boolean>

  loodo option group
  

  -ins_begin <Integer>

  insertion site (pose numbering)
  

  -cap <String>

  cap pdb
  Default: ""
  

  -bot <String>

  bot pdb
  Default: ""
  

  -fragAlength <IntegerVector>

  lengths for loop A
  

  -fragBlength <IntegerVector>

  lengths for loop B
  

  -known <Integer>

  length of known interior region
  

  -fragAnative <String>

  native loop A pdb file
  Default: ""
  

  -fragBnative <String>

  native loop B pdb file
  Default: ""
  

  -gridligpath <String>

  path to gridlig file
  Default: ""
  

  -debug <Boolean>

  dump CapHitB pdbs
  Default: false
  

  -ca_ratio <Real>

  fraction of C-alphas required in active site grid
  Default: 0.5
  

  -distance_tolerance <Real>

  distance cutoff for pairwise Real6 x,y,z comparisons
  Default: 5.0
  

  -euler_tolerance <Real>

  angle cutoff for pairwise Real6 euler angle comparisons
  Default: 15.0
  

  -num_frags <Integer>

  number fragments to pick per frame in library
  Default: 4500
  

  -use_fraglib <String>

  fragment library to use instead of vall database
  

  -use_fraglibsc <String>

  fragment library to use instead of vall database with sidechain torsions specified
  

  -com_in_grid <Boolean>

  cap center-of-mass required to lie in placement grid
  Default: false
  

  -loud <Boolean>

  loud output?
  Default: false
  

  -dump_all_As <Boolean>

  dump passing As
  Default: false
  

  -dump_all_Bs <Boolean>

  dump passing Bs
  Default: false
  

  -caphit_rt_file <String>

  name of CapHit_RT or filtered CapHitRT file
  

• murphp

  -murphp <Boolean>

  murphp option group
  

  -inv_kin_lig_loop_design_filename <String>

  input filename to be used for inv_kin_lig_loop_design
  

• peptide_deriver

  -peptide_deriver <Boolean>

  peptide_deriver option group
  

  -pep_lengths <IntegerVector>

  Length(s) of derived peptides
  Default: ['10']
  

  -skip_zero_isc <Boolean>

  Makes derivation go faster by skipping peptides with 0 interface score
  Default: true
  

  -dump_peptide_pose <Boolean>

  Output pose with peptide cut out (best one for each chain pair)
  Default: false
  

  -dump_cyclic_poses <Boolean>

  Output each cyclic peptide pose (those that are modeled; which is determined by -optimize_cyclic_threshold)
  Default: false
  

  -dump_prepared_pose <Boolean>

  Output each receptor-partner pose as Peptiderive sees it, i.e. after preparation (minimization and disulfide detection)
  Default: false
  

  -dump_report_file <Boolean>

  Send PeptideDeriver output to a file (<input_name>.peptiderive.txt)
  Default: true
  

  -restrict_receptors_to_chains <StringVector>

  Only use chains listed here as receptors. When empty, consider all chains.
  Default: []
  

  -restrict_partners_to_chains <StringVector>

  Only use chains listed here as partners. When empty, consider all chains. For each receptor-partner pair, a peptide is derived from the partner.
  Default: []
  

  -do_minimize <Boolean>

  Perform minimization before everything.
  Default: true
  

  -optimize_cyclic_threshold <Real>

  Choose value of peptide interface score percent of total isc from which to optimize cyclic peptide
  Default: 0.35
  

  -report_format <String>

  The format of the report. Either 'basic' (easily parsable format) or 'markdown' (pretty, readable, but verbose format).
  Default: "markdown"
  

  -report_gzip <Boolean>

  Gzip report file (only if -dump_report_file is enabled)
  Default: false
  

• phil

  -phil <Boolean>

  phil option group
  

  -nloop <Integer>

  No description
  Default: 10
  

  -vall_file <String>

  No description
  

• ralford

  -ralford <Boolean>

  ralford option group
  

• ralford:dump_rotamers

  -dump_rotamers <Boolean>

  dump_rotamers option group
  

  -rsd_index <Integer>

  Dump all of the rotamers for the amino acid at a user-specified position
  Default: 1
  

  -rotamer_info_prefix <String>

  Prefix for output rotamer information file
  Default: "output"
  

  -write_rotamers_to_pdbs <Boolean>

  Write all of the rotamer poses to pdb files
  Default: false
  

  -all_positions <Boolean>

  Option to dump all rotamers at all positions - use with caution
  Default: false
  

• robert

  -robert <Boolean>

  robert option group
  

  -pairdata_input_pdb_list <String>

  Takes in a file containing a list of pdb locations paired with protocol specific data (eg: one disulfide pair)
  Default: ""
  

  -pcs_maxsub_filter <Real>

  minimum normalized maxsub for PCS clustering protocol
  Default: 0.9
  

  -pcs_maxsub_rmsd <Real>

  maxsub calculation's rmsd threshold
  Default: 4.0
  

  -pcs_dump_cluster <Boolean>

  No description
  Default: false
  

  -pcs_cluster_coverage <Real>

  cluster coverage required
  Default: 0.3
  

  -pcs_cluster_lowscoring <Boolean>

  cluster lowest 20% against lowest 50%
  Default: true
  

• rot_anl

  -rot_anl <Boolean>

  rot_anl option group
  

  -tag <String>

  nametag
  Default: "."
  

  -min <Boolean>

  do sc min
  Default: false
  

  -repack <Boolean>

  
  Default: false
  

  -rtmin <Boolean>

  
  Default: false
  

  -scmove <Boolean>

  
  Default: false
  

  -design <Boolean>

  
  Default: false
  

  -dump_pdb <Boolean>

  dump_pdb when pass thresh
  Default: false
  

  -nloop_scmove <Integer>

  base of scmover loop (total=nloop^n_chi)
  Default: 9
  

• smhybrid

  -smhybrid <Boolean>

  smhybrid option group
  

  -add_cavities <Boolean>

  output cavities in result pdbs
  Default: false
  

  -abinitio_design <Boolean>

  do a design run in centroid mode
  Default: true
  

  -fa_refine <Boolean>

  Do nobu's flxbb
  Default: true
  

  -virtual_nterm <Boolean>

  remove Nterm
  Default: false
  

  -debug <Boolean>

  debug
  Default: false
  

  -refine <Boolean>

  don't do bit centroid moves
  Default: false
  

  -centroid_all_val <Boolean>

  mutate all to VAL in centroid mode
  Default: false
  

  -subsubs_attract <Boolean>

  attract subsubs togeher
  Default: false
  

  -linker_cst <Boolean>

  attract N/C termini for linker
  Default: false
  

  -pseudosym <Boolean>

  HACK pseudosymmetry
  Default: false
  

  -design_linker <Boolean>

  allow design on added 'linker' residues
  Default: true
  

  -design <Boolean>

  allow design on added 'linker' residues
  Default: true
  

  -restrict_design_to_interface <Boolean>

  allow design on added 'linker' residues
  Default: false
  

  -restrict_design_to_subsub_interface <Boolean>

  allow design on added 'linker' residues
  Default: false
  

  -design_hydrophobic <Boolean>

  design all hydrophobic
  Default: false
  

  -add_metal_at_0 <Boolean>

  DEPRECATED
  Default: false
  

  -nres_mono <Integer>

  target number of residues per monomer
  Default: 20
  

  -abinitio_cycles <Integer>

  number of abinitio cycles
  Default: 10000
  

  -primary_subsubunit <Integer>

  primary subunut
  Default: 1
  

  -minbb <Integer>

  level of bb min 0=None 1=little 2=all
  Default: 1
  

  -switch_concert_sub <Integer>

  assume prmary subsub is on this subunit for concerted RB moves
  Default: 1
  

  -temperature <Real>

  MC temp for cen fold
  Default: 2.0
  

  -inter_subsub_cst <Boolean>

  add dis csts inter-subsub
  Default: false
  

  -rb_mag <Real>

  magnitude of rb moves
  Default: 1.0
  

  -symm_def_template <File>

  template for symmetry definition file
  

  -symm_def_template_reduced <File>

  template for reduced symmetry definition file
  

  -attach_as_sc <IntegerVector>

  attach the group via side chain
  

  -attach_as_sc_sub <IntegerVector>

  attach the group via side chain in this sub
  

  -chainbreaks <BooleanVector>

  close chainbreak from this subsub to the next
  

  -design_res_files <StringVector>

  files containing designable residues for each component pose
  Default: ""
  

  -fixed_res_files <StringVector>

  files containing fixed residues (no repack even) for each component pose
  Default: ""
  

  -frag_res_files <StringVector>

  files containing residues ok to insert frags into. will have starting ss
  Default: ""
  

  -scattach_res_files <StringVector>

  files containing residues ok to scattach to.
  Default: ""
  

  -rep_edge_files <StringVector>

  files containing residues which are edge strands.
  Default: ""
  

  -virtual_res_files <StringVector>

  files containing residues that should be virtual
  Default: ""
  

  -jumpcut_files <StringVector>

  file specifying jumps and cuts for subsubunits
  Default: ""
  

  -cst_sub_files <StringVector>

  file specifying which subunits are part of a structural unit and shoudl be constrained
  Default: ""
  

  -symm_file_tag <StringVector>

  label for each subunit
  Default: ""
  

  -attach_atom <StringVector>

  attach atom on each subunit
  Default: ""
  

  -add_res_before <StringVector>

  SS to add before each subunit region
  Default: ""
  

  -add_res_after <StringVector>

  SS to add after each subunit region
  Default: ""
  

  -add_ss_before <StringVector>

  residues to add
  Default: ""
  

  -add_ss_after <StringVector>

  SS to add after each subunit region
  Default: ""
  

  -add_atom_at_cen <StringVector>

  SS to add after each subunit region
  Default: ""
  

  -attach_rsd <StringVector>

  attach rsd on each subunit
  Default: ""
  

• threadsc

  -threadsc <Boolean>

  threadsc option group
  

  -src_chain <String>

  Chain of source pdb
  

  -trg_chain <String>

  Chain of target pdb
  

  -src_first_resid <Integer>

  Residue id of first residue in source pdb range
  

  -trg_first_resid <Integer>

  Residue id of first residue in source pdb range
  

  -nres <Integer>

  Number of residues to be threaded
  

  -trg_anchor <Integer>

  anchor residue for backbone threading
  

• ufv

  -ufv <Boolean>

  ufv option group
  

  -left <Integer>

  left endpoint
  

  -right <Integer>

  right endpoint
  

  -ss <String>

  secondary structure string
  

  -aa_during_build <String>

  amino acid string during centroid build
  

  -aa_during_design_refine <String>

  amino acid string during design-refine
  

  -keep_junction_torsions <Boolean>

  when rebuilding loops, keep (approx) the original torsions at the junctions of the loop endpoints
  Default: false
  

  -ufv_loops <File>

  use this multiple loop file in place of specifying single loop options on command line
  

  -use_fullmer <Boolean>

  use full-mer fragments when building loop
  Default: false
  

  -centroid_loop_mover <String>

  the centroid loop mover to use
  Default: "RemodelLoopMover"
  

  -no_neighborhood_design <Boolean>

  only repack the neighborhood of the loop, don't design
  Default: false
  

  -dr_cycles <Integer>

  design-refine cycles
  Default: 3
  

  -centroid_sfx <String>

  filename of the centroid score function to use,
  

  -centroid_sfx_patch <String>

  filename of the centroid score function patch to use,
  

  -fullatom_sfx <String>

  filename of the full-atom score function to use
  

  -fullatom_sfx_patch <String>

  filename of the full-atom score function patch to use
  

• ufv:insert

  -insert <Boolean>

  insert option group
  

  -insert_pdb <File>

  pdb of insert structure
  

  -attached_pdb <File>

  pdb of structure in rigid body relationship with insert structure
  

  -connection_scheme <String>

  enforce type of insertion: choose either n2c or c2n
  

• willmatch

  -willmatch <Boolean>

  willmatch option group
  

  -write_reduced_matchset <StringVector>

  <name> <pdb1> <pdb2> ...
  

  -interface_size <Real>

  num CB-CB within 8A
  Default: 30
  

  -max_dis_any <Real>

  
  Default: 3.0
  

  -max_dis_all <Real>

  
  Default: 2.6
  

  -max_dis_hb <Real>

  
  Default: 3.2
  

  -min_dis_hb <Real>

  
  Default: 2.2
  

  -max_dis_hb_colinear <Real>

  
  Default: 0.7
  

  -max_dis_metal <Real>

  
  Default: 1.0
  

  -max_ang_metal <Real>

  
  Default: 5.0
  

  -clash_dis <Real>

  
  Default: 3.5
  

  -c2_linker_dist <Real>

  
  Default: 3.5
  

  -identical_match_dis <Real>

  
  Default: 0.0001
  

  -chi1_increment <Real>

  
  Default: 10.0
  

  -chi2_increment <Real>

  
  Default: 20.0
  

  -c2_symm_increment <Real>

  
  Default: 20.0
  

  -cb_sasa_thresh <Real>

  
  Default: 20.0
  

  -design_interface <Boolean>

  
  Default: true
  

  -chilist <File>

  
  

  -fixed_res <File>

  
  

  -native1 <File>

  
  

  -native2 <File>

  
  

  -exclude_res1 <File>

  
  Default: ""
  

  -exclude_res2 <File>

  
  Default: ""
  

  -taglist <File>

  
  

  -residues <IntegerVector>

  
  

  -symmetry_d2 <Boolean>

  
  Default: false
  

  -symmetry_c2_dock <Boolean>

  
  Default: false
  

  -splitwork <IntegerVector>

  
  

  -exclude_ala <Boolean>

  
  Default: false
  

  -match_overlap_dis <Real>

  distance under which to consider matches redundant
  Default: 00.20
  

  -match_overlap_ang <Real>

  ang(deg) under which to consider matches redundant
  Default: 10.00
  

  -forbid_residues <IntegerVector>

  disallow residues for matching
  

  -poi <RealVector>

  xyz coords of some site of interest
  

  -poidis <Real>

  poi distance threshold
  

  -homodimer <Boolean>

  examine only homodimer configs
  Default: false
  

  -fa_dun_thresh <Real>

  
  Default: 6.0
  

• testing

  -testing <Boolean>

  testing option group
  

  -HCF <Boolean>

  Cause Rosetta to exit immediately with an error.
  Default: false
  

  -INTEGRATION_TEST <Boolean>

  Meta flag for best-practices flags in integration tests. Don't use on actual runs.
  Default: false