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Release Notes

Rosetta 3.14

  • Numerous changes have been made to support the open repository for Rosetta.

  • The worst9mer filter in RosettaScripts has been renamed to Worst9mer.

New tools and apps:

New Movers, Filters, etc:

Performance:

  • -never_rerun_filters option to avoid final rerun of options with RosettaScripts
  • Bin transitions (e.g. for GenKIC) are laziliy loaded in a threadsafe manner
  • Only generate and validate the XML schema once
  • Load ScoreFunctions from disk once, lazily and in a threadsafe manner.
  • PDB loading was optimized
    • Numerous fixes to speed loading in the default case
    • -in:obey_ssbond skips disulfide detection and assumes SSBOND records are correct
    • -fast_restyping uses a faster method for assigning residue types which may work for simple cases (e.g. just protein residues)

Updates:

  • Additional and improved citations
  • Improved error messages
  • Updates to the included Chemical Components Dictionary from the wwwPDB
  • Performance improvements and generalization to Jacobi loop closure algorithm
  • JumpSelector option added to DdgFilter and ShapeComplementarityFilter
  • New BuriedUnsatisfiedPolarsCalculator options, improved error handling
  • Numerous updates to GALigandDock
  • Membrane
    • Membrane solvation derivative updates.
    • Add membrane options for cartesian_ddg
    • Add support for additional membrane geometries such as micelles, bicelles, vesicles and double vesicles.
    • Add membrane protein support to ensemble docking protocol
  • Glycans
    • Add patch for exocyclic branching from aldofuranoses
    • Add a new scoring column for aglycosylated variants for the glycomutagenesis app
    • Muramic acid (Mur) annotated as O3_LACTYL_SUGAR
    • Add methylated, thiolated & propargyl sugars to database
    • Add glycolylated amino sugars
    • Enable bidirectional glycosicdic linkages
    • Add butyryl acylation patch
  • Improvements to mol2genparams.py
    • Add --comment_bonds flag
  • Improvements to molfile_to_params_polymer.py
  • Update parameters for phenylserine (BB8)
  • Allow residues in PDB input to be split into multiple residues based on database information
  • Allow RandomizeBBByRamaPrePro to be used without a residue selector
  • Various updates to SapConstraintEnergy, AddSapConstraintMover, AddSapMathConstraintMover
  • Allow helical_bundle_predict to take a PsiPred file as an alternative to a helix definition file, for canonical amino acid prediction
  • Additional options related to fragment store handling for ConnectChainsMover, FixAllLoopsMover, NearNativeLoopCloser, Worst9mer, StructProfileMover
  • Additional PSSM options for StructProfileMover
  • Add -edensity::periodicity option for periodic boundary conditions in density
  • Various impovements for MultistageRosettaScripts
  • Add better support for noncanonicals to the SimpleThreadingMover
  • Ensure that the energy_based_clustering app writes out the filenames or other descriptors of poses that it clusters.
  • Added sort_scorefxn option to Disulfidize
  • Added logic option to CompoundStatement to use instead of subelements.
  • Add detect_disulfides option to DeleteRegionMover
  • Add logic option to IfMover
  • RandomMover now has the option of repeats for each mover
  • Add dir option to dumpPDB mover
  • Add residue_selector capability for mergePDBmover
  • Adding new score weights for ReplicaDock2.0 protocol
  • Generalize the virtual residue patch
  • Add Thioether lariat structure prediction to simple_cycpep_predict and SimpleCycpepPredictApplication
  • Add support for other crosslink types to CrosslinkerMover
  • Add "db_file_name" option to SampleRotamersFromPDB
  • Allow RDKitMetric to take a multiple-residue chain (e.g. cyclic peptide).
  • Add a symmetric check for MergePDBMover when using residue_selectors
  • Add support for beta-amino acids in macrocycle structure prediction
  • Adjust improper torsion definitions for cart_bonded such that Rosetta can fix mislabeled Q/N H-atoms
  • Add in ability to measure disorder directly from structure ResidueDisorder
  • Enable NamedAtomPairConstraints in constraint file
  • Allow PARCS to read silent files too
  • Allow Dunbrack probability cutoffs to be changed on a per-packer run basis
  • Update version of RDKit being used.
  • Add support for -density_zscores option on density_tools application
  • Add -bbamide flag to per_residue_solvent_exposure application
  • Add -alternative_score_file option to energy_based_clustering for custom scoring
  • Add metric_to_bfactor option to RunSimpleMetricsMover to assign a per residue metric to the Bfactor
  • Add use_pose_name option to DumpPDB mover
  • Add delta_metrics option to InterfaceAnalyzerMover
  • Custom torsions can now be controlled with the DihedralConstraintGenerator
  • Tar file support added for params file reading.
  • The franklin2019 scorefunction has been updated according to Samanta & Gray
  • The integration with BCL has been updated to use the most recent version of BCL.

Bugfixes:

Build System:

  • Compilation fixes for newer operating systems and compilers
    • Apple Silicon (M1) Macs are now supported
    • Linux arm64 should now be supported
  • Added extras=pytorch and extras=pytorch_gpu builds for integration of PyTorch-based machine learning models
  • Less header inclusion for speeder compile

Other:

Rosetta 3.13

New tools and apps:

  • Scientific benchmarking system rejuvenated (and submitted for publication)
  • trRosetta available in C++ Rosetta now. A TensorFlow build (extras=tensorflow or extras=tensorflow_gpu) supports this.
    • trRosetta application for one-and-done structure prediction from sequence or multiple sequence alignment.
    • trRosettaProtocol mover for structure prediction from sequence or multiple sequence alignment in the context of a larger protocol. (Accessible to RosettaScripts, PyRosetta, or C++ code.)
    • trRosettaConstraintGenerator for applying trRosetta constraints based on sequence or multiple sequence alignment in the context of a larger protocol. (Accessible to RosettaScripts, PyRosetta, or C++ code.)
  • Support for new Mac M1 chipset
  • RosettaSurf (protein surfaces)
  • PyMOL-Rosetta hookup can now be "bounced" off a Gray lab server to allow viewing of Rosetta trajectories when the trajectory source is insufficiently configurable
  • epr/deer handling
  • NDM-1 peptide macrocycle design scripts (via RosettaScripts subrepo)
  • helical_bundle_predict -- Fragment-free structure prediction of helical bundle assemblies. Experimental.
  • auto-DRRAFTER
  • Major updates to Updating-RosettaScripts RosettaScripts - in particular APPLY_TO_POSE no longer exists.
  • CitationManager -- A Rosetta module to track which modules were used in a protocol, and to write information to the tracer at the end indicating which papers should be cited.
  • Jacobi loop closure protocol and Jacobian analysis modules
  • restype_converter
  • https://crash.rosettacommons.org/ and a user-assistant script meant to report to it (Rosetta cannot report anything on its own)

New Movers, Filters, etc:

Database:

  • Carbohydrates: lactyl, triose, tetrose, Aldohexofuranosyls, Modified Aldohexofuranoses, to4 / to7 / to9-Neuraminic acid, Ketopentofuranosyls, Quivonose, Ketohexopyranosyls, Aldopentofuranosyls; GLYCAM codes; many other additions to the database
  • Centroid params files for AIB, ORN, DAB, and DAP (common noncanonicals)

Updated or bugfixed classes and modules:

Other:

  • No more noncannonical spelling of "noncanonical"
  • Toned down the famous "Inaccurate G!" error message. It's still bad but now it yells about it less.
  • Non-recursive coordinate update algorithm replaces old recursive version. Useful when multithreading, because stack space for non-primary threads may be limited. Faster and more efficient in general.
  • ResidueTypes have been updated with an eye towards properties for ML
  • Several general fixes for DNA
  • EnzymaticMovers: Adding parsing of nucleic acid sequences to the EnzymaticMover system

Rosetta 3.12

New apps:

New tools:

Performance:

  • multithreaded packing is available. Note that you must build in multithreaded mode.

Updates and bugfixes:

Rosetta 3.11

New applications

Improvements to applications:

  • Non-canonical design conventions (in all applications) have been made consistent with canonical design conventions: task operations can only be used to disable residue types, not to enable them. PackerPalettes have been introduced as an interface element to define the default set of residue types with which to design in the absence of any task operation, allowing non-canonical designers to specify an expanded set of building blocks with which to work.
  • Support for peptoid macrocycle structure prediction in the simple_cycpep_predict application.
  • GALigandDock: density scoring
  • AntibodyModelerProtocol: LoopModeler compatibility
  • The energy_based_clustering_application can now report the number of unique Ramachandran bin strings observed in the clusters produced.
  • RosettaScripts: Output poses are only rescored automatically if the OUTPUT block says to; otherwise the last scoring data is left intact and reported. Improved behavior in both cases.
  • Silent files now work with hbnet , PyRosetta, and SimpleMetrics
  • FARFAR#
  • RosettaAntibodyDesign nanobody compatibility
  • mp_domain_assembly
  • Implemented a Rosetta thread manager to facilitate multithreaded protocol development and to avoid thread explosions when nested requests for multithreaded code execution are made. (Note that this only affects the threaded builds of Rosetta, built with the extras=cxx11thread option.)

New tools and scorefunctions

Improvements/bugfixes to classes:

Miscellaneous:

  • Scientific tests revivification drive
  • General improvements to centralize disk use and remove repeat access, especially w/r/t scoring. This makes Rosetta more usable on ultra-high-processor-count supercomputers without disk hammering when all threads try to grab scorefunction data at once.
  • Jack Maguire did some serious profiling to hunt for inner-loop slowdowns and garnered several a-few-percent performance gains.
  • Threadsafety improvements, especially for the options system
  • Moving towards Python3 everywhere
  • The Npro atom type was incorrectly listed as a hydrogen bond donor
  • Cadmium has been added to the Rosetta database.
  • Added support for linking Rosetta against Tensorflow (extras=tensorflow option during compilation) to facilitate development of machine learning-based protocols.
  • Considerable refactoring of polycubic interpolation code to fix bugs and permit greater generality.

General bugfixes:

  • We know "Cannot normalize xyzVector of length() zero" is cryptic, it annoys us too. There has been work to catch and re-throw this error with extra data so we can better track down the cause. (The best understood cause is 3 colinear atoms, whose incalculable dihedral causes this error).
  • Rosetta's error handling and reporting system has matured to print debugging backtraces less aggressively for better understood crashes, and dump them to disk when appropriate instead of to terminal.
  • Dunbrack sidechain potentials now properly interpolate well locations as angles (eliminating problems at the -180/180 wraparound point). This is still polylinear interpolation, but could easily be switched to Catmull-Rom splines in the future.
  • Rosetta's option system has been refactored for better thread-safety.
  • Bugfixes for N-methyl amino acids. Support that had been temporarily removed for this modification has now been restored.

Rosetta 3.10

New applications

Scoring function improvements

New features

  • SimpleMetrics are coming online to replace the use of no-action Movers and Filters that were used to calculate values
  • Huge stability improvements to the PDB and mmCIF readers
  • Database directory of RelaxScripts. The RosettaCON2018 RelaxScript is under consideration as the next default script - it improves design quality and runs faster to boot.
  • Protein ensembles in small molecule docking
  • Splice updates
  • InterfaceAnalyzerMover compatible with ligands and generally more stable
  • DensityFitResidueSelector
  • InterfaceHydrophobicResidueContacts filter
  • RosettaDock gains adaptive conformer selection and motif dock score
  • SEWING refactor and new needles (ok, ok, new sub-applications). I don't think it's multithreaded yet.
  • FindGlycanSeqonsMover
  • The simple_cycpep_predict application now supports new cyclization chemistries, including side-chain isopeptide bonds (lariats).
  • Tricks to dump minimization trajectories
  • common flag/config/option file support Custom Configurations

Nonprotein chemistries

Glycans

  • Method to output the IUPAC sequence for an individual glycan
  • RingPlaneFlipMover
  • Glycosylation of lipids and nucleotide diphosphates
  • ShearMover works with glycans now
  • Stepwise works better with sugars

RNA

  • Parametrically generated RNA helices bugfixes
  • RNA-protein ddG calculations.
  • DRRAFTER

Oligoureas

  • Support for oligourea design
  • Support for oligourea structure prediction with the simple_cycpep_predict application

Metals

  • CrosslinkerMover can now place octahedral, tetrahedral, square pyramidal, square planar, trigonal planar, and trigonal pyramidal metals.
  • Improvements for auto_setup_metals - particularly it works with centroid mode, and can be invoked from the new SetupMetalsMover within RosettaScripts protocols.

Updates

  • Rosetta's core and database modules are now threadsafe, permitting development of multi-threaded protocols. Rosetta is not broadly multithreaded (some specialty protocols are) and will not be any time soon.
  • UBQ_Gp_LYX-Cterm compatible with a ResidueSelector from which to sample to choose LYX positions
  • RosettaAntibody can take user-defined CDRs via a JSON input, useful for when the automated regex detection fails
  • CoupledMoves and ClashBasedRepackShell
  • UnsatSel
  • -output_ligands_as_separate_chains, causes Rosetta to reassign chain ID of a ligand when it shares with a peptide chain.
  • SnugDock no longer requires an L_HA chain pattern
  • Enzdes use of PDB headers now more user friendly
  • Cartesian mode minimization and cart_bonded is compatible with per-atom control (mainly used for IUPAC-nomenclature compatability of glycan Movemaps). Fixes for cyclic geometry, D-amino acids, and symmetric glycine behavior.
  • BuriedUnsatisfiedHbondFilter gains ddG_style_dont_recalc_surface
  • PyMOLMover hookup is python3 compatible
  • WriteSSEMover
  • SimpleThreadingMover works with symmetry
  • Major refactor of the parametric code underlying the MakeBundle, BundleGridSampler, and PerturbBundle movers.

Bugfixes

Rosetta 3.9

Scorefunction changes

API changes

  • PyRosetta: xyzMatrix now have .xy properties bound as 'data' instead of set/get functions. So if your code accessed this methods directly you will need to refactor it as m.xx(m.xy()) --> m.xx = m.xy

User friendliness

  • Improved the output formatting for errors - in the vanishingly rare case that an error occurs with Rosetta, you are now more likely to get a useful and interpretable error message.
  • Added Common Flag Configurations to make it easier to run Rosetta often and for a variety of use-cases. running-rosetta-with-options#common-options-and-default-user-configuration
  • Reduced memory use in the most memory-intensive step of the build process. You can now build Rosetta on slightly slimmer machines. You probably should not try running Rosetta on those machines anyway.
  • Exception handling rearranged so that Python users will see the string message in C++-thrown exceptions
  • Long-desired, long-delayed tweaks to the 'released' code end users see. The build system is tweaked to:
    • default to the faster release mode
    • aggressively search for compilers/paths (no need to use .default. any longer)
    • Ignore warnings coming from compilers we've not tested on
  • Made the python infrastructure that comes with the C++ code (not PyRosetta, but Rosetta's Python) more Python 2 vs 3 tolerant

New or updated features

Applications

RosettaScripts tools

Miscellaneous

  • bugfixes to PDB->Pose construction logic arising from missing atoms at termini
  • removed unimplemented fa_plane term. A zero-weight fa_plane term was a feature of a large number of scorefunctions, which was planely wrong. This may cause issues using legacy scoring weight sets with Rosetta 3.9: just remove the unused fa_plane term in your weights file.
  • AlignmentAAFinderFilter filter -- Scans through an alignment, tests all possible amino acids at each position, and generates a file of passing amino acids.
  • AlignmentGapInserterFilter filter -- Scans through an alignment and inserts gaps where positions in the alignment are not representative of the chemical environment of the pose sequence. Useful for removing epistasis from a MSA.
  • NearNativeLoopCloser bugfix
  • bugfixes to Cartesian minimization, the cart_bonded term, and especially those two with symmetric Poses
  • symmetric disulfide scoring bugfix
  • PolymerBondedEnergyContainer bugfix
  • LoopModeler optimize the support for fragment based sampling
  • GenKIC bugfixes
  • remodel bugfixes
  • Backrub bugfix
  • Improvements to silent file reading, enabling the reading of some slightly-corrupted silent files. (There remains a lurking bug causing them to occasionally be written in a corrupted state).
  • Compile fixes for GCC 7.1 and 4.9.
  • ERRASER bugfix
  • ScoringGrids and InterfaceScoreCalculator (for ligands) bugfixes
  • Explicit unfolded state energy calculator bugfixes
  • ABEGO bin scoreterm
  • Implementation of mean-field algorithm to predict rotamer or amino acid probability. Can be used to predict specificity profile for protein-protein or protein-peptide interactions.
  • MonteCarloInterface allows users to set protein-protein interface ddG as the energy criterion in MonteCarlo. This partially addresses the often-requested feature to favor binding energy, not total energy, in design operations.
  • voids_penalty design-centric guidance term - nature abhors a vacuum, but Rosetta tends to ignore them. VoidsPenalty detects underpacked regions in protein cores and favors rotamers to fill those gaps.
  • netcharge design-centric guidance term - a superclass of the older "supercharge" idea, this score term lets you target a desired net charge for your design.
  • Old SEWING deprecated but still functional ahead of its replacement
  • LoopAnalyzerMover bugfixes

Nonprotein chemistries

  • Major bugfixes for rotamer scoring for noncanonical sidechains
  • Improvements to internal glycan handing and IO. (For PDB import use the options -auto_detect_glycan_connections and -alternate_3_letter_codes pdb_sugar. For more information, please see WorkingWithGlycans
  • The handling of non-polymeric chemical connections has been improved/simplified. This includes better handling of LINK records in PDB input, as well as removal of the BRANCH_LOWER_TERMINUS residue variant type.
  • Improvements to both automatic and user-specified handling of metal ions
  • A few more lipids are available for explicit membrane modeling (this is distinct from the implicit membrane scorefunction)
  • Better and automatic writing of LINK records in PDB output
  • Rosetta is more able to figure out missing chemistry data automatically:
    • It can guess at torsion parameters when otherwise missing when scoring the cart_bonded (Cartesian minimization) term
    • It is able to automatically generate centroid (nonpolymeric) residue types when the fullatom type is present - great for split centroid/fullatom protocols where the user has created only the fullatom params file for their ligand.
  • Vikram Mulligan has been absolutely on fire adding nonprotein chemistries for cyclic peptides. (He's now hard at work on fire-retardant peptides):
    • trimesic acid, a three-way crosslinker
    • cyclization via disulfide (instead of simply including disulfides)
    • Oligoureas
    • N-methyl amino acids, for getting rid of that pesky backbone hydrogen bond donor
    • 2-aminoisobutyric acid (AIB), a non-canonical, achiral alpha-amino acid that strongly favours helices (both left- and right-handed). AIB is to ALA as bactrian is to dromedary. (That makes glycine a horse).
  • Glycan Relax - Version 2 GlycanTreeRelax

Rosetta 3.8

New RosettaScripts XML

The XML supporting RosettaScripts has been totally refactored. Rosetta now validates input XML files against an "XML Schema", and can better determine at the start of a run if all XML options are legal and functional. The XML reader can now pinpoint errors much more specifically and offers more helpful error messages.

You can now also get commandline help for XML-enabled classes with the -info flag; e.g. -info PackRotamersMover and a blank, formatted template rosetta script by running the rosetta_script application without giving the -parser:protocol option.

A consequence of this refactoring is that pre-Rosetta3.8 XML scripts are usually no longer legal XML - we offer a tool to convert the old style, pseudo-XML into the current format at tools/xsd_xrw/rewrite_rosetta_script.py (this is in the tools toplevel folder, not the main code folder). The vast majority of classes have complete documentation; when you find one that does not, complain to (doc feedbacks email) and let us know!

JD3

A new Job Distributor, JD3, is ready for use. This is mostly invisible to end users, but will allow more complex protocols to be crafted instead of as multi-step and multi-app instructions. Look forward to cool JD3-enabled apps in future releases.

support for more PDBs

Although most improvements were in Rosetta3.7, we continue to improve the fraction of unmodified PDBs Rosetta can handle. (Don't worry - we've always been able to handle canonical protein well - but we are doing an ever-improving job with strange stuff like the GFP fluorophore, chemically concatenated ligands, glycans, RNA, etc).

Cxx11 builds

Rosetta turned on Cxx11 features in its C++. This deprecates the compatibility of a lot of older compilers. See https://www.rosettacommons.org/docs/latest/build_documentation/Cxx11Support for more information.

Executable naming

We've tweaked the build system such that the built executables are named a little more simply. The tripartite names (rosetta_scripts.default.linuxgccrelease) will work as before, but now the two-part names rosetta_scripts.linuxgccrelease) will always point towards the default build, instead of the most recent build.

beta_nov15

We have a new scorefunction brewing! It doesn't have its official name yet, but it is published. You can try it out with -beta_nov15 on command line and <ScoreFunction name="beta_nov15" weights="beta_nov15"> in RosettaScripts in the meantime. Note that the -beta_nov15 commandline flag is necessary for any use of the new scorefunction, since certain scoring-related objects must be initialized differently (meaning that it is not currently possible to score with talaris2014 and beta_nov15 in the same session of Rosetta.)

New Ramachandran potentials

Rosetta's Ramachandran scoring code has been greatly refactored. The software now supports Ramachandran potentials for arbitrary amino acids. These are lazily loaded, so they do not contribute to Rosetta's memory footprint unless they are needed. The refactored Ramachandran code is now part of the rama_prepro score term in the beta_nov15 scorefunction. The Ramachandran scoring also now allows different Ramachandran potentials for positions preceding proline residues and for positions that do not precede proline residues.

New or updated features

RosettaScripts tools

Miscellaneous

  • Transform mover in ligand docking (bugfixes)
  • JD2 MPIWorkPartitionJobDistributor (the better MPI choice for small MPI runs) splits jobs in a way that's more efficient for restarted runs
  • Changes to Dunbrack library binary format caching. As a consequence, do not install Rosetta 3.8 over an existing installation; you will want this library to be rebuilt on first run.
  • mmCIF input and output
  • Bugfix for constraint files affecting the numbering of PDB-numbered residues from chain A
  • HELIX and SHEET record printing to PDBs (-out::file::output_secondary_structure)
  • LINK record printing to PDBS (-out::file::write_pdb_link_records)
  • Bugfix for resfiles with ligand docking
  • Relax: bugfix to -constrain_relax_to_native_coords
  • Code sanitizers and static analysis tools online (helps us write better, more error-proof code - should be invsible to the end-user)
  • Updated SQLite backend; version to 3.16.2 from 3.7.4
  • bugfixes for various not-specifically-supported compilers (gcc 5.4; gcc 6.2.0, clang 3.9.0, and ICC 14.0)

Nonprotein chemistries

  • The simple_cycpep_predict application has had various bugfixes, and now supports quasi-symmetric sampling for peptides with cN or cN/m symmetries.
  • CycpepSymmetryFilter Filters based on whether a peptide has a desired cyclic (c2, c3, c4, etc.) or mirror cyclic (c2/m, c4/m, c6/m, etc.) symmetry.
  • PeptideCyclizeMover bugfixes
  • Glycans:
    • Updates to GlycanRelax, and new methods for handling connectivity of branched glycans (GlycanTreeSet) - use with PyRosetta: pose.glycan_tree_set()

Rosetta 3.7 (internal notes)

(This section in italics should remain hidden from the public wiki.)

3.7 will be Rosetta 2016.32, http://test.rosettacommons.org/revision?id=108&branch=release, https://github.com/RosettaCommons/main/commit/9005cc64587b4189882337bc87783ab96ead263f. See also [https://wiki.rosettacommons.org/index.php/3.7_release_notes_workspace]

Rosetta 3.7 NOT included in release notes

  • These are items that will be omitted from the release notes as incomplete features, but should be listed once finished for 3.8 or whenever
  • XML schema --> covered in 3.8 release notes
  • JD3 --> covered in 3.8 release notes

Rosetta 3.7

New and updated applications

New features and classes

  • A new introductory tutorial system has been added under the demos/tutorial/ directory. These can also be found online at https://www.rosettacommons.org/demos/latest/
    • The introductory tutorials cover both basic concepts (packing, minimization, fullatom/centroid) as well as demonstrations on how to use some of the most commonly used Rosetta protocols (ab inito, comparative modeling, loop modeling, design, protein-protein docking and protein-ligand docking).
    • Additional demos are now listed thematically, to assist in locating relevant demos.
  • Many new ResidueSelectors
  • PDB reading can handle LINK records in most cases
  • "Spell checking" for options: suggestions for the desired option if the user's options are invalid
  • AACompositionEnergy takes fractional compositions in addition to counted-out compositions
  • New score term to penalize peptide sequences that form aspartimide
  • New script for setting up the pyrosetta environment, and the release of PyRosetta-4

Bugfixes

  • loops::restrict_kic_sampling_to_torsion_string repaired (for KIC loop modeling)
  • BridgeChainsMover repaired to match publication

Rosetta 3.6

After releasing Rosetta 3.5 in 2013, Rosetta transitioned to a weekly release system. Rosetta 3.6 is weekly release v2016.13-dev58602. We are marking it as 3.6 to meet the needs of users that require numbered releases instead of weeklies. This large set of release notes collects changes released in weekly releases since their inception.

New scorefunctions:

Since Rosetta 3.5, the default scorefunction was updated two generations, to Talaris2013 and then to Talaris2014 .
We’ve also updated the default minimizer to LBGFS, which is expected to provide better performance on the average problem.

New applications:

New tools:

  • Batch-distances
  • Residue_energy_breakdown
  • Reference poses: store a pose “snapshot” at a particular point in a protocol, and use the residue numbering in that pose to control behavior of modules at a downstream point, even if the residue numbering has changed (due to loop insertion, etc.).
  • Energy function weight optimization (not suggested for end-user use, but if you’re brave…)
  • A large number of RosettaScripts Movers, Filters, TaskOperations, etc. added. These include:
    • Disulfidize: Add disulfide bonds to a pose, trying all permutations to find best disulfide placement.
    • Perturb by torsion bins (InitializeByBins, PerturbByBins movers): Perturb a conformation based on statistical probability of finding residue i in torsion bin B, and residue i+1 in bin B’.
    • GeneralizedKIC mover: general kinematics-based loop closure for arbitrary chains of atoms that can include stretches of canonical or noncanonical backbone, side-chains, ligands, etc.
    • Parametric design tools (MakeBundle, PerturbBundle, and BundleGridSampler movers; BundleReporter filter): fragment-free sampling of coiled-coil tertiary structures. Fully generalized for strands or helices made of canonical or noncanonical building-blocks.
    • LayerDesign and LayerSelector: design with different sets of residue types depending on burial and/or secondary structure. LayerDesignOperation, LayerSelector
  • FeaturesReporter framework for structural analysis using Rosetta (was in 3.5, but is a more complete system now)

Miscellaneous new features:

  • Rosetta’s Boost version updated from 1.46 - > 1.55
  • Internal smart pointer model altered to match C++11, along with other changes looking forward to C++11
  • Major updates to MR-Rosetta
  • Loop Modeling:
    • Extension of KIC loop modeling to non-canonical backbones (beta amino acids, etc) with GeneralizedKIC (see above).
    • Continued development of next-gen KIC, including compatibility with fragments-based modeling
  • Multiple refactorings in the chemistry layers, allowing:
    • Poses with carbohydrates
    • Better support for ribonucleoprotein
    • Support for all ligands in the PDB’s chemical dictionary (note you must install that dictionary separately)
    • Support for runtime manipulation of chemistry (adding/removing atoms)
    • Support for rotamer libraries with arbitrary numbers of backbone torsion dependencies
    • Automatic setup of bonds to metal ions.
  • Much better support for D-amino acids. Mirror-image conformations now score identically with the talaris2013 and talaris2014 scoring functions. D-residues use rotamer and scoring databases for their L-counterparts.
  • Support for mirror-image symmetry operations in symmetric poses, with proper conversion between D- and L-amino acid residue types.
  • Support for non-pairwise-decomposable score terms during packing
  • New non-pairwise-decomposable score term to guide design that penalizes deviations from a desired residue type composition.
    • New “sequence constraints” to control the residue type composition of a sub-region of a structure (e.g. a protein interface) during design.
  • New neighbor radii for canonical amino acids
  • ResidueSelector hierarchy as a selection syntax
  • FloppyTail now compatible with symmetry
  • Much better support for noncanonical residue linkages, such as N-to-C cylization, sidechain-backbone linkages, etc.
  • Full Database support and documentation (SQLITE3, MySQL, etc)

Performance, usability improvements, bug fixes:

  • 10% speed improvement in etable evaluation (faster scoring). Reduced memory use.
  • Automatic backtrace reporting upon crash, for better debugging
  • Beautification: yes, we finally have a codebase-wide single style format, enforced by an external beautification script
  • Repair of the longstanding “ResidueType explosion” malfeature, reducing memory use dramatically and improving Rosetta boot-up time
  • SASA machinery completely overhauled. Default SASA radii changed to the Reduce set, which include hydrogens by default. It was previously using a radii set that was never published. SASA Calc settings can be changed through options system.
  • New documentation wiki

Rosetta 3.5

Released Sunday, June 2, 2013

  • Major updates to relational database support
  • Many new Movers, Filters, TaskOperations, etc
  • NGK "Next Generation" kinematic loop closure
  • Updates to chemically_conjugated_docking apps UBQ_E2_thioester and neighbors (Saha A, Kleiger G, Lewis S, Kuhlman B, Deshaies RJ. Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate. Molecular Cell. In press.)
  • LOOP_DEFINITIONS tag Loop specification within RosettaScripts
  • OUTPUT tag Rescore-on-output option for RosettaScripts
  • ERRASER package for RNA structure correction with or without experimental electron density (NOTE: collaboration with the PHENIX project; requires PHENIX liscenced and installed separately).
  • ResourceManager allows for different command-line arguments and other centrally-managed resources with different jobs within one instantiation of Rosetta
  • OpenCL support - notice only a very few algorithms feature GPU support; general GPU support is not yet present. previous CUDA support removed
  • Updates to the FloppyTail app
  • pmut_scan app upgraded to have support for Rosetta++ alter_spec mode - it scans for destabilizing rather than stabilizing mutations (particularly at protein-protein interfaces)
  • Linear Memory Interaction Graph now works with symmetric poses
  • Enzyme design at protein-protein interfaces
  • Supercharge application (Lawrence MS, Phillips KJ, Liu DR. Supercharging proteins can impart unusual resilience. J Am Chem Soc. 2007 Aug 22;129(33):10110-2.)
  • 3x1 metal-mediated interface design application (Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc. 2012 Jan 11;134(1):375-85.)
  • New demos ERRASER, favor_native_residue, Protocol captures
  • Scoring
    • -use_bicubic_interpolation smooths issues with binned knowledge-based
    • phi-psi based terms (including Ramachandran, p_aa_pp, and Dunbrack (2002 only)
    • centroid radii bugfixes
    • New RNA scoring potentials, for use with ERRASER and PHENIX
    • -analytic_etable_evaluation (affects fa_rep, fa_atr, fa_sol, fa_intra_rep) offers a major memory reduction and removes a derivative discontinuity, at the cost of some speed
    • sasapack and avge scores from Rosetta++
    • Dunbrack 2010 (Dun10) library added. Dunbrack 2008 (Dun08) library deprecated and removed. Note that Dun10 is only available to academic users as part of the Rosetta download at this time; Dun10 must be separately liscenced for commercial users (LINKY). Feel free to contact us via the forums for assistance in installing the Dun10 library.
    • lbfgs minimizer - more efficient for minimization with many DOFs, especially Relax
    • cartesian minimizer - allows minimization of 3D coordinates instead of internal torsions, including minimization of bond lengths and angles
    • -bbdep_omega - backbone-dependent omega torsion scoring term
  • Tools
    • Python scripts for Rosetta output processing (turning scorefiles into score v. RMSD plots, etc.)
    • pdb2vall package - generates a VALL fragment_picker template database from a specified PDB+chain
    • batch_molfile_to_params.py - used for creating large numbers of ligand paramter files (for virtual screening, etc.), script to load silent files directly into PyMOL.

Rosetta 3.4

Released Sunday, March 25, 2012

  • Point mutant scan application: The purpose of this protocol is to increase the stability of a protein of interest with only single or double point mutants.
  • Non canonical amino acid utilities: This feature includes 2 applications:
    1. MakeRotLib - This application creates a noncanonical amino acid rotamer library
    2. UnfoldedStateEnergyCalculator - This application calculates the explicit unfolded state energies.
  • RNA assembly with experimental pair-wise constraints: This code is intended to take an RNA sequence and secondary structure and then give three-dimensional de novo models of the helices and inter-helical motifs, and then build up the complete model from these parts.
  • RNA 3D structure modeling: Added the applications: rna_cluster, rna_minimize and rna_helix
  • RNA loop modeling with stepwise assembly: This method builds single-stranded RNA loops using a deterministic, enumerative sampling method called Stepwise Assembly.
  • Remodeling RNA crystallographic models with electron density constraint: This code is used for improving a given RNA crystallographic model and reduce the number of potential errors in the model (which can evaluated by Molprobity), under the constraint of experimental electron density map.
  • Chemically conjugated docking : These extensions of the UBQ_E2_thioester protocol allow modeling of chemically conjugated proteins (such as ubiquitin tagged to a target) via isopeptide, thioester, and disulfide linkages.
  • RosettaVIP void identification and packing application: This code is intended to take a pdb file with the coordinates for a structural model of a protein with poor hydrophobic packing, and to return a list of mutations that are predicted to fill cavities in the protein core.
  • Relax pdb with allatom constraints: hese scripts relax a pdb (minimize rosetta score) while keeping atoms as close as possible to the original positions in the crystal. It is designed to be used to prepare a structure for subsequent design in rosetta.
  • Beta strand homodimer design: This code was written for a relatively singular application: finding proteins with surface exposed beta-strands, then trying to make and design a homodimer that will form via that beta-strand.
  • DougsDockDesignMinimizeInterface: This protocol was used in the accompanying manuscript to redesign the protein/peptide interface of Calpain and a fragment of its inhibitory peptide calpastatin.

Rosetta 3.3

Released Wednesday, August 31, 2011

  • Includes comprehensive online documentation for users and for developers
  • A library based object-oriented software suite
  • Easy-to-use applications
  • Flexible to incorporate your own protocols
  • New Applications - Rosetta Antibody, Interface Analyzer, DDG Monomer, Multistate Design, Sequence Recovery, Fragment Picker, Interface Design, RosettaRNA, Pepspec Application.
  • Includes the revolutionary new computer game Foldit in stand-alone version

Rosetta 3.2.1

Released Friday, March 11, 2011

  • New feature in Rosetta - RosettaDNA

Rosetta 3.2

Released Friday, March 11, 2011

  • Includes comprehensive online documentation for users and for developers
  • A library based object-oriented software suite
  • Easy-to-use applications
  • Flexible to incorporate your own protocols New Applications - Comparative Modeling, Flexible Peptide Docking, Symmetry Docking, RosettaMatch, Molecular Replacement, Boinc Minirosetta, Cluster Application.
  • Includes the revolutionary new computer game Foldit in stand-alone version