scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) Modified: Vikram K. Mulligan (vmulligan@flatironinstitute.org) to add support for noncanonicals. This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. Useful when combined with -parser:string_vars option to replace strings within the RosettaScript. For more a more fancy comparative modeling protocol, please see the lovely RosettaCM

References and author information for the SimpleThreadingMover mover:

SimpleThreadingMover Mover's author(s): Jared Adolf-Bryfogle, The Scripps Research Institute, La Jolla, CA [jadolfbr@gmail.com]

<SimpleThreadingMover name="(&string;)" pack_neighbors="(false &bool;)"
        neighbor_dis="(6.0 &real;)" start_position="(&string;)"
        thread_sequence="(&string;)" scorefxn="(&string;)"
        skip_unknown_mutant="(&bool;)" pack_rounds="(5 &positive_integer;)"
        sequence_mode="(oneletter &SequenceMetric_output_modes;)" />

pack_neighbors: Option to pack neighbors while threading. By default, only the mutated residues, and not the neighbors, are repacked.
neighbor_dis: Distance to repack neighbor side chains. Repack shell distance for each threaded residue. Default 6.0 Angstroms.
start_position: (REQUIRED) Position to start thread. PDB numbering (like 30L) or Rosetta pose numbering. PDB numbering parsed at apply time to allow for pose-length changes prior to apply of this mover
thread_sequence: (REQUIRED) The residue sequence that we will be grafting. This can be provided as one-letter codes (e.g. "RSTX[DASP]LNE", comma-separated three-letter codes (e.g. "ARG,SER,THR,DAS,LEU,ASN,GLU"), base-names (e.g. "ARG,SER,THR,DASP,LEU,ASN,GLU"), or full names (e.g. "ARG,SER:N_Methylation,THR,DASP,LEU,ASN,GLU"), depending on the setting for sequence_mode.
scorefxn: Optional Scorefunction name passed - setup in score function block
skip_unknown_mutant: Skip unknown amino acids in thread_sequence string instead of throwing an exception.
pack_rounds: Number of packing rounds for threading. Set this to 0 to skip all packing, in which case the new side-chains will likely be in very poor conformations. Defaults to 5.
sequence_mode: The format for the input sequence. Allowed output formats are: oneletter, threeletter, basename, or fullname.

scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover_type