SimpleThreadingMover

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SimpleThreadingMover

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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.

Details

It does the threading by calling the MutateResidueMover, and then does a repacking. Optionally repack neighbors so we save one more step.

A sequence can be provided in one of several formats, with the input format specified with the sequence_mode option. The table below gives the available sequence modes, and shows how to specify the tetrapeptide sequence L-aspartate, L-phenylalanine, D-tryptophan, D-alanine.

Sequence mode	Input sequence description	Example
oneletter	A string of amino acid one-letter codes. Additional '-' characters indicate that a position is to be skipped in the thread. An 'X', followed by a full basename in square brackets (e.g. `X[ORN]`) can be used to specify non-canonical building-blocks.	DFX[DTRP]X[DALA]
threeletter	A string of amino acid three-letter codes, separated by commas. No whitespace should be included. Additional '-' characters indicate that a position is to be skipped in the thread. A '-' indicates a position to be skipped.	ASP,PHE,DTR,DAL
basename	A string of amino acid base names, separated by commas. No whitespace should be included. Additional '-' characters indicate that a position is to be skipped in the thread. A '-' indicates a position to be skipped.	ASP,PHE,DTRP,DALA
fullname	A string of full amino acid names, including any variant types. Additional '-' characters indicate that a position is to be skipped in the thread.	ASP:NtermProteinFull,PHE,DTRP,DALA:CtermProteinFull

The default is 5 rounds of packing. If the sequence would be threaded past the C-terminus, the returned pose will have the sequence threaded up to the end of the pose - additional residues will not be added or modeled.

SimpleThreadingMover supports symmetric poses.

Overview

In order to run this protocol, you just need to specify the place to start - in rosetta or PDB numbering - and the sequence.
We will parse the PDB numbering on apply time in case there are any pose-length changes until then. Pass the option to repack neighbors for packing.

   <SimpleThreadingMover name="threader" start_position="24L" thread_sequence="TGTGT--GTGT" pack_neighbors="1" neighbor_dis="6"  pack_rounds="5"/>

SimpleThreadingMover