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SimpleThreadingMover

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com)

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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

<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;)" />
  • pack_neighbors: Option to pack neighbors while threading
  • neighbor_dis: Distance to repack neighbor side chains. Repack shell distance for each threaded residue
  • 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) One letter amino acid sequence we will be grafting. Currently only works for canonical amino acids
  • scorefxn: Optional Scorefunction name passed - setup in score function block
  • skip_unknown_mutant: Skip unknown amino acid in thread_sequence string instead of throwing an exception
  • pack_rounds: Number of packing rounds for threading. Must be at least 1 so that substitutions are applied.

Details

It does the threading by allowing the task to only enable these residues and then does a repacking. Optionally repack neighbors so we save one more step.

A sequence is just a string, additional '-' charactors denote to skip this position in the thread. Default is 5 rounds of packing.

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"/>

See Also