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Updating documentation for SimpleThreadingMover. #36

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Updating documentation for SimpleThreadingMover.
vmullig Sep 17, 2019
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Reverting unwanted change.
vmullig Sep 17, 2019
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15 changes: 9 additions & 6 deletions scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover_type.md
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Expand Up @@ -4,21 +4,24 @@ _Autogenerated Tag Syntax Documentation:_

---
Author: Jared Adolf-Bryfogle ([email protected])
Modified: Vikram K. Mulligan ([email protected]) 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

```xml
<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;)" />
skip_unknown_mutant="(&bool;)" pack_rounds="(5 &positive_integer;)"
sequence_mode="(oneletter &SequenceMetric_output_modes;)" />
```

- **pack_neighbors**: Option to pack neighbors while threading
- **neighbor_dis**: Distance to repack neighbor side chains. Repack shell distance for each threaded residue
- **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) One letter amino acid sequence we will be grafting. Currently only works for canonical amino acids
- **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 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.
- **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.

---