From 89f120f4f46e3a2332792d68a358241dfa6e7ae8 Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Tue, 17 Sep 2019 19:31:20 -0400 Subject: [PATCH 1/2] Updating documentation for SimpleThreadingMover. --- .../xsd/filter_FragmentScoreFilter_type.md | 2 +- .../xsd/mover_SimpleThreadingMover_type.md | 15 +++++++++------ 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md index cf17faf3b..2886446e5 100644 --- a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md +++ b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md @@ -13,7 +13,7 @@ Filter based on any score that can be calculated in fragment_picker. outputs_name="(pose &string;)" csblast="(&string;)" blast_pgp="(&string;)" placeholder_seqs="(&string;)" sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)" - vall_path="(/scratch/benchmark/W.hojo-1/rosetta.Hojo-1/master/main/database//sampling/vall.jul19.2011.gz &string;)" + vall_path="(/home/vmulligan/rosetta_devcopy_local/Rosetta/main/database//sampling/vall.jul19.2011.gz &string;)" frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)" n_candidates="(1000 &non_negative_integer;)" print_to_pdb="(false &xs:boolean;)" diff --git a/scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover_type.md b/scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover_type.md index 974318b12..33c1730cb 100644 --- a/scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover_type.md +++ b/scripting_documentation/RosettaScripts/xsd/mover_SimpleThreadingMover_type.md @@ -4,21 +4,24 @@ _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 ```xml + 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. --- From 648ee00c9a0a861d29684d61300c3af9c14df72c Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Tue, 17 Sep 2019 19:33:36 -0400 Subject: [PATCH 2/2] Reverting unwanted change. --- .../RosettaScripts/xsd/filter_FragmentScoreFilter_type.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md index 2886446e5..cf17faf3b 100644 --- a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md +++ b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md @@ -13,7 +13,7 @@ Filter based on any score that can be calculated in fragment_picker. outputs_name="(pose &string;)" csblast="(&string;)" blast_pgp="(&string;)" placeholder_seqs="(&string;)" sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)" - vall_path="(/home/vmulligan/rosetta_devcopy_local/Rosetta/main/database//sampling/vall.jul19.2011.gz &string;)" + vall_path="(/scratch/benchmark/W.hojo-1/rosetta.Hojo-1/master/main/database//sampling/vall.jul19.2011.gz &string;)" frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)" n_candidates="(1000 &non_negative_integer;)" print_to_pdb="(false &xs:boolean;)"