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Author: Jared Adolf-Bryfogle (firstname.lastname@example.org) Modified: Vikram K. Mulligan (email@example.com) 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
<SimpleThreadingMover name="(&string;)" pack_neighbors="(false &bool;)" neighbor_dis="(6.0 ℜ)" start_position="(&string;)" thread_sequence="(&string;)" scorefxn="(&string;)" skip_unknown_mutant="(&bool;)" pack_rounds="(5 &positive_integer;)" sequence_mode="(oneletter &SequenceMetric_output_modes;)" />
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.
|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.
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"/>