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Author: Jared Adolf-Bryfogle (firstname.lastname@example.org) 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;)" />
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. 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"/>