Motifgraft is a is a rosetta implementation which grafts a motif from a source structre into new scaffolds. In order to use motifgraft, three input structures are needed:
- Motif, which is the fragment (or fragments) that the user want to graft.
- Context, which is the protein (or proteins) that interact with the motif.
- Pose (or list of poses), that is the scaffold in which the mover will try to insert the Motif.
I am now trying to use motifgraft to graft a fragment from a complex structure which contains three chains (chain A, H and L) to a set of new scaffolds (around 400 structures). According to the tutorial of motifgraft (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/MotifGraftMover), a XML code for input looks like:
<MotifGraft name="motif_grafting" context_structure="./contextStructure.pdb" motif_structure="./motif_2NM1B.pdb" RMSD_tolerance="1.0" NC_points_RMSD_tolerance="1.0" clash_score_cutoff="5" full_motif_bb_alignment="1" revert_graft_to_native_sequence="1" allow_repeat_same_graft_output="0" />
I select 20 residues in chain H in my source complex structure, save it as a seperate pdb file, and use this file as the input for the option "motif_structure"; Because this motif interact with chain A, I save chain A as a seperate pdb file and use it as the input for the option "context_structure" . Are these input files correct for the MotifGraft Mover?
What I cannot understand now is that these is no option for the input of Pose (scaffold) in the above example xml code. The pose in my situation is a set of structures which I save in a directory named "pose". How should I provide this pose information to the MotifGraft Mover?
Another question is that which rosetta command should be used to call the MotifGraft Mover. I guess it is "rosetta_scripts.default.linuxgccrelease". The name of my input xml code file is "motifgraft.xml", and I guess I should write the command as the following:
$ROSETTA3/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol motifgraft.xml
Am I correct?
Thank you in advance