Hello all, I am working on using PyRosetta to improve a homology-derived protein structure, in which the disulfide bonds are not in their ideal configuration. After playing around with the refinement.py script in the tutorials, I noticed that it was leaving the disulfides untouched in the output results. I noticed in the manual (under TaskFactory) that PyRosetta/Rosetta disables cysteine repacking by default. It wasn't clear to me how to disable this behavior. I tried the following after initializing the packmover:
rr = RestrictResidueToRepacking()
rr.include_residue( 4 )
rr.include_residue( 13 )
tf = standard_task_factory()
...with residues 4 and 13 being the bonded cysteines. It slows the script down tremendously, leading me to believe that I am doing it incorrectly (or this is something I shouldn't be touching).