I often have a disruptive mutation, say a selection winner has leucine to a proline, where design, backrub and even Remodel (with finding neighbours) give a pose with an empirically discordant poor score. Doing a Relax fixes things, but relax is dangerous as it is may find a better minimum for an unrelated loop (say as a helix).
I have been trying to write a Rosetta script to energy-minimize the side chain and backbone of a model but restricted to the neighbourhood of the residue mutated, but I cannot manage. The mutateResidue works fine, but the constrained bb minizing movers do not. How does one get FastRelax, MinMover or other backbone mover to accept the neighbourhood residue selector?
I have tried a few diverse things and found that neighborhood or StoreResidueSubset are not okay in a movemap, BackrubDD does not accept task_operation and so forth...
You will want to use the MoveMapFactory, which accepts a ResidueSelector, and then pass that to the MinMover or FastRelax. In order to not have deletarious downstream effects resulting from the foldtree, I suggest using cartesian mode - IE a cartesian scorefunction and passing the option cartesian=1. Check this for more: https://www.rosettacommons.org/node/10383