Is there a way of doing SequenceRelax on a loop?
So far I have managed to do simple energy minimization with the attached script:
from rosetta import *
pose = Pose("test_in.pdb")
mm4060 = MoveMap()
loop = Loop(15,24,20)
minmover = MinMover()
scorefxn = create_score_function('standard')
but I would really like to do something more like SequenceRelax to allow side chain repacking and gradient minimization (while ramping up ) if this is possible. I am also not sure how many steps of minimization MinMover does each time I apply it as it continues to find a better minimum each time I call it with apply().
Also it seems to me that the bond lengths and angles do not change with the my attached script except at the cut point but ideally I would like these to move as well if possible.
I hope these questions make sense and I am not asking anything too simple - I do not want to make large scale changes to my loop using CCD, etc just to find a local minimum for a loop conformation I already have.
thanks in advance for your help!