I'm trying to understand the D070_Refinement.py code posted by the Gray lab on PyRosetta.org. In short, the code basically makes small stabilizing backbone perturbations and repacks the sidechain of random residues in your pose. However, I don't know how many residues get perturbed/repacked. What input parameter specifies the # of residues that get perturbed? The "cycles" parameter is set 9 and is fed to the RepeatMover() function and the comments say that "cycles" affects the amount of sampling, but I'm not don't think think this is what I'm looking for.
Does the PyJobDistributor have any control over the # of residues to perturb? Or is only for parallel processing?
Thanks in advance,