Help! I am trying to energy minimize a protein with distance restraints in cartesian space. Instead of making nice regular bonds and bond angles, I get an arginine side chain that looks like a pitchfork and a phenylalanine ring that looks like somebody stepped on it. After having tried different weight sets and minimizers (FastRelax, MinMover), I am frustrated and need some advice. Has anyone successfully regularized a distorted structure in pyRosetta with the setting MinMover.cartesian(True) ? I don't see any bond length or bond angle weights in any of the wts files.
I am attaching an image showing pitchfork Arg and squashed Phe.
Here is the python script.
rosetta.init(extra_options="-ignore_unrecognized_res -extra_res_fa data/CRO.params data/HOH.params -mute all")
pose = rosetta.pose_from_pdb("1d3b.pdb")
mm = rosetta.MoveMap()
scorefxn = rosetta.create_score_function("score12_full")
minmover = rosetta.MinMover(mm, scorefxn, 'dfpmin_armijo_nonmonotone', 0.01, True)