I am trying to replicate some of the examples of the PyRosetta manual and tutorial. I have several problems with the LoopMover_Perturb_CCD. See the code below
1) I am getting the same conformation 10 times (instead of 10 different conformations). Conformations looks the same and have the same energy. Is LoopMover_Perturb_CCD not properly working in PyRosetta or what I am doing wrong?
2) The two commented lines do not work. When uncommented I get the "object has no attribute" message. PyRosetta manual indicates that "randomize_loop(True)" option exist (the other one, I just trying to guess the correct option). How do I get which options are available for a specific function?
3) When applying "switch_to_standard.apply(pose)" I get sidechains with a lots of bumps. I guess I need to minimize the conformations after switching from centroid. I have to use add a minimizer mover or there is and option in LoopMover_Perturb_CCD to minimize and/or recover sidechains properly?
Thanks in advance.
from rosetta import *
pose = pose_from_pdb('test.pdb')
scorefxn_std = create_score_function('standard')
scorefxn_low = create_score_function_ws_patch('cen_std', 'score4L')
frag_set = ConstantLengthFragSet(3, 'frag_test')
switch_to_centroid = SwitchResidueTypeSetMover('centroid')
switch_to_standard = SwitchResidueTypeSetMover('fa_standard')
loop_A = Loop(20,30, 25)
sample_loops = Loops()
loop_perturb = LoopMover_Perturb_CCD(sample_loops, scorefxn_low, frag_set)
- for ite in range(0, 10):
- pose.dump_pdb('test_%03d.pdb' % ite)