- This topic has 2 replies, 2 voices, and was last updated 10 years, 3 months ago by Anonymous.
August 17, 2013 at 1:58 am #1695Anonymous
I am still relatively new to PyRosetta so excuse my ignorance if the answer to this question is obvious.
I would like to do protein design calculations and the material I have read uses PackRotamersMover. I’m having no problems running these calculations. But I am not sure how to do some minor minimization of the structure after each design move when I apply PackRotamersMover. So when the algorithm outputs at the end that it built X rotamers at Y positions, I would like for it to have done X minimizations too.
Any help with this matter is much appreciated.
August 17, 2013 at 9:57 pm #9207Anonymous
You’re looking for the MinPacker (see protocols.simple_moves.MinPackMover for the friendliest interface). It works exactly like the PackRotamersMover, except that every time it considers a rotamer, it minimizes it first. (It does this throughout the simulated annealing, though, not during the initial build, as minimization will be context dependent.)
August 22, 2013 at 10:31 pm #9223Anonymous
Thanks so much for the advice. Here is the list of commands that I used in case it can help someone else.
In : from rosetta import *
In : rosetta.init()
In : pose = pose_from_pdb(“filename.pdb”)
In : scorefxn = create_score_function(“standard”)
In : print scorefxn(pose)
In : task = TaskFactory()
In : task.push_back(InitializeFromCommandline())
In : task.push_back(ReadResfile(“filename.resfile”))
In : s_mover = SequenceMover()
In : design_mover = MinPackMover()
In : design_mover.task_factory(task)
In : design_mover.score_function(scorefxn)
In : s_mover.add_mover(design_mover)
In : s_mover.apply(pose)
In : print pose.residue(90).name()
In : print pose.residue(135).name()
In : scorefxn.show(pose)
In : pose.dump_pdb(“filename-redesign.pdb”)
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