Minimization of structure after each trial move in PackRotamersMover

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    • August 17, 2013 at 1:58 am #1695
      Anonymous

        Hi,

        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.

        Troy Wymore

      • August 17, 2013 at 9:57 pm #9207
        Anonymous

          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 #9223
          Anonymous

            Thanks so much for the advice. Here is the list of commands that I used in case it can help someone else.

            In [1]: from rosetta import *

            In [2]: rosetta.init()

            In [3]: pose = pose_from_pdb(“filename.pdb”)

            In [4]: scorefxn = create_score_function(“standard”)

            In [5]: print scorefxn(pose)

            In [6]: task = TaskFactory()

            In [7]: task.push_back(InitializeFromCommandline())

            In [8]: task.push_back(ReadResfile(“filename.resfile”))

            In [9]: s_mover = SequenceMover()

            In [10]: design_mover = MinPackMover()

            In [11]: design_mover.task_factory(task)

            In [12]: design_mover.score_function(scorefxn)

            In [13]: s_mover.add_mover(design_mover)

            In [14]: s_mover.apply(pose)

            In [15]: print pose.residue(90).name()
            SER

            In [16]: print pose.residue(135).name()
            VAL

            In [17]: scorefxn.show(pose)

            In [18]: pose.dump_pdb(“filename-redesign.pdb”)

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