Displaying side-chain rotamers in PyMol

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    • #2002

        What is the most elegant way to display rotamers in PyMol?

        This is a spin-off from this question.

        I have a basic implementation working here. I had the most problems since doing r.pose_from_sequence(‘Z’) was not working.

        Any suggestions about improving this are welcome.


        def display_rotamers(pose, rotamers,  pymol_mover):

            “””Displays al the rotamers (allready built) at a given rotamers.resid()

            using the given pymol_mover


            #there must be a better way to create a one amino acid pose, but I can’t find it

            #Problem is with R1A or Z residue. pose_from_sequence does not seem to work

            #doing r.pose_from_sequence(‘Z’) reports that residue can not be found 

            short_pose = r.pose_from_sequence(‘G’, auto_termini=False)

            mut = r.MutateResidue(1 , rotamers.rotamer(1).name3())


            short_pose.copy_segment(1, pose, 1, rotamers.resid())

            old_keep_history = pymol_mover.keep_history()


            #add the rotamers as pymol states. remember the old keep_history setting


            short_pose.pdb_info().name(rotamers.rotamer(1).name1()+str( rotamers.resid()))


            for i in range1(rotamers.num_rotamers()):

                #print rotamers.rotamer(i).chi()









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