Displaying side-chain rotamers in PyMol

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    • #2002
      Anonymous

        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())

            mut.apply(short_pose)    

            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

            pymol_mover.keep_history(True)

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

            

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

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

                short_pose.residue(1).set_all_chi(rotamers.rotamer(i).chi())

                

                #short_pose.pdb_info().name(rotamers.rotamer(i).name1()+str(i))

                pymol_mover.apply(short_pose)

         

            pymol_mover.keep_history(old_keep_history)

         

         

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