Cannot get PyMOL_mover to work on MacOS

Member Site Forums PyRosetta PyRosetta – General Cannot get PyMOL_mover to work on MacOS

Viewing 2 reply threads
  • Author
    Posts
    • #1161
      Anonymous

        I’ve trying to set up the PyRosetta PyMOL viewer on a MacOS 10.7.3, 64 bit system, but I cannot get PyRosetta to send graphics(?) to PyMOL. The current setup is:
        PyRosetta 2.011 [r46035]
        Python 2.7.1
        PyMOL 1.5.0

        I start PyMOL:
        PyMOL>cd /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/
        cd: now in /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit
        PyMOL>run /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/PyMOLPyRosettaServer.py
        PyMOL <---> PyRosetta link started!
        at 127.0.0.1 port 65000

        Running through the walkthrough in Baugh et al I get:
        >>> from rosetta import*
        >>> init()
        Found rosetta_database at /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/rosetta_database, using it…
        PyRosetta 2.011 [r46035] retrieved from: https://svn.rosettacommons.org/source/trunk/rosetta/rosetta_source
        (C) Copyright Rosetta Commons Member Institutions.
        Created in JHU by Sergey Lyskov and PyRosetta Team.

        core.init: Mini-Rosetta version 46035 from https://svn.rosettacommons.org/source/trunk/rosetta/rosetta_source
        core.init: command: app -database /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/rosetta_database -ex1 -ex2aro
        core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=860947739 seed_offset=0 real_seed=860947739
        core.init.random: RandomGenerator:init: Normal mode, seed=860947739 RG_type=mt19937
        >>>pose=Pose()
        >>>pose=pose_from_pdb(pose,”1d4l.clean.pdb”)
        core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 41

        core.pack.pack_rotamers: IG: 11316 bytes
        >>> pymover=PyMOL_Mover()
        >>> pymover.apply(pose)
        File ““, line 1, in
        Boost.Python.ArgumentError: Python argument types in
        PyMolMover.apply(PyMOL_Mover, NoneType)
        did not match C++ signature:
        apply(PyMolMover_exposer_callback {lvalue}, core::pose::Pose )
        apply(protocols::moves::PyMolMover {lvalue}, core::pose::Pose )
        apply(PyMolMover_exposer_callback {lvalue}, core::pose::Pose {lvalue} )
        apply(protocols::moves::PyMolMover {lvalue}, core::pose::Pose {lvalue} )

        Alternatively I get:
        Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
        [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
        Type “help”, “copyright”, “credits” or “license” for more information.
        >>> from rosetta import*
        >>> init()
        Found rosetta_database at /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/rosetta_database, using it…
        PyRosetta 2.011 [r46035] retrieved from: https://svn.rosettacommons.org/source/trunk/rosetta/rosetta_source
        (C) Copyright Rosetta Commons Member Institutions.
        Created in JHU by Sergey Lyskov and PyRosetta Team.

        core.init: Mini-Rosetta version 46035 from https://svn.rosettacommons.org/source/trunk/rosetta/rosetta_source
        core.init: command: app -database /Users/cno/software/PyRosetta.MacOSX.Lion-r46035.64Bit/rosetta_database -ex1 -ex2aro
        core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1519591611 seed_offset=0 real_seed=1519591611
        core.init.random: RandomGenerator:init: Normal mode, seed=1519591611 RG_type=mt19937
        >>> protease = Pose()
        >>> pose_from_pdb( protease , “1d4l.clean.pdb” )
        ….
        >>> pymover = PyMOL_Mover()
        >>> pymover.apply( protease )
        #Note that no error occurs now!??! Doing it again make pymol talk:
        >>> pymover.apply(protease)
        PyMOL: Buffer clean up: ‘x00x00x00x00x00x00x00x00x00x00x00x00x00x00x00x00x00x00’
        scorefxn=create_score_function(“standard”)
        >>> scorefxn=create_score_function(“standard”)
        >>> scorefxn(protease)
        -157.13907398742094
        >>> pymover.apply(protease)
        >>> pymover.send_energy(protease)
        PyMOL:
        Selector-Error: Invalid selection name “1d4l.clean.pdb”.
        1d4l.clean.pdb and chain A and resi 1<--
        Coloring failed… did you forget to send geometry first?

        Hope you can help. Thanks

      • #6642
        Anonymous

          I think you hitting the bug that we discovered and fixed recently. Please try new binaries, they should work. Its available here http://graylab.jhu.edu/pyrosetta/downloads/release/PyRosetta.MacOSX.Lion-r47373.64Bit.tar.bz2 (you will need to enter the same name and password that you used to download previous version). Let us know how it goes.

        • #6654
          Anonymous

            That fixed the problem! Thanks

        Viewing 2 reply threads
        • You must be logged in to reply to this topic.