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PyMOL

  • Description

    a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

  • Usage

    To list all executables provided by PyMOL, run: $ sbgrid-list pymol Copy to clipboard

  • Usage Notes

    SBGrid non-profit laboratories in North America, Europe, Asia, and Australia have full access to the official incentive builds of PyMOL.

    The SBGrid Consortium PyMOL license is provided with PyMOL in the SBGrid software installation.

    Pymol is installed with the APBS plugin. Your PDB must be in the following format:

    1. No water or ligand molecules
    2. B-factors < 100
    3. No alternative conformations
    4. No partial occupancies

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install pymol Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Citation Note

    Please cite PyMol as follows, editing the version number in accordance with your usage: Schrodinger, LLC. 2010. The PyMOL Molecular Graphics System, Version X.X.

  • Webinars

    PyMOL

    Presenter: Thomas Stewart, Ph.D., Schrödinger
    Topic: A new approach to visual presets in PyMOL (upcoming in PyMOL 3.0)

    Recorded on March 1, 2022
    Host: Pete Meyer

    PyMOL

    Topic: Communicating your research results using PyMOL
    Presenter: Daniel Cappel, Senior Applications Scientist, Schrödinger, Inc.

    Host: Jason Key
    Recorded on September 13, 2016

    PyMOL

    Topic: PyMOL Demo, Hints, and New Features
    Presenter: Thomas Holder, PyMOL Developer, Schrodinger

    Recorded on March 7, 2013

  • Keywords

    Visualization

  • Default Versions

    Linux 64:  3.0.4 (1.0 GB)
    OS X INTEL:  3.0.4 (531.0 MB)

  • Other Versions

      Linux 64:

      1.7.6.6 (392.2 MB) , 1.8.6.0 (493.7 MB) , 2.2.3 (526.1 MB) , 2.5.0_openvr (1.0 GB) , 2.5.5 (837.0 MB) , 2.6.0 (1.1 GB) , 3.0.0 (1.0 GB) , 3.0.2 (1.0 GB)

    • OS X INTEL:

      1.7.6.6 (256.9 MB) , 1.8.6.0 (888.0 MB) , 2.2.3 (438.4 MB) , 2.5.5 (482.8 MB) , 2.5.5_legacy (482.7 MB) , 2.6.0 (549.4 MB) , 3.0.0 (527.6 MB) , 3.0.2 (527.4 MB)
    • Common files size: 2.1 MB

  • Developers

    Thomas Stewart

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