PyMOL Support


Professional Support


  • PyMOL Incentive User Area

    Incentive PyMOL subscribers receive access to documentation, installation instructions, and narrated screencasts through the PyMOL Incentive User Area.

  • Schrödinger Technical Support

    PyMOL incentive subscribers can contact us with technical questions using the online contact form or by e-mailing help@schrodinger.com.

  • Personalized Support and Training Sessions

    PyMOL representatives are available for personalized support and training sessions at your site. Contact us for more information.


Community-Sponsored Resources


  • The PyMOLWiki

    Visit the PyMOLWiki for tutorials, scripts, plugins, answers to frequently asked questions, and more. A user-maintained knowledge base, the PyMOLWiki is full of helpful information.

  • PyMOL Users Mailing List

    Users can also subscribe to the PyMOL Users Mailing List to participate in conversations with a dedicated base of knowledgeable users, and to stay up-to-date on the latest PyMOL tips and news. Thousands of archived conversations can also be browsed through this Mailing List.


Citing PyMOL, AxPyMOL, and JyMOL


Please see citation instructions for publications.

PyMOL Installation


On Windows

On a Mac

  • Double-click on *.dmg file
  • Drag PyMOL icon to Applications folder

On Linux

  • Unpack the .tar.bz2 file, e.g.: tar -jxf PyMOL-2.0.2_0-Linux-x86_64.tar.bz2
  • Run PyMOL with: cd pymol; ./pymol

With existing Anaconda installation

  • We recommend Python 2.7 for production use
  • conda install -c schrodinger pymol
  • conda install -c schrodinger qt # required on Linux with Anaconda 4.4!
    The Anaconda 4.4 qt package on Linux has broken OpenGL support, use the package from the schrodinger channel. The package is also fixed in Anaconda 5.0.0 and in conda-forge.

License installation

  • Download the license file. Save it on your workstation and then navigate to it when PyMOL prompts you for a license.

Supported Operating Systems and Hardware


PyMOL v2.0

  • 64-bit Windows 7 or newer
  • 64-bit macOS 10.9+
  • 64-bit Linux, including CentOS 6+, Ubuntu 12.04+, and others (glibc 2.12+)

AxPyMOL v1.8

  • Microsoft Windows XP, Vista, Win7, Win8, Win10
  • Microsoft Office 2003 to 2016
  • 32-bit and 64-bit where available

Frequently Asked Questions

How to do silent installation on Windows?

The Windows installer is based on Conda, silent mode installation is documented here: https://conda.io/docs/user-guide/install/windows.html#install-win-silent
An alternative noinstall-bundle is also available (unzip and run - this version will not create start menu entries): https://pymol.org/installers/PyMOL-2.0.4_0-Win64-portable.zip

Plugins are not initialized by default. Is there a setting?

This was a conservative approach for the initial release of PyMOL 2.0. There is no setting yet to skip the manual initialization. We'll remove the extra step in a future update.

Can the license file be installed globally instead of per user?

Yes, the license file can be placed at $PREFIX/share/pymol/license.lic

What do I do with my new license file?

Don't open it. Save it on your workstation and then navigate to it when PyMOL prompts you for a license.

Where is AxPyMOL 2.0?

The improvements in PyMOL 2.0 don't affect AxPyMOL, that's why we haven't released AxPyMOL 2.0 (yet). AxPyMOL 1.8.6 is compatible with session files from PyMOL 2.0

3Dconnexion Space Navigator does not work

PyMOL 2.0 currently has no built-in space navigator support. Support is available in MacPyMOL 1.8.6, and on Linux with the spaceball plugin.

Will PyMOL also work with other Python installations (system Python, Homebrew, MacPorts, etc.)?

Most likely not. But if you miss a Python package, it's very likely available from Anaconda Cloud! All our bundles are based on the Anaconda Python distribution and ship with the conda package manager.

Does PyMOL support Python 3?

We recommend Python 2.7 for production use! Python 3.6 packages for macOS and Linux are available in our Anaconda channel. Be advised that issues with PyMOL session files and third party plugins or scripts are possible.

Can PyMOL 2.0 export Session Files for PyMOL 1.x?

Yes, use the pse_export_version setting (no support yet for Python 3.6)

Known Issues

"D-Bus library appears to be incorrectly set up"

Fixed in 2.0.4, please download the new version.

PyMOL won't launch because of conflicting PYTHONHOME and QT_PLUGIN_PATH

Fixed in 2.0.4, please download the new version.

Quad-buffered stereo not working in Linux

Fixed in 2.0.1, please download the new version. Please force stereo mode by using '-S' command line flag.

Panel docking on macOS

Undocking "docked" panels (e.g. Builder, Volume Editor) by dragging their title bar breaks redocking.
Workaround: Always undock by using the icon in the title bar.

On Windows, some "old" plugin windows (e.g. APBS Tools2.1) can't be moved or resized

The plugins work, but moving/resizing the window will cause a threading error and PyMOL will crash

On Linux with default Anaconda installation: "RuntimeError: OpenGL initialization failed"

Solution: install qt package from schrodinger channel: conda install -c schrodinger qt

Citing PyMOL, JyMOL and AxPyMOL


Citation Format

Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the version number in accordance with your usage. If you use BibTex or EndNote, download the handy citation files below.

  • PyMOL

    The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.

  • JyMOL

    The JyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.

  • AxPyMOL

    The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.8 Schrödinger, LLC.

BibTex Files

For help with BibTex see:

EndNote Files