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PyMOL Installation


On Windows

  • Interactive: Execute the .exe installer and follow the setup wizard
  • Non-interactive (alternative): Equivalent to Miniconda installer
    start /wait "" PyMOL-2.3.4_0-Windows-x86_64.exe /InstallationType=AllUsers /S /D=C:\Programs\PyMOL
  • ZIP Archive: Unzip and run PyMOLWin.exe (does not create start menu entries)

On a Mac

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

On Linux

  1. Unpack the .tar.bz2 file, e.g.: tar -jxf PyMOL-2.2.0_0-Linux-x86_64.tar.bz2
  2. Run PyMOL with: cd pymol; ./pymol

With existing Anaconda installation

  • For PyMOL 2.5+: Transition from previous versions may not work. All dependencies, including python, are based off of conda-forge. More information
    conda install -c schrodinger -c conda-forge pymol
  • For PyMOL 2.4 and older:
    conda install -c schrodinger pymol
  • Hint: Conda works great with isolated environments

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 v3.0+

  • 64-bit Windows 10 or newer
  • 64-bit macOS 12+, including Apple Silicon (M1, M2) with Rosetta 2
  • 64-bit Linux, including CentOS 7+, Ubuntu 20.04+, and others (glibc 2.12+)

PyMOL v2.4+

  • 64-bit Windows 10 or newer
  • 64-bit macOS 10.12+, including Apple Silicon (M1) with Rosetta 2
  • 64-bit Linux, including CentOS 7+, Ubuntu 18.04+, and others (glibc 2.12+)

PyMOL v2.0+

  • 64-bit Windows 7 or newer
  • 64-bit macOS 10.10+
  • 64-bit Linux, including CentOS 6+, Ubuntu 12.04+, and others (glibc 2.12+)

AxPyMOL v2.0+

  • Microsoft 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?

See non-interactive installation.

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

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

  • On Windows: C:\ProgramData\PyMOL\share\pymol\license.lic
  • On macOS: /Applications/PyMOL.app/Contents/share/pymol/license.lic (not gatekeeper-friendly)
    or: /Library/Application Support/Schrodinger/licenses/*.lic (gatekeeper-friendly, since PyMOL 2.2.2)
  • On Linux: $HOME/anaconda3/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.

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.

Can PyMOL 2.0/3.0 export Session Files for PyMOL 1.x/2.x?

Yes, use the pse_export_version setting (please let us know if you experience issues with Python 3).

PyMOL v3.0 Known Issues:

Timeline

  • Occasional crash when reintiailizing PyMOL with scene keyframes in place.
  • Custom programs are currently in preview and will currently not be saved with session file.
  • Timeline actions are not undoable.

Contents Panel

  • ASHLC submenus can occasionally fail to hide properly, resulting in overlapping or floating submenus
    • Workaround: The legacy interface can be toggled under the "Display" system menu
  • Groups within groups are not currently supported
  • Items within groups cannot be reordered
  • Contents panel responsiveness can slow when dealing with a significant number of entries

Presets

  • The presets panel is currently in preview and significant changes to the interface may be implemented in the future
  • Presets cannot be restored individually
  • Certain settings from an applied preset will remain set when another preset is applied

Pre-v3.0 Known Issues:

Previous conda installation workflow not compatible with PyMOL 2.5

For PyMOL 2.5: Transition from previous versions may not work. All dependencies, including python, are based off of conda-forge. More information
Remove all relevant dependencies or create a new environment and:
conda install -c schrodinger -c conda-forge pymol
or
conda install -c schrodinger -c conda-forge pymol-bundle

On macOS: Movie export with ffmpeg broken

The on-demand installation of ffmpeg may install an incompatible version (Error message: dyld: Library not loaded: @rpath/libopenh264.5.dylib). This can be fixed by running the following command in a terminal: /Applications/PyMOL.app/Contents/bin/conda install conda-forge::ffmpeg

On Windows with Intel Graphics: Colors are faded (issue #15)

Set the precomputed_lighting setting (fixed in PyMOL 2.3.0)

Quad-buffered stereo not auto-detected on Linux

Fixed in 2.1.0, please download the new version.
Also make sure your conda environment has pyqt=5.6 (not 5.9).
With pyqt>=5.9 you need to launch PyMOL with pymol -S

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

Fixed in 2.4.0, please download the new version.

.pymolpluginsrc.py invalid syntax error on startup

Remove the file ~/.pymolpluginsrc.py (fixed in PyMOL 2.3.1)

On Windows: UnicodeDecodeError on startup

Remove the file %USERPROFILE%\.pymol\winfiletypes_done.txt (fixed in PyMOL 2.3.1)

On Linux: ImportError: libnsl.so.1

Issue on a default Fedora installation. Please do sudo dnf install libnsl

Citing PyMOL and AxPyMOL


Citation Format

Please cite PyMOL and AxPyMOL 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 3.0 Schrödinger, LLC.

  • AxPyMOL

    The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 3.0 Schrödinger, LLC.

BibTex Files

For help with BibTex see:

EndNote Files