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tar -jxf PyMOL-2.2.0_0-Linux-x86_64.tar.bz2
cd pymol; ./pymol
conda install -c schrodinger pymol
The Windows installer is based on Conda, silent mode installation is documented here:
An alternative noinstall-bundle is also available (unzip and run - this version will not create start menu entries): https://pymol.org/installers/PyMOL-2.2.0_0-Win64-portable.zip
Yes, the license file can be placed at
C:\ProgramData\PyMOL\share\pymol\license.lic on Windows)
(Alternative gatekeeper-friendly location on macOS, since PyMOL 2.2.2:
Don't open it. Save it on your workstation and then navigate to it when PyMOL prompts you for a license.
AxPyMOL 2.0.7 is now available.
Please upgrade to PyMOL 2.1 (see driver installation instructions)
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.
Python 3.6 packages are available in our Anaconda channel. Be advised that issues with PyMOL session files and third party plugins or scripts are possible.
Yes, use the pse_export_version setting (please let us know if you experience issues with Python 3.6).
Fixed in 2.1.0, please download the new version.
Also make sure your conda environment has pyqt=5.6 (not 5.9).
Undocking "docked" panels (e.g. Builder, Volume Editor) by dragging their title bar breaks redocking.
Fixed in 2.2.0, please download the new version.
The plugins work, but moving/resizing the window will cause a threading error and PyMOL will crash
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.
The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 2.0 Schrödinger, LLC.
For help with BibTex see: