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Please see citation instructions for publications.
tar -jxf PyMOL-2.0.1_0-Linux-x86_64.tar.bz2
cd pymol; ./pymol
conda install -c schrodinger pymol
conda install -c schrodinger qt # required on Linux!
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-2.0.1_0-Win64-portable.zip
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.
Yes, the license file can be placed at
Don't open it. Save it on your workstation and then navigate to it when PyMOL prompts you for a license.
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
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.
Once a volume is loaded, The "C" color button menu in the object panel has a "panel" entry, as well as some presets.
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.
Fixed in 2.0.1, please download the new version.
Fixed in 2.0.1, please download the new version. Please force stereo mode by using '-S' command line flag.
Seen on Windows with certain Intel HD graphics drivers. We are working on a fix.
Floating panels (like the volume editor) should be dockable by dragging them over the PyMOL Window. On macOS, this sometimes doesn't work, panels simply won't dock. Useful hints welcome.
The plugins work, but moving/resizing the window will cause a threading error and PyMOL will crash
Workaround: Don't use the pre-packaged PyMOL bundle. Install Miniconda (2.7 64-bit)
and then install pymol with
conda install -c schrodinger pymol
Solution: install qt package from schrodinger channel:
conda install -c schrodinger qt
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.
The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
The JyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.
The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.8 Schrödinger, LLC.
For help with BibTex see: