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tar -jxf PyMOL-2.1.0_0-Linux-x86_64.tar.bz2
cd pymol; ./pymol
conda install -c schrodinger pymol
conda install -c schrodinger qt # required on Linux with Anaconda 4.4!
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-2.1.0_0-Win64-portable.zip
Please upgrade to PyMOL 2.1 (This was a conservative approach for the initial release of PyMOL 2.0)
Yes, the license file can be placed at
C:\ProgramData\PyMOL\share\pymol\license.lic on Windows)
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.
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.
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.
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.
The plugins work, but moving/resizing the window will cause a threading error and PyMOL will crash
Solution: install qt package from schrodinger channel:
conda install -c schrodinger qt
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: