Install PyMOL

Binary from official website

Download PyMOL package from the official website maintained by Schrödinger. This incentive binary version has bundled Python environment and necessary packages.

We recommend using this version of PyMOL due to the easy installation.

Pre-built open-source version

Conda (miniconda/anaconda)[Mac/Linux/Win] users

Open-source pymol has released package on conda.

Please run in the terminal

$ conda create -n pymol-opensource
$ conda activate pymol-opensource
$ conda install -c conda-forge pymol-open-source
$ conda install -c anaconda numpy
$ pymol

Mac OS users

Latest PyMOL is available in the third-party package managers like Homebrew and MacPorts. See https://pymolwiki.org/index.php/MAC_Install.

For Apple Silicon M1/M2 users, Homebrew is a good choice to install PyMOL via “brew install pymol”.

Linux users

Latest PyMOL can be installed via the native package manager (e.g. yum, pacman) of the Linux distribution. See https://pymolwiki.org/index.php/Linux_Install.

For Ubuntu-based distros (e.g. Ubuntu, Pos OS), PyMOL 2.5+ is available in the software repository for 22.04 LTS and later versions. Therefore, it can be easily installed via “sudo apt install python3-pymol”.

PyMOL from Snap and Flatpak package managers has not been tested and it might have issue when installing LModeA-nano as a plugin.

Windows users

Christoph Gohlke from UC Irvine provides the pre-built open-source version of PyMOL for Windows on his website.

Instructions on how to install this pre-compiled PyMOL can be found at

• https://pymolwiki.org/index.php/Windows_Install#Open-Source_PyMOL

• https://omicx.cc/posts/2021-04-20-install-pymol-windows/

• https://www.youtube.com/watch?v=B5GbuAND3IQ

For LModeA-nano to function properly, the PyQt5 package should be installed. One may try “pip install pyqt5” if LModeA-nano has problem while launching.

Compile open-source version

For Linux users who are familiar with compiling programs, it is possible to build the open-source PyMOL from source code on GitHub. Detailed instructions can be found at https://pymolwiki.org/index.php/Linux_Install#Install_from_source.

Note

To make LModeA-nano properly work, the Python environment which compiles the PyMOL source code needs the numpy package installed.