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

Mac OS users

Latest PyMOL is available in the third-party package managers like Homebrew and MacPorts. See

Linux users

Latest PyMOL can be installed via the native package manager (e.g. yum, pacman) of the Linux distribution. See

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

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


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