PyMOL, a cross-platform molecular graphics tool, has been widely used for three-dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing, and making movies.

PyMOL Plugins are user-developed modules that extend PyMOL’s capabilities via the Tcl/Tk user interface. In order to use them, you’ll need an Tcl/Tk-based version of PyMOL (on Macs, this means either using Fink or the X11/Hybrid version: copy and rename MacPyMOL. to PyMOLX11Hybrid).

To install from a local file, click the “Choose file…” button. A file chooser will appear. Select the file and press Open. PyMOL will install the script/plugin for you.

Pre-compiled Open-Source PyMOL is available free from Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine. Install the latest version of Python 3 for Windows (e.g., by going to http://www.python.org/downloads/ and choosing the x64 EXE installer).

Package managers. Open-Source PyMOL is available free of charge and may be readily installed via the Homebrew (recommended), MacPorts, or Fink package managers.

Run a Python script from the PyMOLWiki

1. Load a protein structure, e.g. by typing into the PyMOL command line: fetch 1ubq.
2. The bbPlane.py script added the new bbPlane command to PyMOL, type it into the PyMOL command line and hit Enter bbPlane.

Apart from the possible trademark issue, since the original PyMOL was licensed under a permissive license, anyone is free to include it in a commercial product that expands on the code as long as the original code is freely available.

Moreover, pymol also provides free licence for students. For Windows, you can get precompiled open source PyMOL from http://www.lfd.uci.edu/~gohlke/pythonlibs/. You can find the open source version on GitHub: https://github.com/schrodinger/pymol-open-source to install under Linux.

Order PyMOL and AxPyMOL Online Educational subscriptions to PyMOL are available at no cost to full-time students and educators teaching full-time students.

However, PyMOL comes with a python distribution that should be located in this directory. ( E:/{my/folder/directory}/pymol2/PyMOL-2.3. 2_81-Win64-portable-py37/PyMOL/python.exe ). This has the PyMOL python package amongst others (NumPy, BioPython.

PyMOL (Schrödinger, 2015) is one of the most popular molecular graphics programs in the bioinformatics and structural biology communities.

PyMOL is one of the few open-source model visualization tools available for use in structural biology. The Py part of the software’s name refers to the program having been written in the programming language Python.

PyMOL Plugins need to be installed in the following directory: On Windows, this is usually: On Macintosh, with MacPyMOL launching in X11/Hybrid mode, you need to right-click and “Show Package Contents” on the PyMOLX11Hybrid bundle and copy the plugin into:

The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate “-X #” (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support.

Plugins are external modules that add functionality to PyMOL. Plugins can be single Python files (*.py) or directories with an __init__.py file (see PluginArchitecture ). Looking for available Plugins?

To run PyMOL with a native PyQt library (linked against macOS OpenGL framework, not against XQuartz), it needs to be built with the –osx-frameworks option: To use the electrostatics plugin, you will need APBS and its dependencies.