PyMOL is one of a few open-source visualization tools available for use in structural biology. The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language.

PyMOL has the ability to load, manipulate and visualize molecules from a variety of formats and sources. The program can easily be controlled using a menu-driven GUI, or from a large number of commands and/or scripts. A built-in raytracer is available to generate high-quality images of the views generated in the GL portion of the GUI.

PyMOL uses OpenGL Extension Wrangler Library (GLEW) and Freeglut, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver (apbs).

Install this application to view, analyze, and prepare graphics images of proteins and experimental strucural data (e.g. crystallographic, NMR and electron microscopy based).