We have a campus-wide license agreement for PyMOL.  Access to the license keys are limited to current students, faculty, and staff at Stanford.As a subscribing organization, we have access to the latest version of the software, including beta versions, as well as official documentation for using it.  The current license agreement is valid through 12/31/2024.   Please note that AxPyMOL was dropped when we renewed our license agreement. 

Download software and get license key

To get the license key for PyMOL, please send a request to the Science Library using your @Stanford email address.  Please also include your Stanford ID number in the request.

PyMOL 2 — molecular visualization system (PC, Mac, Linux). Please note: you must be on-campus or connected via VPN when downloading and installing but no VPN connection is required when using the software.

• Download PyMOL 2

• PyMOL on the iPad (free)

AxPyMOL - plugin for Windows PowerPoint that enables presentation of 3-D molecular data without having to "tab out" of PowerPoint slides.  Please contact the Science Library

• Download AxPyMOL (Stanford only) (no longer available after 12/31/2021)

Help / Documentation

• PyMOL 2 FAQs
• PyMOLWiki [Current news, tutorials, plugins, scripts]
• About PyMOL 2
• About AxPyMOL (no longer available after 12/31/2021)
• PyMOL Documentation (access limited to subscribers, registration required, request access from the Science Library using your @Stanford email address.