Access to PyMOL and AxPyMOL software is limited to current students, faculty, and staff at Stanford.

PyMOL software is available on the cluster computers located in libraries, dorms, and the academic virtual desktop.

Stanford Libraries has a campus-wide site license for PyMOL and AxPyMOL. Please note: you must be on-campus or connected via VPN when downloading and installing but no network connection is required when using the software.

License keys are available to all current students, faculty, and staff at Stanford. 

• Stanford email address: Send a request to the Science Library using your @stanford.edu or @slac.stanford.edu email address. 

Our site license enables Stanford users to download software, access documentation, installation instructions, and narrated screencasts through the PyMOL Incentive User Area.  Please request Invoice Number, Invoice User Name, and Invoice Password from the Science Library, providing the same personal information that you would do when requesting a PyMOL license key.  After filling out the online registration form, you will be sent a personalized link by email for accessing  "incentive" content.

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)

Stanford Libraries provides site-licensed access to AxPyMOL, a Windows-only plug-in for embedding 3D images and animations into PowerPoint presentations.  You must register and login to the "incentive" content area in order to download the software.