Guides
Wayfinders for our collections, tools, and servicesCHEM 143: The Chemical Principles of Life II: Molecular visualization tools
Visualizing molecules in 3D
We have a campus-wide license agreement for PyMOL and AxPyMOL. 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 license agreement is valid through 12/31/2024.
License Keys
Access to the license keys are limited to current students, faculty, and staff at Stanford. The license key for PyMOL 2 is located on the Download PyMOL 2 page. To get the license key for AxPyMOL, please send a request to sciencelibrary@stanford.edu using your @Stanford email address. Please also include your Stanford ID number in the request.
Download
PyMOL 2 — molecular visualization system (PC, Mac, Linux).
- Download PyMOL 2 (Stanford only)
- Download PyMOL 2 license file (Stanford only)
- PyMOL 2 FAQs
- PyMOLWiki [Current news, tutorials, plugins, scripts] | PyMOL DokuWiki [Legacy documentation]
- About 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 Grace Baysinger,
- Download AxPyMOL (Stanford only)
- About AxPyMOL
Tutorials
- PyMOL tutorials (YouTube, by Molecular Memory)
3D and 2D views for Caffeine monohydrate
Access WebCSD
WebCSD is the web interface to Cambridge Structural Database (CSD) without the need to install any software. Contains published crystallographic data on organic, organometallic, and metal complex structures whose 3D structures have been determined using X-ray diffraction or neutron diffraction. Updated weekly, WebCSD is available to Stanford students, faculty, and staff.
Features of WebCSD
- Substructure searching
- Similarity searching (only available in WebCSD)
- Text/numeric searching (journal reference, compound name, all text)
- Reduced cell searching
- Database browsing
- Customizable 3D display using embedded viewer (Elemental by Dotmatrics) — no local software installation required. External viewers also supported.
- Single pane results window
- Easy structure and result export features
