Skip to Main Content

CHEM 143: The Chemical Principles of Life II: Molecular visualization tools

This guide contains resources to help students learn about biochemistry and to complete class projects.

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 using your @Stanford email address.  Please also include your Stanford ID number in the request.


PyMOL 2 — molecular visualization system (PC, Mac, Linux). 

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,


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 weeklyWebCSD 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


View WebCSD Tutorials (on YouTube)