Skip to Main Content

Software Licensed by the Science Library: Features and Tools

The Robin Li and Melissa Ma Science Library has purchased campus-wide site licenses for several products. Access to all of these products is limited to current Stanford students, faculty, and staff.

Features of PyMol

VIEW 3D Molecular Structures: Data can be represented in nearly 20 different ways. Spheres provides a CPK-like view, surface and mesh provide more volumetric views, lines and sticks put the emphasis on bond connectivity, and ribbon and cartoon are popular representations for identifying secondary structure and topology. PyMOL's quick demo, accessible through the built-in Wizard menu, gets users started with all of the standard representations. 

RENDER Figures Artistically: An internal ray caster for ray tracing, a graphics technique that enhances shadows and smooths jagged edges, enables the creation of high-resolution 3-D images. With one simple command, users can create custom-­sized and custom-­resolution images in PyMOL. Click here to browse the PyMOLWiki Cover Gallery of publication-quality images that have been generated using PyMOL.

ANIMATE Molecules Dynamically: It's easier than ever to create animations, enabling users to convey molecular results with more impact. Watch the following movies for a glimpse of PyMOL's animation capabilities:

   ► See more movies here

EXPORT PyMOL Geometry: With one simple save command, PyMOL can export geometry data to VRML, Virtual Reality Markup Language. VRML can be used to generate interactive vector graphics and movies using Maya, PovRay and even 3D printers.
PRESENT 3D Data with AxPyMOL: Streamlining presentations just became a lot easier with AxPyMOL, a plugin for Windows PowerPoint that enables presentation of 3-D molecular data without having to "tab out" of PowerPoint slides. During presentation, the PyMOL shows can be manipulated within PowerPoint to display structures using multiple vantage points and rendering schemes set up in advance.

Built-in Tools

  • FreeMOL, including the APBS (Adaptive Poisson-Boltzmann Solver) Plugin for PyMOL
  • RigiMOL, a proprietary molecular morphing software product
  • Open-source implementation of the MMFF94 (Merck Molecular Force Field)
  • MPEG encoder for simplified moviemaking

Additional Conveniences

  • Clipboard support for copying and pasting of images in Windows and Mac
  • A "one window" native user interface with a Tcl/Tk/X11 option (MacPyMOL)
  • Direct export of QuickTime movies (Mac only)
  • For Schrödinger Users: PyMOL for Maestro to easily export data to PyMOL
  • Built-in MTZ Map Reading (and auto loading)
  • Stereochemical labeling (R/S enantiomers)
  • Improved atom typing (MOL2 and MacroModel)
  • Improved real-time rendering quality
  • Improved real-time rendering speed
  • Improved 'undo' command
  • Optimized anaglyph coloring
  • New mouse modes for moving lights
  • Ambient occlusion
  • Surface color smoothing
  • Improved feedback on the 'clean' command
  • Reads compressed PyMOL session files and compressed Maestro files
  • ...and more