PyMOL Links

Please submit by mail them with a one line summary to warren@delsci.com

• PyMOL Wiki
  An awesome site maintained by Jason Vertrees.

• eMovie: a storyboard-based tool for making molecular movies
  by Eran Hodis, Gideon Schreiber, Kristian Rother and Joel L. Sussman
• Robert Campbell's PyMOL Script Repository
  A very nice collection of scripts for coloring and crystallography.
• Kristian Rother's Scripts at Bioinformatik
  Including ScriptBox, a one-click script launching tool.
• Gareth Stockwell's PyMOL Scripts at the EBI
  Density slider, rendering, movies, etc.
• Michael Lerner's Useful PyMOL Scripts page
  Including APBS electrostatics interfacing code.
• Cameron Mura's PyMOL Page
  includes a number of helpful examples.

• Movie HOWTO page (David Cooper)
• PyMOL Tips (Kristian Rother)
• PyMOL Tutorial for Windows (Carly Huitema) [mirror]
• Using Alternative Input Devices with PyMOL (Zac Panepucci)
• Gareth Stockwell's PyMOL page at the EBI
• Also, be sure to check out the PyMOL Scripts and Programs Page

• DynMap: a python-based program that generates maps of functional groups present in a protein and visualize them using dynamic parameters (Giacomo Bastianelli)
• Sequence to Structure: display, manipulate, and interconnect RNA data from the sequence to the structure (Fabrice Jossinet)
• STRAP: sequence alignment tool (Christoph Gille)
• NUCCYL: high-quality nucleic acid cartoons (Luca Jovine)

STRAP

NUCCYL

• Flexweb: Analysis of Flexibility in Biomolecules and Networks Provides PyMOL scripts for analyzing protein flexibility and dynamics.
• PROView: A Viewer for RAPTOR / PROSPECT Pro (Bioinformatics Solutions, Inc.), Screenshot, & Related Movie
• PLANET: A Metaphorics Cabinet Server (Metaphorics LLC)

PROView

PLANET

• The Yale Morph Server
  They're using PyMOL for some of their animations.
• AISMIG
  An Interactive Server-side Molecular Image Generator

• Apple's Article on GNU/Darwin and PyMOL

• Marc Saric has compiled an awesome comparison of available molecular graphics programs, including PyMOL. Note that some of the programs he reviews are platform-specific or only free for noncommercial purposes.

• Workarounds
  Tips for compiling PyMOL on various platforms.
   
• Darwin/MacOSX Port of PyMOL
  Michael Love's maintains this port of PyMOL along with other useful scientific packages.
   
• Fink version of PyMOL
  Reportedly easier to install than the above...

• CCP4
  One of the top crystallography packages. PyMOL reads binary CCP4 maps.
   
• CNS
  One of the top crystallography packages. PyMOL reads ASCII format CNS maps.
   
• GAMESS-US
  A powerful, free and open-source ab initio package. PyMOL can write limited input files for GAMESS and interpret GAMESS output, but is far from a front-end at this point. There is also a PyMOL/GAMESS-UK project underway.
   
• ISIS (MDL Information Systems)
  PyMOL can display both 2D and 3D MOL and SD files written by MDL's ISIS suite for chemical informatics. PyMOL is a great tool for viewing virtual ligand screening results on a protein surface.
   
• Macromodel (Schrodinger)
  PyMOL makes an excellent front end to Batchmin provided that you have a means of assigning MMFF atom types for arbitrary structures and are comfortable with batchmin scripts. PyMOL reads and writes Macromodel coordinate files.
   
• Molscript (Avatar Software)
  Although PyMOL is a free replacement for much of Molscript, Molscripts generates uniquely beautiful geometries that can be fed into PyMOL (or Raster3D) for viewing and rendering. It is still worth the inconvenience if you simply must have the absolute highest quality.
   
• X-PLOR
  One of the top crystallography packages. PyMOL reads ASCII format XPLOR maps.
   

• CACTVS
  An excellent free and partially open-source chemistry package.
   

• MMTK
  A Python-based Molecular Modeling Tool-Kit. It is only a matter of time before PyMOL and MMTK are combined, like chocolate and peanut butter coming together. We just need someone who knows both packages to make the dream come true.
   

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