PyMOL Links

This page contains links to various user-maintained internet sites pertaining to PyMOL. Please submit by mail them with a one line summary to warren@delsci.com

NOTE: Links last verified September 13, 2009.

• PyMOL Wiki
  The main community-run site for PyMOL, founded by Jason Vertrees, Ph.D.

• Cameron Mura's PyMOL Page
  includes a number of helpful examples.
• 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.
• Movie HOWTO page (David Cooper)

• Fink: Open-Source PyMOL for Mac OS X.
• GNU/Darwin: Michael Love's port of Open-Source PyMOL and many other scientific software packages.
• Debian:Open-Source PyMOL for Debian (Ubuntu).
• Fedora Open-Source PyMOL for Fedora (RedHat).

• 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)

• Flexweb: Analysis of Flexibility in Biomolecules and Networks Provides PyMOL scripts for analyzing protein flexibility and dynamics.
• PLANET: A Metaphorics Cabinet Server (Metaphorics LLC)

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

This is a collection of key software packages which interoperate with PyMOL

• CCP4
  A top crystallography package. PyMOL reads binary CCP4 maps.
• PHENIX
  Another top crystallography package. PyMOL integrates with PHENIX in various ways.
• CNS
  Another top crystallography package. PyMOL reads ASCII format CNS / X-PLOR maps.
• Maestro (Schrodinger)
  PyMOL can read Maestro files and there is a Maestro Plugin available.
• Molscript (Avatar Software)
  Although PyMOL superceeds Molscript in many ways, Molscript still generates uniquely beautiful geometries that can be fed into PyMOL (or Raster3D) for viewing and rendering. It may still be worth the inconvenience if you simply must have the absolute highest quality.
• MMTK
  A Python-based Molecular Modeling Tool-Kit.