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Citing PyMOL, AxPyMOL, and JyMOL
Please see citation instructions for publications.
Links to External Sites
PyMOL Scripts, Programs, and Tips
Cameron Mura's PyMOL Page: includes 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 great 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)
Open-Source PyMOL Ports
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).
Tools Enhanced with PyMOL: Open-Source and Open-Access
DynMap: a python- based program that generates maps of functional groups in a protein and visualizes them using dynamic parameters (Giacomo Bastianelli)
Sequence to Structure: display, manipulate, and interconnect RNA data from a sequence to structure (Fabrice Jossinet)
STRAP: sequence alignment tool (Christophe Gille)
NUCCYL: high-quality nucleic acid cartoons (Luca Jovine)
Tools Enhanced with PyMOL: Closed-Source and Restricted Access
Flexweb: Analysis of Flexibility in Biomolecules and Networks: provides PyMOL scripts for analyzing protein flexibility and dynamics.
PLANET: A Metaphorics Cabinet Server (Metaphorics LLC)
Image and Animation Galleries
Software Packages that Interoperate with PyMOL
Maestro (Schrödinger): PyMOL reads Maestro files; a Maestro Plugin is available.
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.
Molscript (Avatar Software): although PyMOL supercedes Molscript in many ways, Molscript still generates uniquely beautiful geometries that can be fed into PyMOL (or Raster3D) for viewing and rendering.
MMTK: a Python-based Molecular Modeling Tool-Kit