PyMOL Links
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PyMOL Wiki
- PyMOL Wiki
An awesome site maintained by Jason Vertrees.
PyMOL Scripts and Programs
Contributed PyMOL User Pages
Open-Source and/or Open-Access Tools Enhanced with PyMOL
Closed-Source and/or Restricted-Access Tools Enhanced with PyMOL
Off-Site Image and Animation Galleries
Articles about PyMOL
Ports
"Supported" Packages (assembly required in some cases)
- 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.
Unrelated Free or Open-Source Packages (Editor's Choice)
- 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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