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Revision as of 16:04, 26 November 2008 by Inchoate (talk | contribs)
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Welcome to the PyMOL Wiki
We are the community-based support site for the popular molecular visualization program, PyMOL.


New Users
New users are encouraged to join. Feel free to add any appropriate content; make an account and get started!
Quick Links
Table of Contents -- updated! Index of all pages PyMOL Cheat Sheet: PDF | Wiki Page
Tutorials Commands Settings: All | Documented
Script Library Plugins See All Categories
Frequently Asked Questions Gallery | Covers About PyMOL
Track: Bugs Feature Req Support Req
News and Updates (archive)
Wiki
♦ We got our 2,000,000th page view!
♦ Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
♦ New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).
♦ New category about PyMOL performance: making the impossible possible, and the difficult easier/faster.
♦ Information about PyMOL and Stereo 3D Displays.
♦ Massively restructured the TOPTOC and make the OLD_TOPTOC for the older version. Still need to add more content to the TOPTOC.
♦ Added a simple script for removing specific alternately located atoms.
♦ Added a starter gallery of PyMOL-created Journal Covers.
♦ Added some information on how PyMOL handles Nonstandard_Amino_Acids.
♦ Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been very fortunate to have hosting from BitGnome.Net; they've done an incredible job!
Gallery -- Did you make a cool image? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).
070920nature.pdf.jpg Sample Cover from the Covers gallery.
PyMOL
♦ PyMOL now comes with some builtin examples: look in the examples directory of your source tree.
group command has been added.
♦ The truly awesome grid_mode setting has been added.
Ellipsoids representation added for drawing thermal ellipsoids.
Gm1.png Screenshot of Grid Mode in action.
Scripts & Plugins
♦ Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with LoadDir.
LigAlign -- Ligand-based active site alignment and comparison.
♦ Added a simple script for finding the center or mass, or moving a selection to the origin.
ImmersiveViz -- Headtracking user interface for PyMOL (watch the video)!
Colorama --a PyMOL plugin which allows to color objects using adjustable scale bars
ProMOL plugin added. Catalytic site prediction, other tools. Redirects to website.
EMovie plugin added. Easy movies in PyMol using a GUI.
DYNMAP plugin page created. Check it out!
EZ-Viz
COLORAMA-screenshot.jpg Screenshot of Colorama.