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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!). 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. 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. ♦ PDB Web Services Script -- Example using PyMOL and the PDB Web Services. ♦ 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 Screenshot of Colorama.