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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)

PyMOL ♦ PyMOL now integrates seamlessly with MS Powerpoint. See Axpymol. ♦ 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 Caver showing cavities.

Scripts & Plugins ♦ Modevectors — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects. ♦ Pucker — finds the sugar pucker information (phase, amplitude, pucker) for a given selection. ♦ GetNamesInSel — find the names of all objects in a selection. ♦ CalcArea — find the area of any given object/selection; ♦ ConnectedCloud — find connected clouds of objects in PyMOL. ♦ MakeVinaCommand — Use PyMOL to create a valid command line for the new Vina docking software. ♦ DrawBoundingBox — Draw a bounding box around your selection. ♦ Locate loaded PyMOL objects that are nearby some other object with FindObjectsNearby. ♦ 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. Screenshot of DrawBoundingBox in action. Wiki ♦ Documented a few more settings. Also, check out the cool, Huge_surfaces page for handling very large objects and representing them as surfaces, in PyMOL. ♦ 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. Sample Cover from the Covers gallery.