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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 Index of all pages PyMOL Cheat Sheet: PDF | Wiki Page Tutorials Commands Settings: All | Documented Script Library — updated! Plugins See All Categories Frequently Asked Questions Gallery | Covers About PyMOL Track: Bugs Feature Req Support Req

News and Updates (archive)

PyMOL ♦ PyMOL 1.2 is out! ♦ Check out the artist who integrates PyMOL into his work. ♦ If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with Texture_fonts. ♦ 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 ♦ alphaToAll — Expands your desired alpha-carbon property down to all atoms in the residue. ♦ interfaceResidues — Finds interface residues in a complex. ♦ FindSurfaceResidues — Find and show (if you want) surface exposed resiues in PyMOL. ♦ ToGroup — Converts a multistate object into a group of single state objects. ♦ FindSeq — Find sequence or regular expression of amino acids in a protein. ♦ 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 ♦ Labels page was thoroughly refurbished. ♦ The Wiki experienced a few moments of downtime due to system maintenance. The downtime was <10 minutes. ♦ Please note the "Go" and "Search" buttons in the search bar. They're not the same, and entering text and hitting ENTER is the same as using the "Go" button. Please try using the "Search" button; we're using a new search engine and it has cool new features. ♦ 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.