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Welcome to the PyMOL Wiki!

The community-run support site for the PyMOL molecular viewer.

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 ! Plugins See All Categories Frequently Asked Questions Gallery | Covers About PyMOL Track: Bugs Feature Req Support Req GoogleSearch !

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News and Updates (archive)

PyMOL ♦ PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See Installing PyMOL under Fink. ♦ PyMOL now has a Set command for basic settings, and a Set_bond command for bond-only settings. ♦ Space— new command to control PyMOL's usage of color spaces. ♦ CGOCylinder— information on CGO cylinders and circles in 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. Example image from SuperSym, showing cell, symmetry mates and symmetry axes.

Scripts, Plugins & Tutorials ♦ Save2traj — plugin for saving objects to a dcd trajectory file! ♦ SuperSym — plugin for visualizing lots and lots of space groups! ♦ Autodock_Plugin — New PyMOL plugin for interacting with AutoDock (including AutoDock Vina) and visualizing results. ♦ Spectrumbar — powerful new script for making custom spectrum bars in PyMOL. ♦ CollapseSel — simple script to compress selection lists: eg. instead of i. 1+2+3+4+5 you get 1-5. ♦ CgoCircle — draw CGO circles in PyMOL; surround objects or selections with circles. ♦ MovieSchool — PyMOL Wiki's Movie School. Learn how to make movies in PyMOL! ♦ 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. Example image from the new script, Spectrumbar. Wiki ♦ Added the new GoogleSearch widget for better searching on the 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! Sample Cover from the Covers gallery.