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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.
Caver.png 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.
DrawMinBB.png 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.
080701 h.a.steinberg biochemie.jpg Sample Cover from the Covers gallery.