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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[ConnectedCloud]] -- find connected clouds of objects in PyMOL.
| style="padding: 3px 5px 10px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[MakeVinaCommand]] -- Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
| style="padding: 3px 5px 10px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[DrawMinBoundingBox]] -- Draw the minimum bounding box around your selection.
| style="padding: 3px 5px 10px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[DrawMinBoundingBox]] — Draw the minimum bounding box around your selection.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
| style="padding: 3px 5px 10px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
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| style="padding: 3px 5px 10px 15px;"| ♦ Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
| style="padding: 3px 5px 10px 15px;"| ♦ Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦  [[PDB Web Services Script]] -- Example using PyMOL and the PDB Web Services.
| style="padding: 3px 5px 10px 15px;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦  [[LigAlign]] -- Ligand-based active site alignment and comparison.
| style="padding: 3px 5px 10px 15px;"| ♦  [[LigAlign]] — Ligand-based active site alignment and comparison.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
| style="padding: 3px 5px 10px 15px;"| ♦ Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.

Revision as of 08:55, 20 March 2009

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
♦ 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.
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
♦ 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.
♦ DrawMinBoundingBox — Draw the minimum 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 DrawMinBoundingBox in action.
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