Main Page: Difference between revisions

Revision as of 14:11, 30 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.

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.

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.
♦ 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.

@@ Line 97: / Line 97: @@
 | style="padding: 3px 5px 10px 15px;"| &diams; [[MakeVinaCommand]] &#8212; Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
 |-
-| style="padding: 3px 5px 10px 15px;"| &diams; [[DrawMinBoundingBox]] &#8212; Draw the minimum bounding box around your selection.
+| style="padding: 3px 5px 10px 15px;"| &diams; [[DrawBoundingBox]] &#8212; Draw a bounding box around your selection.
 |-
 | style="padding: 3px 5px 10px 15px;"| &diams; Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
@@ Line 109: / Line 109: @@
 | style="padding: 3px 5px 10px 15px;"| &diams; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
 |}
-|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawMinBoundingBox]] in action.
+|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
 |}
 |}