Main Page: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 56: Line 56:
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
| style="padding: 2px 5px 0px 15px;"| ♦ '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
|-
| style="padding: 2px 5px 0px 15px;"| ♦ PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[group]] command has been added.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
|}
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Image_large.png|125px]] Screenshot of [[Caver]] showing cavities.
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Image_large.png|125px]] Screenshot of [[Caver]] showing cavities.
Line 81: Line 73:
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSurfaceResidues]] — Find and show (if you want) surface exposed resiues in PyMOL.
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSurfaceResidues]] — Find and show (if you want) surface exposed resiues in PyMOL.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[ToGroup]] — Converts a multistate object into a group of single state objects.
| style="padding: 2px 5px 0px 15px;"| ♦ [[ToGroup]] — Converts a multistate object into a group of single state objects.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
|-
| style="padding: 2px 5px 10px 15px;"| ♦ [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
| style="padding: 2px 5px 10px 15px;"| ♦ [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
| style="padding: 2px 5px 0px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|-
| style="padding: 2px 5px 0px 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: 2px 5px 0px 15px;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
|-
| style="padding: 2px 5px 0px 15px;"| ♦  [[LigAlign]] — Ligand-based active site alignment and comparison.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ 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 [[DrawBoundingBox]] in action.
|}
|}
{|style="background-color: transparent;" width="100%"
{|style="background-color: transparent;" width="100%"
Line 127: Line 97:
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ We got our '''2,000,000th''' page view!
| style="padding: 2px 5px 0px 15px;"| ♦ We got our '''2,000,000th''' page view!
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ 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).
|-
| style="padding: 2px 5px 0px 15px;"| ♦ New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
|}
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
|}
|}
|}
|}

Revision as of 04:47, 2 July 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 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.
Image large.png 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.
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!
Science090410.jpg Sample Cover from the Covers gallery.
Retrieved from "https://pymolwiki.org/index.php?title=Main_Page&oldid=6964"