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! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
|-
|-
| [[TOPTOC|'''Table of Contents''']] -- ''updated!''
| [[TOPTOC|'''Table of Contents''']]
|| [[Special:Allpages|Index of all pages]]
|| [[Special:Allpages|Index of all pages]]
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
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|| '''Settings''': [[Settings|All]]  | [[:Category:Settings|Documented]]
|| '''Settings''': [[Settings|All]]  | [[:Category:Settings|Documented]]
|-
|-
| [[:Category:Script_Library|'''Script Library''']]
| [[:Category:Script_Library|'''Script Library''']] — ''updated!''
|| [[:Category:Plugins|'''Plugins''']]
|| [[:Category:Plugins|'''Plugins''']]
|| [[:Special:Categories| See All Categories]]
|| [[:Special:Categories| See All Categories]]
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|-
|-
| style="padding: 3px 5px 10px 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: 3px 5px 10px 15px;"| ♦ PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
| style="padding: 2px 5px 0px 15px;"| ♦ PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[group]] command has been added.
| style="padding: 2px 5px 0px 15px;"| ♦ [[group]] command has been added.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
| style="padding: 2px 5px 0px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
| style="padding: 2px 5px 0px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
|}
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
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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;"| ♦ [[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 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: 3px 5px 10px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
| style="padding: 2px 5px 0px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
| style="padding: 2px 5px 0px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
| style="padding: 2px 5px 0px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
| style="padding: 2px 5px 0px 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: 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: 3px 5px 10px 15px;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
| style="padding: 2px 5px 0px 15px;"| ♦ [[DrawBoundingBox]] — Draw a 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: 2px 5px 0px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
|-
|-
| 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: 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: 3px 5px 10px 15px;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
| style="padding: 2px 5px 0px 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: 2px 5px 0px 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: 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.
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance.  The downtime was <10 minutes.
| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance.  The downtime was <10 minutes.
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; '''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.
| style="padding: 2px 5px 0px 15px;"| &diams; '''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.
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; 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.
| style="padding: 2px 5px 0px 15px;"| &diams; 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.
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; We got our '''2,000,000th''' page view!
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
| style="padding: 2px 5px 0px 15px;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
|-
|-
| style="padding: 3px 5px 10px 15px;"| &diams; 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;"| &diams; 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: 3px 5px 10px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
| style="padding: 2px 5px 0px 15px;"| &diams; 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:080701_h.a.steinberg_biochemie.jpg|125px]] Sample Cover from the [[Covers]] gallery.
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:080701_h.a.steinberg_biochemie.jpg|125px]] Sample Cover from the [[Covers]] gallery.
|}
|}
|}
|}

Revision as of 09:24, 30 April 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 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
♦ 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!
♦ 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.
Retrieved from "https://pymolwiki.org/index.php?title=Main_Page&oldid=6413"