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- 12:16, 29 October 2007 diff hist +17 Publication Quality Images →See Also
- 12:12, 29 October 2007 diff hist +47 m Main Page →Welcome to the PyMOL Wiki
- 12:08, 29 October 2007 diff hist +18 PDB Loader Service →Comments
- 12:01, 29 October 2007 diff hist +39 m Caver
- 12:01, 29 October 2007 diff hist +63 N Category:Surfaces and Voids New page: = Overview = Page for detecting surfaces and voids in proteins. current
- 12:00, 29 October 2007 diff hist -29 m Main Page →News
- 11:59, 29 October 2007 diff hist +299 Older News →Older News
- 11:58, 29 October 2007 diff hist -54 m Main Page →News
- 11:54, 29 October 2007 diff hist +40 Super
- 11:54, 29 October 2007 diff hist +5 m Cealign plugin
- 11:53, 29 October 2007 diff hist +36 Cealign plugin
- 11:53, 29 October 2007 diff hist +50 Kabsch
- 11:53, 29 October 2007 diff hist +107 N Category:Structure Alignment New page: == Overview == PyMOL and its third party software offer some good options for quality structure alignments. current
- 11:52, 29 October 2007 diff hist +24 TOPTOC →PyMolWiki Top-Level Table Of Contents
- 11:51, 29 October 2007 diff hist +39 Align
- 11:49, 29 October 2007 diff hist -10 TOPTOC →PyMolWiki Top-Level Table Of Contents
- 11:48, 29 October 2007 diff hist +5,578 N Plugins Tutorial New page: ==Learn By Example== This tutorial is a more sophisticated version of the PDB Loader Service plugin that is bundled with PyMol. It is a relatively simple plugin, but should prove to b...
- 11:45, 29 October 2007 diff hist +1,487 N Python Integration New page: ==Launching Python programs from PyMOL == Running a Python script from PyMOL, usually the command: <source lang="python"> run script.py </source> Is enough. Of course, the file script.py needs to be in ...
- 11:44, 29 October 2007 diff hist -10 TOPTOC →PyMolWiki Top-Level Table Of Contents
- 11:43, 29 October 2007 diff hist +372 N Surfaces and Voids New page: Help with integrating output from programs that generate/analyse surfaces and voids in molecules. See also: #http://sourceforge.net/search/?group_id=4546&words=cavity&type_of_search=mlis...
- 11:42, 29 October 2007 diff hist -20 TOPTOC →PyMolWiki Top-Level Table Of Contents
- 11:42, 29 October 2007 diff hist +1,185 N Software Codecs New page: == Codecs == I've made movies with the DivX codec and those, in my experience, make the best movies. They take a while to encode, and are large, but have the best output quality. ===Mpl...
- 11:41, 29 October 2007 diff hist -10 m TOPTOC →PyMolWiki Top-Level Table Of Contents
- 11:40, 29 October 2007 diff hist +3,788 N PovRay New page: ==Nice PovRay settings== I typically use the make_pov.py script and "run" it from pymol once to load the function, and then I do ''make_pov('povray.inp')'' to create the povray.inp file. T...
- 18:48, 28 October 2007 diff hist +404 Talk:Main Page
- 18:46, 28 October 2007 diff hist -14 Slerpy Updated a link.
- 18:44, 28 October 2007 diff hist 0 TOPTOC →PyMolWiki Top-Level Table Of Contents
- 18:44, 28 October 2007 diff hist -5 TOPTOC →PyMolWiki Top-Level Table Of Contents
- 18:42, 28 October 2007 diff hist +5,298 N Making Movies New page: ==Encoding video files== ===Animated GIF=== Quality note: Converting to video generally leads to a loss of quality and inflated file sizes. Gif animation gives a good alternative, retaini...
- 06:43, 25 October 2007 diff hist +14 N User:Shiran009 New page: Idiot spammer. current
- 09:55, 12 October 2007 diff hist +177 N Category talk:Software Movies New page: This page isn't being indexed. It should be broken down into its component pages and then those should be linked from here. I wonder how many other pages this is happening to. current
- 12:58, 3 October 2007 diff hist +51 m Talk:Displaying Biochemical Properties
- 12:58, 3 October 2007 diff hist +38 Talk:Displaying Biochemical Properties
- 16:31, 24 September 2007 diff hist +45 Command Line Options
- 16:30, 24 September 2007 diff hist +1 Command Line Options
- 11:41, 20 September 2007 diff hist +57 Cartoon smooth loops →Overview
- 11:40, 20 September 2007 diff hist +250 Cartoon smooth loops
- 09:30, 17 September 2007 diff hist +253 Main Page →News
- 09:26, 17 September 2007 diff hist -103 m Main Page →PyMol
- 09:25, 17 September 2007 diff hist +103 Main Page →Plugins/Scripts
- 14:52, 18 August 2007 diff hist +70 Kabsch →Caveats
- 17:43, 17 August 2007 diff hist +280 m Extend
- 17:14, 17 August 2007 diff hist +61 m Transparency →Overview
- 17:13, 17 August 2007 diff hist +120 Transparency →Overview
- 12:57, 17 August 2007 diff hist +471 MAC Install →Stereo
- 11:54, 31 July 2007 diff hist +646 N Cycle valence New page: ===DESCRIPTION=== '''cycle_valence''' cycles the valence on the currently selected bond. ===USAGE=== <source lang="python"> cycle_valence [ h_fill ] </source> ''h_fill'' = 0; do not update hydrogens...
- 11:49, 31 July 2007 diff hist -16 Torsion
- 11:44, 31 July 2007 diff hist +34 Helicity check
- 11:41, 31 July 2007 diff hist -47 Main Page
- 11:38, 31 July 2007 diff hist -135 m Main Page →Links of Interest
- 16:29, 24 July 2007 diff hist +150 Talk:Cealign plugin
- 00:01, 19 July 2007 diff hist -611 Main Page →Plugins/Scripts
- 20:20, 11 July 2007 diff hist -15 m PyMOLWiki:Searching Removing all content from page current
- 19:55, 9 July 2007 diff hist -2 m Main Page →PyMol
- 18:51, 6 July 2007 diff hist +295 m Label →DESCRIPTION
- 18:48, 6 July 2007 diff hist 0 m Hide Cmd hide moved to Hide: Removing the old cmd prefix.
- 18:47, 6 July 2007 diff hist +32 m Show →PYMOL API
- 18:46, 6 July 2007 diff hist +37 Show →DESCRIPTION
- 00:58, 5 July 2007 diff hist -599 Main Page
- 00:43, 5 July 2007 diff hist +49 Main Page
- 00:43, 5 July 2007 diff hist +633 N DYNMAP New page: ==DYNMAP== DYN-MAP is a PyMol v0.99 plug-in that generates maps of functional groups present in a protein and visualize them using dynamic parameters. Why DYNMAP could be useful: * Visuali... current
- 13:48, 11 June 2007 diff hist +42 N User:Wwwzhudan New page: Idiot spammer. Account suspended. Moron. current
- 13:48, 11 June 2007 diff hist -1,082 m Talk:Main Page Reverted edits by Wwwzhudan (Talk); changed back to last version by Inchoate
- 13:43, 7 June 2007 diff hist +251 Nm Cell New page: == Overview == The unit '''cell''' may be shown by using the '''show''' command. <gallery> Image:Unit_cell.png|Example protein (1N6H) show in the unit cell shown with '''show cell'''. </g... current
- 13:40, 7 June 2007 diff hist +21 N File:Unit cell.png Showing the unit cell current
- 10:00, 4 June 2007 diff hist +12 Png →USAGE
- 10:00, 4 June 2007 diff hist +129 Png
- 09:56, 4 June 2007 diff hist +138 N Super New page: === Overview === '''super''' aligns two selections. '''super''' is more robust and accurate than '''align'''. For syntax, see align.
- 09:56, 4 June 2007 diff hist +200 Align
- 09:10, 14 May 2007 diff hist +175 Zero residues →OVERVIEW
- 14:33, 7 May 2007 diff hist +348 m Zero residues
- 18:10, 14 April 2007 diff hist 0 m Cealign plugin
- 18:10, 14 April 2007 diff hist +61 Cealign plugin →Introduction
- 18:05, 14 April 2007 diff hist 0 N File:Cealign-0.8-RBS.zip current
- 18:04, 14 April 2007 diff hist 0 N File:Cealign-0.8-RBS.tar.bz2 current
- 18:03, 14 April 2007 diff hist -3,595 m Cealign plugin →Updates
- 18:03, 14 April 2007 diff hist -480 m Cealign plugin
- 18:01, 14 April 2007 diff hist +4 Main Page
- 18:01, 14 April 2007 diff hist +229 Cealign plugin →The Code
- 13:54, 11 April 2007 diff hist +154 m Talk:Practical Pymol for Beginners →TODO:
- 23:09, 7 April 2007 diff hist -10 m Cealign plugin →Results From v0.7
- 23:09, 7 April 2007 diff hist -636 Cealign plugin →Results From v0.2
- 23:02, 7 April 2007 diff hist -1,461 m Cealign plugin →Multiple Structure Alignments
- 22:27, 7 April 2007 diff hist +49 m Cealign plugin →Comparison to PyMol
- 22:26, 7 April 2007 diff hist -106 m Cealign plugin →Comparison to PyMol
- 22:25, 7 April 2007 diff hist 0 N File:Cealign ex1.png current
- 22:15, 7 April 2007 diff hist -2 m Cealign plugin →Introduction
- 22:15, 7 April 2007 diff hist -58 m Cealign plugin →Introduction
- 00:44, 7 April 2007 diff hist -251 Main Page →PyMol
- 00:36, 7 April 2007 diff hist -16 m Cealign plugin →Coming Soon
- 00:36, 7 April 2007 diff hist 0 N File:Cealign-0.7.zip current
- 00:36, 7 April 2007 diff hist 0 N File:Cealign-0.7.tar.bz2 current
- 00:35, 7 April 2007 diff hist +127 Cealign plugin →The Code
- 00:19, 7 April 2007 diff hist 0 N File:1cew 1mol.png current
- 00:18, 7 April 2007 diff hist 0 N File:V7 1oan 1s6n.png current
- 00:17, 7 April 2007 diff hist 0 N File:V7 1a15 1b50.png current
- 00:12, 7 April 2007 diff hist 0 N File:V7 2sim 1nsb.png current
- 00:12, 7 April 2007 diff hist 0 N File:V7 1ten 3hhr.png current
- 00:11, 7 April 2007 diff hist 0 m Cealign plugin →Results From v0.7
- 00:11, 7 April 2007 diff hist 0 N File:V7 1rlw 1byn.png current
- 00:10, 7 April 2007 diff hist +1 Cealign plugin →Results From v0.7
- 00:09, 7 April 2007 diff hist 0 N File:V7 1fao 1eaz.png current
- 00:08, 7 April 2007 diff hist 0 N File:V7 1cew 1mol.png current
- 00:05, 7 April 2007 diff hist 0 N File:V7 1cbs 1hmt.png current
- 00:04, 7 April 2007 diff hist -207 Cealign plugin →Results From v0.6
- 15:21, 3 April 2007 diff hist +88 m User:Inchoate
- 12:44, 2 April 2007 diff hist +1,247 N Zero residues New page: == OVERVIEW == This script will renumber all the residues such that the first one is numbered 0. This is often helpful when dealing with alignments. == EXAMPLE == <source lang="python"> zero_residues ...
- 12:38, 2 April 2007 diff hist +9 Category:Script Library
- 12:27, 2 April 2007 diff hist +183 Category:Script Library
- 14:41, 29 March 2007 diff hist +30 Cealign plugin
- 01:34, 27 March 2007 diff hist +1,581 Cealign plugin →Directions
- 01:24, 27 March 2007 diff hist +87 Main Page →PyMol
- 01:10, 27 March 2007 diff hist +46 Cealign plugin →2007-03-27
- 01:09, 27 March 2007 diff hist +296 Cealign plugin →Updates
- 01:06, 27 March 2007 diff hist 0 N File:Cealign-0.6.zip current
- 01:06, 27 March 2007 diff hist +126 Cealign plugin →The Code
- 01:05, 27 March 2007 diff hist 0 N File:Cealign-0.6.tar.bz2 current
- 12:37, 26 March 2007 diff hist +128 m Cealign plugin →Results From v0.6
- 12:36, 26 March 2007 diff hist +2 m Cealign plugin →Results From v0.6
- 12:36, 26 March 2007 diff hist +766 Cealign plugin →Results From v0.2
- 12:35, 26 March 2007 diff hist 0 N File:V6 1cew 1mol.png current
- 12:34, 26 March 2007 diff hist 0 N File:V6 2sim 1nsb.png current
- 12:33, 26 March 2007 diff hist 0 N File:V6 1ten 3hhr.png current
- 12:29, 26 March 2007 diff hist 0 N File:V6 1rlw 1mol.png current
- 12:27, 26 March 2007 diff hist 0 N File:V6 1oan 1s6n.png current
- 12:24, 26 March 2007 diff hist 0 N File:V6 1a15 1b50.png current
- 12:20, 26 March 2007 diff hist 0 N File:V6 1cbs 1hmt.png current
- 12:18, 26 March 2007 diff hist +30 N File:V6 1eaz fao.png cealign v0.6 for 1eaz and 1fao current
- 12:09, 26 March 2007 diff hist +95 m Cealign plugin →Coming Soon
- 23:05, 25 March 2007 diff hist +58 m Cealign plugin
- 19:28, 19 March 2007 diff hist +1,150 Cealign plugin →Troubleshooting
- 07:23, 12 March 2007 diff hist +160 Talk:Main Page →New
- 07:20, 12 March 2007 diff hist +2,935 m Main Page Reverted edits by Fggf (Talk); changed back to last version by Inchoate
- 07:17, 12 March 2007 diff hist +8 Nm User:Fggf New page: Spammer. current
- 14:27, 11 March 2007 diff hist +682 m Objects and Selections →Objects and Selections
- 13:56, 9 March 2007 diff hist +45 Seq view overlay
- 13:54, 9 March 2007 diff hist +331 N Seq view overlay New page: === OVERVIEW === The '''seq_view_overaly''' setting controls whether or not the background of the sequence viewer is opaque or not. === USAGE === <source lang="python"> # make the sequence viewer back...
- 13:54, 9 March 2007 diff hist +234 Seq view →Overview
- 13:49, 9 March 2007 diff hist +540 N Seq view label mode New page: ===OVERVIEW=== The '''seq_view_label_mode''' setting controls the display of the sequence viewer in PyMOL. Currently, the settings are: * 0 = Just the object name and chosen sequence form...
- 13:45, 9 March 2007 diff hist +278 N Seq view label color New page: ===OVERVIEW=== The '''Seq_view_label_color''' setting controls the setting of the color that the information about the sequence in displayed in. ===USAGE=== <source lang="python"> # make the informatio...
- 13:43, 9 March 2007 diff hist +615 N Seq view format New page: === OVERVIEW === The '''seq_view_format''' setting controls how PyMOL displays the sequence viewer. (To turn on the sequence viewer, type, '''set seq_view, on'''.) The available formats ...
- 16:37, 8 March 2007 diff hist +838 N Atom name wildcard New page: ==OVERVIEW== This setting controls whether or not PyMOL will respect wildcards ("*"). PyMOL automatically disables the asterisk wildcard for atom names in PDB structures read which contai...
- 16:33, 8 March 2007 diff hist +4 Settings
- 16:30, 8 March 2007 diff hist +910 m Isomesh →NOTES
- 15:05, 8 March 2007 diff hist -17 m Mesh quality →Syntax
- 15:05, 8 March 2007 diff hist +29 m Mesh quality →Overview
- 19:30, 7 March 2007 diff hist +246 Cealign plugin →Updates
- 19:28, 7 March 2007 diff hist +1,058 Cealign plugin →Multiple Structure Alignments
- 12:47, 7 March 2007 diff hist +229 m Dss →NOTES
- 12:44, 7 March 2007 diff hist +99 m Dss →EXAMPLES
- 12:43, 7 March 2007 diff hist +12 m Dss →DESCRIPTION
- 19:44, 5 March 2007 diff hist +630 N Ray shadows New page: === OVERVIEW === The '''ray_shadows''' setting determines whether or not PyMOL will ray trace shadows. This is also related to the '''ray_shadow''' setting. === SYNTAX === <source lang="python"> # tur...
- 19:43, 5 March 2007 diff hist 0 N File:Ray shadow on.png current
- 19:42, 5 March 2007 diff hist 0 N File:Ray shadow off.png current
- 19:34, 5 March 2007 diff hist +1 Fragment →DESCRIPTION
- 19:31, 5 March 2007 diff hist 0 m Color →B-Factors
- 19:30, 5 March 2007 diff hist +5 m Cartoon color →Overview
- 19:27, 5 March 2007 diff hist +208 m Seq view
- 19:25, 5 March 2007 diff hist +32 Rms cur →USAGE
- 19:24, 5 March 2007 diff hist +9 m Mesh lighting
- 19:23, 5 March 2007 diff hist -1 m Iterate →DESCRIPTION
- 19:22, 5 March 2007 diff hist +30 System →PYMOL API
- 19:22, 5 March 2007 diff hist +47 System →USAGE
- 19:21, 5 March 2007 diff hist +16 m System →DESCRIPTION
- 16:14, 4 March 2007 diff hist -8 m Cartoon Helix Settings →Overview
- 16:12, 4 March 2007 diff hist +1 Cartoon oval quality →Overview
- 16:11, 4 March 2007 diff hist +7 m Cartoon flat cycles →Overview
- 16:11, 4 March 2007 diff hist +29 Cartoon side chain helper →Overview
- 16:07, 4 March 2007 diff hist +95 m Cartoon ring mode →Syntax
- 16:06, 4 March 2007 diff hist -1 Cartoon ring mode →Syntax
- 16:05, 4 March 2007 diff hist +105 m Cartoon ring mode →Overview
- 16:04, 4 March 2007 diff hist +36 Fetch →Example
- 19:58, 26 February 2007 diff hist -1 Cartoon nucleic acid color →Syntax
- 15:58, 24 February 2007 diff hist -22 Fog start →Syntax
- 15:57, 24 February 2007 diff hist -50 Fog →Syntax
- 15:57, 24 February 2007 diff hist -67 Fit →SEE ALSO
- 15:55, 24 February 2007 diff hist +124 N Talk:Fork New page: =Fix= This page should be fixed. It's called '''Fork''', but the text calls it '''spawn''' and the example shows '''run'''! current
- 15:53, 24 February 2007 diff hist +3 Read Molstr
- 15:50, 24 February 2007 diff hist 0 Align →NOTE
- 15:50, 24 February 2007 diff hist +119 Align →DESCRIPTION
- 15:49, 24 February 2007 diff hist +14 m Align →SEE ALSO
- 15:49, 24 February 2007 diff hist +32 Alter State →EXAMPLES
- 15:48, 24 February 2007 diff hist +5 Alter State →DESCRIPTION
- 15:47, 24 February 2007 diff hist +1 m Backface cull
- 02:46, 24 February 2007 diff hist +366 N Cd New page: == DESCRIPTION == Changes PyMOL's current working directory. This useful command allows the user to set the current working directory without having to leave PyMOL. == USAGE == <source lang="python">...
- 02:43, 24 February 2007 diff hist +434 Ls
- 02:43, 24 February 2007 diff hist -12 Pwd
- 02:39, 24 February 2007 diff hist +84 Orthoscopic →Overview
- 02:38, 24 February 2007 diff hist +77 Orthoscopic →Overview
- 02:37, 24 February 2007 diff hist +16 Line smooth →Overview
- 02:34, 24 February 2007 diff hist +3 m Cartoon color →Overview
- 02:24, 24 February 2007 diff hist +24 Ray →DESCRIPTION
- 02:15, 24 February 2007 diff hist +57 Split states →Example
- 02:12, 24 February 2007 diff hist +15 Order →EXAMPLES
- 02:11, 24 February 2007 diff hist +676 Set name →DESCRIPTION
- 13:52, 23 February 2007 diff hist +326 PyMOLWiki:About →Site
- 13:49, 23 February 2007 diff hist +99 PyMOLWiki:Community Portal →How to Get Involved
- 13:48, 23 February 2007 diff hist +148 PyMOLWiki:Community Portal →What to Do
- 13:44, 23 February 2007 diff hist +67 Fetch →Overview
- 13:44, 23 February 2007 diff hist +93 Fetch →Syntax
- 13:43, 23 February 2007 diff hist +121 Fetch →Example
- 13:43, 23 February 2007 diff hist +32 Fetch →Syntax
- 13:42, 23 February 2007 diff hist +575 Ball and Stick
- 13:32, 23 February 2007 diff hist +440 N Ribbon smooth New page: ==Overview== This PyMOL setting determines smoothly how PyMOL draws ribbons. Turning ''on'' the setting smooths out the ribbons and make the image look cleaner. The setting is by default...
- 13:29, 23 February 2007 diff hist +3 Settings
- 13:25, 23 February 2007 diff hist -5 Ray
- 13:20, 23 February 2007 diff hist -16 Ray →Examples
- 13:20, 23 February 2007 diff hist +45 Ray →Examples
- 13:19, 23 February 2007 diff hist +20 Ray →Simple=
- 13:19, 23 February 2007 diff hist +297 Ray →Examples
- 13:18, 23 February 2007 diff hist -250 Ray →EXAMPLES
- 13:18, 23 February 2007 diff hist +447 Ray →Ray-Tracing modes
- 13:14, 23 February 2007 diff hist +697 Ray →Perspective Example Images
- 13:13, 23 February 2007 diff hist -620 m Ray →Ray-Tracing modes
- 13:12, 23 February 2007 diff hist +154 Ray →Ray-Tracing modes
- 13:12, 23 February 2007 diff hist -174 m Ray →Examples
- 13:11, 23 February 2007 diff hist +201 Ray →EXAMPLES
- 13:10, 23 February 2007 diff hist +345 m Ray →DESCRIPTION
- 13:07, 23 February 2007 diff hist +824 Transparency
- 13:04, 23 February 2007 diff hist +49 N File:Surfall 065.png Showing the entire surface with 65% transparency. current
- 13:02, 23 February 2007 diff hist +47 N File:Surf065.png Example showing partial surface transparencies. current
- 12:51, 23 February 2007 diff hist -25 Lines →See Also
- 12:51, 23 February 2007 diff hist +730 Lines
- 12:44, 23 February 2007 diff hist +78 Label →DESCRIPTION
- 03:05, 23 February 2007 diff hist +209 Measure Distance
- 03:03, 23 February 2007 diff hist +4 Measure Distance
- 03:03, 23 February 2007 diff hist +195 Measure Distance
- 03:01, 23 February 2007 diff hist +11 Show →SEE ALSO
- 03:01, 23 February 2007 diff hist +282 Show →EXAMPLES
- 02:59, 23 February 2007 diff hist +201 Show →DESCRIPTION
- 02:56, 23 February 2007 diff hist +46 Iterate →EXAMPLES
- 02:55, 23 February 2007 diff hist +578 Translate →EXAMPLES
- 02:49, 23 February 2007 diff hist +151 Hide →EXAMPLES
- 02:48, 23 February 2007 diff hist +23 Hide →DESCRIPTION
- 02:48, 23 February 2007 diff hist +11 Sphere scale →Syntax
- 02:47, 23 February 2007 diff hist +138 Sphere scale →Syntax
- 02:45, 23 February 2007 diff hist +144 Get View →DESCRIPTION
- 02:44, 23 February 2007 diff hist 0 Set View →DESCRIPTION
- 02:44, 23 February 2007 diff hist +332 Set View →DESCRIPTION
- 02:41, 23 February 2007 diff hist +16 Mpng →DESCRIPTION
- 02:39, 23 February 2007 diff hist +6 Orthoscopic
- 16:04, 20 February 2007 diff hist +155 Kabsch →Update
- 16:03, 20 February 2007 diff hist +64 Kabsch →The New Code
- 16:01, 20 February 2007 diff hist +63 Cealign plugin →2007-02-20
- 16:01, 20 February 2007 diff hist +924 Cealign plugin →Updates
- 15:59, 20 February 2007 diff hist +127 Cealign plugin →The Code
- 15:59, 20 February 2007 diff hist 0 N File:Cealign-0.5.zip current
- 15:59, 20 February 2007 diff hist 0 N File:Cealign-0.5.tar.bz2 current
- 15:57, 20 February 2007 diff hist +82 Main Page →PyMol
- 19:42, 19 February 2007 diff hist +285 Publication Quality Images →High Resolution (DPI) Images