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- 17:41, 1 April 2009 diff hist +58 m Pucker Just made small edits to make the text more clear; also added some "source" stmts
- 17:38, 1 April 2009 diff hist +149 Main Page
- 17:37, 1 April 2009 diff hist +36 Pucker
- 19:53, 31 March 2009 diff hist +122 m Talk:Huge surfaces current
- 16:22, 23 March 2009 diff hist +653 Load →NOTES
- 16:22, 23 March 2009 diff hist -321 Load →DESCRIPTION
- 16:09, 23 March 2009 diff hist +320 Load
- 14:39, 23 March 2009 diff hist -1 GetNamesInSel
- 14:39, 23 March 2009 diff hist -1 GetNamesInSel
- 14:38, 23 March 2009 diff hist +435 GetNamesInSel
- 14:36, 23 March 2009 diff hist +116 GetNamesInSel
- 11:54, 21 March 2009 diff hist +6 Label
- 09:55, 20 March 2009 diff hist +263 Main Page
- 09:52, 20 March 2009 diff hist +634 N CalcArea New page: =Overview= This code will calculate the area of a given selection. If you have a bunch of disparate selections, or one selection made up of various objects then you can use this to find t...
- 09:48, 20 March 2009 diff hist +747 N GetNamesInSel New page: = Overview = This script returns the list of object names that exist in any given selection. For example, if you have 100 objects loaded (viz. ligand poses from small molecule docking) an...
- 12:33, 19 March 2009 diff hist +96 Align →NOTE
- 18:00, 18 March 2009 diff hist +219 Linux Install
- 12:00, 17 March 2009 diff hist +68 Surface →Calculating a partial surface
- 11:59, 17 March 2009 diff hist +85 Get area
- 11:57, 17 March 2009 diff hist +34 ConnectedCloud
- 09:58, 15 March 2009 diff hist +41 Advanced Scripting
- 09:29, 11 March 2009 diff hist +125 Commands
- 09:28, 11 March 2009 diff hist +20 Pymolrc
- 16:23, 2 March 2009 diff hist +124 FindObjectsNearby
- 22:21, 28 February 2009 diff hist +324 As
- 22:17, 28 February 2009 diff hist +43 Nonstandard Amino Acids current
- 22:15, 28 February 2009 diff hist +50 N Category:Biochemical Properties New page: Information about Biochemical Properties in PyMOL. current
- 18:01, 27 February 2009 diff hist -3 Main Page
- 17:42, 27 February 2009 diff hist +175 Category:Script Library
- 17:41, 27 February 2009 diff hist +44 ConnectedCloud
- 17:41, 27 February 2009 diff hist +115 Main Page
- 17:40, 27 February 2009 diff hist +3,845 N ConnectedCloud New page: = Overview = ConnectedCloud grows a cloud of objects that are "connected." Two objects are "connected" if they are within the user-defined cutoff, radius. It starts with a selection,...
- 17:30, 27 February 2009 diff hist +14 N File:ConnectedCloud2.png objects found. current
- 17:29, 27 February 2009 diff hist +24 N File:ConnectedCloud.png Connected cloud to find. current
- 16:55, 26 February 2009 diff hist +3 Main Page
- 16:51, 24 February 2009 diff hist +126 Main Page
- 15:44, 24 February 2009 diff hist +270 N Category:Launching New page: = Overview = PyMOL can be launched in various ways. You can start it normally, from an icon or the commandline. You can also run it in headless mode from scripts and from within a separa... current
- 15:42, 24 February 2009 diff hist +24 Command Line Options
- 09:44, 24 February 2009 diff hist +175 Main Page
- 09:42, 24 February 2009 diff hist +3,302 N MakeVinaCommand New page: = Overview = [http://vina.scripps.edu/ Vina] is a new, very fast, molecular docking program, written by Oleg Trott. In order to run Vina, you should have [http://mgltools.scripps.edu/down...
- 09:16, 24 February 2009 diff hist -48 3DNA →Invoking
- 13:16, 20 February 2009 diff hist +139 Main Page
- 13:14, 20 February 2009 diff hist +33 DrawBoundingBox
- 13:13, 20 February 2009 diff hist +5,532 N DrawBoundingBox New page: = OVERVIEW = Draws the minumum bounding box around your selection. <gallery> Image:DrawMinBB.png|Example min BB </gallery> = Example = <source lang="python"> run ~/drawMinBoundingBox.py ...
- 13:11, 20 February 2009 diff hist +17 N File:DrawMinBoundBox.tar.bz2 Draw min BB code. current
- 13:09, 20 February 2009 diff hist +20 N File:DrawMinBB.png Example of the minBB current
- 12:07, 6 February 2009 diff hist +11 Surface solvent
- 13:42, 29 January 2009 diff hist +140 Main Page
- 13:40, 29 January 2009 diff hist +2,084 N FindObjectsNearby New page: == Overview == This script returns the names of all objects (in state 1) that are within a certain cutoff distance from your provided target. For example, if you load an MD trajectory and...
- 16:34, 28 January 2009 diff hist +13 As
- 16:34, 28 January 2009 diff hist +1,407 N Show as New page: == DESCRIPTION == (History: Python 2.6 came out with the keyword as which is also a PyMOL keyword. So, we had to change the PyMOL-named keyword to show_as.) show_as turns on ...
- 11:25, 27 January 2009 diff hist +271 Get Title
- 10:01, 27 January 2009 diff hist +117 Property Selectors →General
- 10:00, 27 January 2009 diff hist +63 Selection Macros →General
- 12:30, 23 January 2009 diff hist +159 Cealign plugin →Discussion
- 12:07, 22 January 2009 diff hist +26 m Cealign plugin →Fit vs. optAlign
- 12:05, 22 January 2009 diff hist +2,324 Cealign plugin →Comparison to PyMol
- 09:52, 19 January 2009 diff hist -76 Split states
- 09:52, 19 January 2009 diff hist +556 Split states →Using
- 09:25, 19 January 2009 diff hist +296 Windows Install
- 09:23, 19 January 2009 diff hist +548 Ray →Performance
- 09:21, 19 January 2009 diff hist -2 m Talk:Ray
- 09:20, 19 January 2009 diff hist +488 Talk:Ray New section: Cool idea
- 09:16, 19 January 2009 diff hist +28 Viewport
- 09:14, 19 January 2009 diff hist +116 N Category:Concepts New page: = Introduction = PyMOL has a few basic concepts that are worth knowing. Those currently documented are listed here. current
- 09:13, 19 January 2009 diff hist +68 N Category:States New page: PyMOLWiki pages related to the concept of using States in PyMOL. current
- 09:12, 19 January 2009 diff hist +20 Defer builds mode current
- 09:12, 19 January 2009 diff hist +20 Pseudoatom
- 09:12, 19 January 2009 diff hist +20 Script Tutorial
- 09:12, 19 January 2009 diff hist +20 Modeling and Editing Structures
- 09:12, 19 January 2009 diff hist +20 Practical Pymol for Beginners
- 09:11, 19 January 2009 diff hist +20 Ribbon color
- 09:11, 19 January 2009 diff hist +20 Split states
- 09:11, 19 January 2009 diff hist +20 Set Dihedral
- 09:11, 19 January 2009 diff hist +20 Editing atoms
- 09:10, 19 January 2009 diff hist +20 Isosurface
- 09:10, 19 January 2009 diff hist +20 Isomesh
- 09:10, 19 January 2009 diff hist +20 Isolevel
- 09:10, 19 January 2009 diff hist +20 Isodot
- 09:10, 19 January 2009 diff hist +20 Load traj
- 09:09, 19 January 2009 diff hist +20 Load Model
- 09:09, 19 January 2009 diff hist +20 Mset
- 09:09, 19 January 2009 diff hist +20 Map double
- 09:09, 19 January 2009 diff hist +20 Origin
- 09:09, 19 January 2009 diff hist +20 Orient
- 09:09, 19 January 2009 diff hist +20 Rotate
- 09:09, 19 January 2009 diff hist +20 Read Pdbstr
- 09:09, 19 January 2009 diff hist +20 Read Molstr
- 09:08, 19 January 2009 diff hist +20 Set Title
- 09:08, 19 January 2009 diff hist +20 Set name
- 09:08, 19 January 2009 diff hist +20 Save
- 09:08, 19 January 2009 diff hist +20 Scene
- 09:08, 19 January 2009 diff hist +20 Translate
- 09:08, 19 January 2009 diff hist +20 Unset
- 09:08, 19 January 2009 diff hist +20 Get Title
- 09:08, 19 January 2009 diff hist +20 Get Pdbstr
- 09:08, 19 January 2009 diff hist +20 Get Distance
- 09:08, 19 January 2009 diff hist +20 Get Dihedral
- 09:07, 19 January 2009 diff hist +20 Get Angle
- 09:07, 19 January 2009 diff hist +20 Clip
- 09:07, 19 January 2009 diff hist +20 Get Extent
- 09:07, 19 January 2009 diff hist +20 Zoom
- 09:07, 19 January 2009 diff hist +20 Set
- 09:07, 19 January 2009 diff hist +20 Dss
- 09:07, 19 January 2009 diff hist +20 Intra rms cur
- 09:07, 19 January 2009 diff hist +20 Intra rms
- 09:06, 19 January 2009 diff hist +20 Intra fit
- 09:06, 19 January 2009 diff hist +20 Single-word Selectors
- 09:06, 19 January 2009 diff hist +20 Load
- 09:06, 19 January 2009 diff hist +20 Create
- 09:06, 19 January 2009 diff hist +20 Center
- 09:06, 19 January 2009 diff hist +20 Simple Scripting
- 09:06, 19 January 2009 diff hist +20 Alter State
- 09:05, 19 January 2009 diff hist +20 Iterate State
- 09:04, 19 January 2009 diff hist +49 Color →Color States Individually
- 09:04, 19 January 2009 diff hist +523 Color →Getting Atom Colors
- 09:02, 19 January 2009 diff hist -5 Color →Expanding to Surface
- 09:01, 19 January 2009 diff hist +1,238 N States New page: = Introduction to States = Working with States in PyMOL is a very common task. A State is one particular conformation of an object. For example, one could load an NMR ensemble an...
- 08:54, 19 January 2009 diff hist +20 All states current
- 08:47, 19 January 2009 diff hist +19 Count States
- 08:45, 19 January 2009 diff hist +165 All states →Example
- 08:43, 19 January 2009 diff hist +32 All states
- 15:37, 8 January 2009 diff hist +185 All states
- 23:48, 30 December 2008 diff hist +80 N Talk:Fetch New page: * This is an important command. Update it to current version and give examples. current
- 21:13, 18 December 2008 diff hist +33 Huge surfaces
- 21:12, 18 December 2008 diff hist -88 Main Page
- 21:04, 18 December 2008 diff hist +6 Main Page
- 21:02, 18 December 2008 diff hist +209 Main Page
- 21:01, 18 December 2008 diff hist +172 Surface →Creating a Closed Surface
- 20:59, 18 December 2008 diff hist +1,315 N Huge surfaces New page: = Overview = PyMOL can render '''very large''' surfaces of proteins, using a few tricks. First off, you should know that because of the size, you do not get the level of accuracy that you...
- 20:58, 18 December 2008 diff hist +51 N File:Large surface approx.png Approximation, using Gaussians, of a large surface. current
- 20:57, 18 December 2008 diff hist +26 N File:Large surface.png Example of a large surface current
- 20:42, 18 December 2008 diff hist +341 N Cartoon putty radius New page: = Overview = cartoon_putty_radius sets the base putty radius. = Usage = <source lang="python"> # set a base radius of 1.0 (will be scaled based on B factors) set cartoon_putty_radius,... current
- 20:39, 18 December 2008 diff hist +379 N Cartoon putty transform New page: = Overview = This setting determines how PyMOL renders the transformation of original values into putty related settings. = Usage = <source lang="python"> # absolute linear scaling from ...
- 20:37, 18 December 2008 diff hist +3 Cartoon putty scale min
- 20:37, 18 December 2008 diff hist 0 Cartoon putty scale max
- 20:37, 18 December 2008 diff hist +397 N Cartoon putty scale max New page: = Overview = cartoon_putty_scale_max sets the max scale that PyMOL will use for rendering cartoon putty. = Usage = <source lang="python"> # set a max scale set cartoon_putty_scale_ma...
- 20:36, 18 December 2008 diff hist +400 N Cartoon putty scale min New page: = Overview = cartoon_putty_scale_min sets the minimum scale that PyMOL will use for rendering cartoon putty. = Usage = <source lang="python"> # set a minimum scale set cartoon_putty_s...
- 10:59, 17 December 2008 diff hist +14 N User:Wowgoldgate New page: Loser spammer. current
- 16:04, 2 December 2008 diff hist +2 Older News
- 16:04, 2 December 2008 diff hist +1,330 Older News
- 16:04, 2 December 2008 diff hist -1,900 Main Page
- 16:01, 2 December 2008 diff hist +128 Main Page
- 16:00, 2 December 2008 diff hist +29 PDB Web Services Script
- 16:00, 2 December 2008 diff hist +581 PDB Web Services Script
- 15:46, 2 December 2008 diff hist +1,388 N PDB Web Services Script New page: == Overview == A short snippet of code utilizing the new PDB Web Services. == The Code == <source lang="python"> import pymol from pymol import stored, cmd import SOAPpy import string # ...
- 17:04, 26 November 2008 diff hist +90 Main Page
- 23:12, 24 November 2008 diff hist +2,895 Help:Contents
- 14:44, 14 November 2008 diff hist -4,206 Settings
- 10:09, 13 November 2008 diff hist +102 Color →Getting Atom Colors
- 10:07, 13 November 2008 diff hist +139 Color →Expanding to Surface
- 07:39, 12 November 2008 diff hist +14 N User talk:Rs2play New page: Idiot spammer. current
- 14:07, 11 November 2008 diff hist +54 Rotate →DESCRIPTION
- 14:07, 11 November 2008 diff hist +9 Rotate →SEE ALSO
- 14:06, 11 November 2008 diff hist +3 Turn
- 16:32, 10 November 2008 diff hist +96 Category:Script Library
- 16:31, 10 November 2008 diff hist +2,803 N FilterByMol New page: == Overview == This script filters through all the PDBs in the parent dir (you can easily the the directory it scans). For each molecule, it saves '''just''' the ligands/heteroatoms (excl...
- 15:31, 10 November 2008 diff hist +86 Help:Contents
- 15:28, 10 November 2008 diff hist +384 Selection Algebra
- 15:27, 10 November 2008 diff hist +385 PyMOLWiki talk:Community Portal New section: Answer: New Pages
- 13:25, 10 November 2008 diff hist -491 Selection Algebra →Examples
- 13:23, 10 November 2008 diff hist +108 N Talk:Selection Algebra New page: * This should be cleaned up. One of PyMOL's most powerful features is the selections and selection algebra. current
- 13:14, 10 November 2008 diff hist +193 Selection Algebra
- 18:57, 8 November 2008 diff hist +378 Cealign plugin →The Function SimpAlign() is not found
- 16:55, 4 November 2008 diff hist 0 LoadDir →The Code
- 08:04, 30 October 2008 diff hist 0 Surface →Performance
- 08:04, 30 October 2008 diff hist +601 Surface →Creating a Closed Surface
- 15:12, 20 October 2008 diff hist -1 Get Position
- 15:12, 20 October 2008 diff hist +249 N Get Position New page: == Overview == Get_Position gets the 3D coordinates of the center of the viewer window.. == Syntax == <source lang="python"> # print the coordinates for center of mass zoom print cmd....
- 12:08, 20 October 2008 diff hist +383 Ribbon width
- 12:07, 20 October 2008 diff hist 0 N File:Rw3.png current
- 12:07, 20 October 2008 diff hist 0 N File:Rw2.png current
- 12:06, 20 October 2008 diff hist 0 N File:Rw1.png current
- 11:34, 20 October 2008 diff hist 0 LoadDir
- 11:33, 20 October 2008 diff hist +138 Category:Script Library
- 11:30, 20 October 2008 diff hist +55 LoadDir →The Code
- 10:58, 20 October 2008 diff hist +139 LoadDir →The Code
- 10:57, 20 October 2008 diff hist +237 LoadDir →Examples
- 10:36, 20 October 2008 diff hist +95 LoadDir →Example
- 10:15, 20 October 2008 diff hist +265 N Talk:LigAlign New page: * Great tool. I think this would be more useful for the users if they could load two objects into PyMOL and simply use it there. I had a session open with about 50 proteins and '''ligali...
- 09:54, 20 October 2008 diff hist 0 Main Page
- 09:54, 20 October 2008 diff hist +37 LoadDir
- 09:53, 20 October 2008 diff hist +167 Main Page
- 09:52, 20 October 2008 diff hist +21 N LoadAll LoadAll moved to LoadDir: Oops, wrong name.
- 09:52, 20 October 2008 diff hist 0 m LoadDir LoadAll moved to LoadDir: Oops, wrong name.
- 09:52, 20 October 2008 diff hist +197 LoadDir →Overview
- 09:51, 20 October 2008 diff hist +1 m LoadDir →Example
- 09:50, 20 October 2008 diff hist +1,776 N LoadDir New page: == Overview == Load all files of the suffix '''suff''' from the directory '''dirName''', where '''suff''' and '''dirName''' are function parameters. == Example == <source lang="python"> ...
- 09:13, 20 October 2008 diff hist -21 Cealign plugin →It Worked A Second Ago!
- 09:12, 20 October 2008 diff hist +22 Cealign plugin →It Worked A Second Ago!
- 09:12, 20 October 2008 diff hist +794 Cealign plugin →Short Alignments Don't Work
- 09:10, 20 October 2008 diff hist +26 N File:Rewind.png Showing the rewind button. current
- 20:54, 15 October 2008 diff hist +36 Modeling and Editing Structures
- 20:54, 15 October 2008 diff hist +36 Displaying Biochemical Properties →Align proteins with CA fit
- 13:52, 15 October 2008 diff hist +154 m Main Page
- 21:28, 14 October 2008 diff hist -7 Cealign plugin →Syntax
- 13:49, 14 October 2008 diff hist +427 N Builder New page: = Overview = The Builder is a PyMOL GUI menu that allows you to easily build up structures by hand from various elements like atoms, fragments, rings, amino acids, etc. You can also a...
- 13:48, 14 October 2008 diff hist +11 N File:Builder1.png Builder on. current
- 13:47, 14 October 2008 diff hist +14 N File:Builder0.png Builder button current
- 13:41, 14 October 2008 diff hist 0 Abort
- 13:40, 14 October 2008 diff hist +2 Feedback →NOTES
- 13:40, 14 October 2008 diff hist +2 Feedback
- 10:40, 13 October 2008 diff hist +468 Linux Install →Problems
- 10:35, 13 October 2008 diff hist +515 Linux Install →Compiling By Hand
- 08:36, 6 October 2008 diff hist +63 N Talk:Windows Install New page: = Updates = * This page needs an example ~/.pymolrc file on it. current
- 23:59, 3 October 2008 diff hist +173 PyMOLWiki:Community Portal →Editing current
- 23:55, 3 October 2008 diff hist -129 PyMOLWiki:Community Portal →Get Involved
- 23:55, 3 October 2008 diff hist +12 PyMOLWiki:Community Portal →You Should Know
- 23:54, 3 October 2008 diff hist +298 PyMOLWiki:Community Portal →Making Edits
- 23:53, 3 October 2008 diff hist -1,397 PyMOLWiki:Community Portal →Features
- 23:52, 3 October 2008 diff hist +244 PyMOLWiki:Community Portal →Editing Tricks
- 23:42, 3 October 2008 diff hist +3,726 PyMOLWiki:Community Portal →How to Get Involved
- 21:28, 3 October 2008 diff hist -2 m Covers Fixed external link
- 21:12, 30 September 2008 diff hist -3 CheatSheet current
- 21:11, 30 September 2008 diff hist +21 N Talk:ProMOL New page: * This looks defunct.
- 21:09, 30 September 2008 diff hist +4 Dot radius current
- 21:08, 30 September 2008 diff hist +11 Ray Tracing current
- 21:05, 30 September 2008 diff hist +209 Show
- 08:25, 29 September 2008 diff hist +164 Isomesh →USAGE
- 21:43, 27 September 2008 diff hist +198 Main Page
- 19:22, 27 September 2008 diff hist +1 Main Page
- 19:22, 27 September 2008 diff hist +236 m Main Page
- 21:41, 26 September 2008 diff hist +145 Talk:Covers current
- 21:40, 26 September 2008 diff hist +110 Covers
- 21:38, 26 September 2008 diff hist +71 m Covers
- 21:35, 26 September 2008 diff hist +413 Covers
- 20:08, 26 September 2008 diff hist +358 Covers
- 20:05, 26 September 2008 diff hist +179 Covers
- 20:02, 26 September 2008 diff hist +216 Covers
- 20:00, 26 September 2008 diff hist +110 Covers
- 19:59, 26 September 2008 diff hist +676 Covers
- 19:50, 26 September 2008 diff hist +154 Covers
- 19:43, 26 September 2008 diff hist +190 Ray
- 19:42, 26 September 2008 diff hist +28 N File:Ray2.png Another ray tracing example. current
- 19:40, 26 September 2008 diff hist +14 N File:Ray1.png Example ray on current
- 19:40, 26 September 2008 diff hist +30 N File:Noray.png Normal image. No ray tracing. current
- 19:37, 26 September 2008 diff hist +54 Apropos
- 16:03, 25 September 2008 diff hist +78 N Talk:Covers New page: * Need to link to the image cover pages instead of the cover-pages themselves.
- 19:14, 24 September 2008 diff hist +1 Helicity check
- 18:45, 24 September 2008 diff hist +62 Helicity check
- 18:41, 24 September 2008 diff hist -1 CBC
- 17:47, 24 September 2008 diff hist +32 Selection Algebra →Intro
- 16:45, 24 September 2008 diff hist +95 Color
- 16:44, 24 September 2008 diff hist +22 m List Colors
- 12:06, 24 September 2008 diff hist -35 m Button →NOTES
- 12:03, 24 September 2008 diff hist +2 Fog current
- 12:02, 24 September 2008 diff hist +33 Sphere color
- 12:01, 24 September 2008 diff hist +3 m Cartoon color →Syntax current
- 12:00, 24 September 2008 diff hist +26 Cartoon color
- 16:33, 23 September 2008 diff hist +179 Main Page