User contributions
Jump to navigation
Jump to search
- 14:01, 7 June 2016 diff hist +911 User:Jaredsampson Update current
- 13:31, 7 June 2016 diff hist +341 Linux Install →Get latest source from SVN: Add HTTP protocol as alternative to troubleshoot sf.net SVN connection.
- 01:44, 28 March 2016 diff hist +124 Cartoon →Various Transparency Levels: include mention of "extract"
- 02:19, 26 February 2016 diff hist +19 COLLADA Include first version to support COLLADA.
- 12:36, 2 December 2015 diff hist -1,602 Selection Algebra →Selection Operator/Modifier Table: converted to wiki markup and made several minor edits (e.g. periods at end of "effect" column sentences.)
- 00:28, 10 November 2015 diff hist +372 MAC Install →With xquartz intalled: This is untested, but just updating the flags to the current syntax listed in the homebrew/homebrew-science/pymol.rb formula.
- 00:19, 10 November 2015 diff hist -250 MAC Install →Switch stereo: Renamed section, and rewrote most of the content because latest homebrew install no longer switches the stereo/mono paradigm as previously described.
- 00:08, 10 November 2015 diff hist -75 MAC Install →3. Install PyMOL.: latest version doesn't require multiple install commands--everything is handled by the install script (apparently)
- 00:06, 10 November 2015 diff hist +153 MAC Install →2. Install Xquartz.: add homebrew cask option to install Xquartz
- 23:17, 29 August 2015 diff hist -1 PYMOL PATH →Contents: typo
- 15:18, 29 August 2015 diff hist +21 Plugin Manager add Plugins category
- 17:36, 13 August 2015 diff hist +40 Plane Wizard Improve handling of auto_zoom setting (store original setting, then re-set it).
- 23:22, 7 June 2015 diff hist +158 Plugins →Using Fink: Change title of section to reflect additonal package managers. Fix link for Fink, add links for MacPorts and Homebrew. Update install example to refer to pymol-py27 fink package and remove unnecessary tags.
- 17:02, 7 June 2015 diff hist +8 Pytms Correct link to raw plugin file in repo.
- 16:41, 7 June 2015 diff hist +21 Pytms Add plugins category.
- 18:52, 20 May 2015 diff hist +2,502 N Collada geometry mode Created current
- 12:21, 20 May 2015 diff hist +3 Modeling and Editing Structures →Adding and using your own fragments: clarified that editing modules/pmg_tk/skins/normal/__init__.py would add a menu item, not a hotkey.
- 10:31, 6 May 2015 diff hist -8 Mset →EXAMPLES: fixed python comments to use # instead of //
- 12:12, 16 April 2015 diff hist +161 MAC Install →3. Install PyMOL.: Added sentence to indicate the end of the installation process.
- 12:08, 16 April 2015 diff hist +31 MAC Install →1. Install homebrew.: updated homebrew install command per https://developer.github.com/changes/2014-04-25-user-content-security/
- 18:52, 29 September 2014 diff hist +3,624 N COLLADA Created page
- 17:54, 13 August 2014 diff hist -23 User:Jaredsampson
- 14:47, 13 August 2014 diff hist +128 Elbow angle →Syntax: added rationale for default limit residues current
- 15:00, 12 August 2014 diff hist +159 Cealign plugin →Comparison to PyMol: Whoops...fixed text to go with image order. Added PDB links.
- 14:49, 12 August 2014 diff hist 0 m Cealign plugin →Comparison to PyMol: switched order of images for logical flow (align, then cealign)
- 13:08, 28 July 2014 diff hist +60 Outline →Example: added "Automation" heading. Added `outfile` variable in imagemagick script, and adjusted filenames for consistency.
- 12:51, 24 July 2014 diff hist +1,644 N Outline Created page
- 12:47, 24 July 2014 diff hist +77 N File:Outline cleaned.png Cleaned-up version of Outline_composite.png, with extra outline lines erased. current
- 12:45, 24 July 2014 diff hist +53 N File:Outline composite.png Composite of Outine_base.png and Outline_overlay.png. current
- 12:42, 24 July 2014 diff hist +127 N File:Outline overlay.png Cytochrome C (3cyt) residues within 2Å of Lys85 are outlined in yellow, using `ray_trace_mode` and `ray_trace_color` settings. current
- 12:39, 24 July 2014 diff hist +46 N File:Outline base.png Surface representation of Cytochrome C (3cyt). current
- 12:50, 28 June 2014 diff hist +34 Get View →SEE ALSO: added Model_Space_and_Camera_Space
- 12:14, 28 June 2014 diff hist +5 Move current
- 09:36, 28 June 2014 diff hist 0 m View →Function Key Presets: capitalized title current
- 09:35, 28 June 2014 diff hist +15 View →VIEWS: made section title reflect contents
- 13:17, 5 June 2014 diff hist +16 Ray opaque background →Examples: eliminated abbreviation in setting name current
- 13:16, 5 June 2014 diff hist +84 Png →Transparent Backgrounds: added example of ray_opaque_background setting
- 13:11, 5 June 2014 diff hist +36 Png →DPI Setting: updated to account for integrated width, height, and ray arguments
- 13:06, 5 June 2014 diff hist +485 Png →USAGE: updated with additional parameters
- 13:01, 5 June 2014 diff hist +57 Png →PYMOL API: updated API to match `help png` output and include defaults
- 12:56, 5 June 2014 diff hist +43 Png →USAGE: added brackets and defaults for keyword arguments
- 12:52, 5 June 2014 diff hist -19 Optimize →Local optimization: moved image to top of section, added Usage heading
- 12:46, 5 June 2014 diff hist +404 Optimize →Local optimization: fixed a few typos, added default values from script, added PyMOL API section.
- 19:15, 11 April 2014 diff hist +11 Enable changed to definition list format
- 18:51, 11 April 2014 diff hist +206 Disable added examples, improved description, added default='all'
- 18:42, 11 April 2014 diff hist +443 Enable Added more examples and description of `parents` argument.
- 12:30, 9 April 2014 diff hist -1 Morph fix typo
- 11:14, 28 February 2014 diff hist +2,131 N Colorblindfriendly Added basic page for Colorblindfriendly.py script
- 17:01, 25 February 2014 diff hist +730 MAC Install →PyMOL in brew: Updated homebrew link. Expanded installation section. Added "brew tap homebrew/dupes", which enables Tcl/Tk installation.
- 13:32, 19 February 2014 diff hist +383 Model Space and Camera Space Added links to other PW pages. Removed unnecessary line breaks. Updated some language for clarity. current
- 12:29, 19 February 2014 diff hist +380 N Talk:Translate Questioning two statements in the Notes section current
- 12:12, 19 February 2014 diff hist +4 m Translate →EXAMPLES: Added example numbers. Moved Example 1 description below its heading. current
- 12:09, 19 February 2014 diff hist -94 Translate →ARGUMENTS: corrected list of arguments from 1.7.0.0 `help translate`
- 15:49, 5 January 2014 diff hist +1,062 N Geometry export mode Added basic description, example, and syntax for geometry_export_mode setting. current
- 15:26, 5 January 2014 diff hist +256 Settings added alphabetic index for easier browsing
- 15:10, 5 January 2014 diff hist -241 Template:Columns-list Blanked the page current
- 15:09, 5 January 2014 diff hist +241 N Template:Columns-list Created page with "<includeonly>{{div col | cols = {{{cols|{{{1|}}}}}} | colwidth = {{{colwidth|}}} | rules = {{{rules|}}} | small = {{{small|}}} | style = {{{style|}}} | content = {{{2|{{{1|..."
- 14:19, 1 January 2014 diff hist +22 N Set view redirect to existing page current
- 14:17, 1 January 2014 diff hist +26 N Count states redirect to existing page current
- 14:15, 1 January 2014 diff hist +22 N Get view redirect to existing page current
- 14:14, 1 January 2014 diff hist +18 m Gallery fix broken links to Get_View
- 10:54, 21 November 2013 diff hist -3 m Save →SEE ALSO
- 10:54, 21 November 2013 diff hist +162 Save →Details: updated list of auto-detected formats [from modules/pymol/exporting.py]; added default state = -1
- 10:42, 21 November 2013 diff hist +10 Load →SEE ALSO
- 10:19, 21 November 2013 diff hist +77 m Practical Pymol for Beginners →The Python MiniShell: corrected typo, added <code> tags to commands instead of bold font weight
- 10:03, 21 November 2013 diff hist 0 m Practical Pymol for Beginners changed capitalization of PyMOL
- 13:41, 6 November 2013 diff hist +37 Elbow angle →Basic usage: added link to COM
- 13:32, 6 November 2013 diff hist +33 Average b →code: adjusted string outputs to use string formatting instead of concatenation; adjusted whitespace around operators
- 15:24, 29 October 2013 diff hist +169 Get Names added "how to tell whether or not object is enabled" as posted by Jason on pymol-users
- 13:08, 10 October 2013 diff hist 0 m Fuse fix typo
- 00:56, 18 September 2013 diff hist +1 m MAC Install →PyMOL Install from Source, Using Fink: fixed typo
- 11:46, 2 August 2013 diff hist +2 m Command Line Options fixed typos
- 19:09, 26 April 2013 diff hist +754 Covers added Structure Nov 2009 cover. Began to sort by year and suggested a standardized format: Image|Description [link ''Journal'', Volume, Issue, Date].
- 11:56, 26 April 2013 diff hist +136 N File:20091111 Structure cover.jpg Cover of the 11 November 2009 issue of Structure. Artwork by Jared Sampson, Xiangpeng Kong lab, New York University School of Medicine. current
- 17:01, 5 October 2012 diff hist +23 Elbow angle →Syntax
- 12:35, 6 July 2012 diff hist +2 Git install scripts →Adding Pymol-script-repo to PyMOL search path: clarified date of rev 3997
- 15:14, 15 June 2012 diff hist +22 Elbow angle →Included Example: added user link
- 15:13, 15 June 2012 diff hist -2 Elbow angle changed release license to BSD
- 15:13, 15 June 2012 diff hist +62 Elbow angle →Included Example: converted to infobox again (read that the old template had been deprecated)
- 15:05, 15 June 2012 diff hist -22 Elbow angle →Included Example: restored original infobox from PymolScriptRepoDownload template
- 15:00, 15 June 2012 diff hist +2 Elbow angle →Included Example: moved infobox down to be in same place as included pml script source
- 14:58, 15 June 2012 diff hist +19 Elbow angle →Examples: added infobox for example pml script
- 14:55, 15 June 2012 diff hist -1,110 Elbow angle →Examples: added include tag to refer to example script
- 11:37, 15 June 2012 diff hist +45 User:Jaredsampson updated profile. added list of scripts.
- 23:53, 14 June 2012 diff hist +786 Elbow angle Added Implementation section
- 23:13, 14 June 2012 diff hist 0 m Elbow angle →Syntax: capitalized PyMOL
- 23:13, 14 June 2012 diff hist +171 Elbow angle →Syntax: added description of object argument
- 23:10, 14 June 2012 diff hist 0 m Elbow angle →Examples: fixed capitalization of Abnum to match Dr. Martin's page
- 23:09, 14 June 2012 diff hist +232 Elbow angle →Examples: changed order of image and script to make the page look nicer. clarified explanation of arguments and importance of correct numbering and chain ids.
- 17:33, 14 June 2012 diff hist +448 Elbow angle added syntax section
- 17:25, 14 June 2012 diff hist +1,404 Elbow angle →Examples: added contents of example script
- 17:22, 14 June 2012 diff hist +443 Elbow angle →Examples: added more details to first example, and better explanation for Pymol-script-repo example
- 15:17, 8 June 2012 diff hist +814 N Transformations Basic description of script added. Explained basic import and started a list of scripts using transformations.py. current
- 14:54, 8 June 2012 diff hist -42 Elbow angle →Examples: Updated description of visualization, removed orient command from example.
- 14:53, 8 June 2012 diff hist +27 Elbow angle →Examples: updated gallery heights and widths
- 14:52, 8 June 2012 diff hist -3 Elbow angle →Examples: updated link to second image
- 14:47, 8 June 2012 diff hist +171 File:Stanfield.png current
- 14:45, 8 June 2012 diff hist +200 N File:Stanfield.png Example PDBs from Stanfield, et al., JMB 2006 as shown in Fig. 1 of that paper. elbow_angle.py was used to calculate the elbow angles and draw a representation of the vectors used in the calculation.
- 14:42, 8 June 2012 diff hist -31 Elbow angle →Examples: removed gallery dimensions
- 14:37, 8 June 2012 diff hist +1 Elbow angle
- 14:29, 8 June 2012 diff hist +81 N File:Elbow angle 3ghe.png View of the elbow_angle vector representation for the Fab fragment from PDB 3ghe. current
- 14:24, 8 June 2012 diff hist -203 Elbow angle removed reference to github example script
- 14:23, 8 June 2012 diff hist +1,415 N Elbow angle Added the page for elbow_angle.py script in Pymol-script-repo
- 10:45, 1 May 2012 diff hist -2 m Iterate →Details: fixed typos and removed orphaned colons.
- 14:57, 14 February 2012 diff hist +291 Set name →User Comments/Examples: added comment comparing set_name to shell mv
- 11:27, 26 January 2012 diff hist +14 MAC Install →Mighty Mouse: changed title to include magic mouse
- 11:26, 26 January 2012 diff hist +545 MAC Install →Mighty Mouse: added link to MagicPrefs for 3-button Magic Mouse functionality, and description of Emulate three button mouse setting for X11
- 11:29, 5 December 2011 diff hist +37 m Single-word Selectors →More selectors
- 11:29, 5 December 2011 diff hist +104 Single-word Selectors →More selectors: added a couple more descriptions to the list
- 11:26, 5 December 2011 diff hist +138 Single-word Selectors added list of selectors (from Selector.c in source), excluding deprecated forms
- 14:29, 9 March 2011 diff hist -1 m Category:Structural Biology Scripts fixed typo in word "dependent" current
- 13:07, 2 February 2011 diff hist +37 m Ideas →Low-Level Enhancement Ideas (Mostly C-oriented): +1 for highlighting salt bridges
- 14:02, 9 December 2010 diff hist +5 User:Jaredsampson
- 14:01, 9 December 2010 diff hist -369 User:Jaredsampson
- 13:36, 9 December 2010 diff hist +296 Stereo mode Added example stereo_mode settings, since none were listed before.
- 15:01, 26 October 2010 diff hist +143 N Talk:Align Asking a question
- 13:35, 7 September 2010 diff hist +197 Orient →EXAMPLES: added a second image and <code> tags current
- 13:29, 7 September 2010 diff hist +61 N File:1hiw orient2.png Demonstration of orient command with 1hiw, two trimers shown. current
- 13:19, 7 September 2010 diff hist +431 Orient provided an example of orient for a model with NCS symmetry
- 13:15, 7 September 2010 diff hist +62 N File:1hiw orient.png Demonstration of orient command with NCS symmetry of PDB 1hiw. current
- 12:59, 7 September 2010 diff hist +305 N Talk:Orient Question about "principal components" criteria current
- 11:39, 11 August 2010 diff hist 0 Ray →Modes
- 11:38, 11 August 2010 diff hist +126 Ray →Modes
- 11:59, 17 June 2010 diff hist -10 m Label position replaced spelling of aangstrom(?) with Å current
- 15:15, 20 April 2010 diff hist +1 m Cealign plugin →Discussion: fixed reference to "Calign" to "Cealign"
- 12:11, 9 April 2010 diff hist +4 User:Jaredsampson
- 12:10, 9 April 2010 diff hist +22 User:Jaredsampson
- 12:10, 9 April 2010 diff hist +529 N User:Jaredsampson Created page with 'Jared Sampson. I'm a lowly research technician with 5 years of experience in crystallography in 2 labs. I'm by no means an expert, but I'm gradually picking up tricks here and …'
- 11:58, 9 April 2010 diff hist 0 m Hash max →Exmaple: typo correction
- 13:42, 26 March 2010 diff hist -1 m Selection Algebra →Selection Operator/Modifier Table: fixed formatting for "s1 in s2" description
- 17:28, 21 January 2010 diff hist +4 Advanced Coloring →CMYK-safe Colors: inserted word "not" to make the meaning of the sentence about RGB vs CMYK accurate.
- 18:34, 25 August 2009 diff hist 0 m Cealign plugin →Discussion
- 12:27, 25 August 2009 diff hist +282 Talk:Cealign plugin →Disparity in description of first pair of figures: new section
- 15:30, 21 July 2009 diff hist 0 m Settings fixed grammar/spelling in first sentence (incredible >> incredibly)