User contributions for Jaredsampson

2 December 2015

• 12:3612:36, 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.)

10 November 2015

• 00:2800:28, 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.
• 00:1900:19, 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.
• 00:0800:08, 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)
• 00:0600:06, 10 November 2015 diff hist +153‎ MAC Install ‎ →‎2. Install Xquartz.: add homebrew cask option to install Xquartz

29 August 2015

• 23:1723:17, 29 August 2015 diff hist −1‎ PYMOL PATH ‎ →‎Contents: typo
• 15:1815:18, 29 August 2015 diff hist +21‎ Plugin Manager ‎ add Plugins category

13 August 2015

• 17:3617:36, 13 August 2015 diff hist +40‎ Plane Wizard ‎ Improve handling of auto_zoom setting (store original setting, then re-set it).

7 June 2015

• 23:2223:22, 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.
• 17:0217:02, 7 June 2015 diff hist +8‎ Pytms ‎ Correct link to raw plugin file in repo.
• 16:4116:41, 7 June 2015 diff hist +21‎ Pytms ‎ Add plugins category.

20 May 2015

• 18:5218:52, 20 May 2015 diff hist +2,502‎ N Collada geometry mode ‎ Created current
• 12:2112:21, 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.

6 May 2015

• 10:3110:31, 6 May 2015 diff hist −8‎ Mset ‎ →‎EXAMPLES: fixed python comments to use # instead of //

16 April 2015

• 12:1212:12, 16 April 2015 diff hist +161‎ MAC Install ‎ →‎3. Install PyMOL.: Added sentence to indicate the end of the installation process.
• 12:0812:08, 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/

29 September 2014

• 18:5218:52, 29 September 2014 diff hist +3,624‎ N COLLADA ‎ Created page

13 August 2014

• 17:5417:54, 13 August 2014 diff hist −23‎ User:Jaredsampson ‎No edit summary
• 14:4714:47, 13 August 2014 diff hist +128‎ Elbow angle ‎ →‎Syntax: added rationale for default limit residues current

12 August 2014

• 15:0015:00, 12 August 2014 diff hist +159‎ Cealign plugin ‎ →‎Comparison to PyMol: Whoops...fixed text to go with image order. Added PDB links.
• 14:4914:49, 12 August 2014 diff hist 0‎ m Cealign plugin ‎ →‎Comparison to PyMol: switched order of images for logical flow (align, then cealign)

28 July 2014

• 13:0813:08, 28 July 2014 diff hist +60‎ Outline ‎ →‎Example: added "Automation" heading. Added `outfile` variable in imagemagick script, and adjusted filenames for consistency.

24 July 2014

• 12:5112:51, 24 July 2014 diff hist +1,644‎ N Outline ‎ Created page
• 12:4712:47, 24 July 2014 diff hist +77‎ N File:Outline cleaned.png ‎ Cleaned-up version of Outline_composite.png, with extra outline lines erased. current
• 12:4512:45, 24 July 2014 diff hist +53‎ N File:Outline composite.png ‎ Composite of Outine_base.png and Outline_overlay.png. current
• 12:4212:42, 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
• 12:3912:39, 24 July 2014 diff hist +46‎ N File:Outline base.png ‎ Surface representation of Cytochrome C (3cyt). current

28 June 2014

• 12:5012:50, 28 June 2014 diff hist +34‎ Get View ‎ →‎SEE ALSO: added Model_Space_and_Camera_Space
• 12:1412:14, 28 June 2014 diff hist +5‎ Move ‎No edit summary current
• 09:3609:36, 28 June 2014 diff hist 0‎ m View ‎ →‎Function Key Presets: capitalized title current
• 09:3509:35, 28 June 2014 diff hist +15‎ View ‎ →‎VIEWS: made section title reflect contents

5 June 2014

• 13:1713:17, 5 June 2014 diff hist +16‎ Ray opaque background ‎ →‎Examples: eliminated abbreviation in setting name current
• 13:1613:16, 5 June 2014 diff hist +84‎ Png ‎ →‎Transparent Backgrounds: added example of ray_opaque_background setting
• 13:1113:11, 5 June 2014 diff hist +36‎ Png ‎ →‎DPI Setting: updated to account for integrated width, height, and ray arguments
• 13:0613:06, 5 June 2014 diff hist +485‎ Png ‎ →‎USAGE: updated with additional parameters
• 13:0113:01, 5 June 2014 diff hist +57‎ Png ‎ →‎PYMOL API: updated API to match `help png` output and include defaults
• 12:5612:56, 5 June 2014 diff hist +43‎ Png ‎ →‎USAGE: added brackets and defaults for keyword arguments
• 12:5212:52, 5 June 2014 diff hist −19‎ Optimize ‎ →‎Local optimization: moved image to top of section, added Usage heading
• 12:4612:46, 5 June 2014 diff hist +404‎ Optimize ‎ →‎Local optimization: fixed a few typos, added default values from script, added PyMOL API section.

11 April 2014

• 19:1519:15, 11 April 2014 diff hist +11‎ Enable ‎ changed to definition list format
• 18:5118:51, 11 April 2014 diff hist +206‎ Disable ‎ added examples, improved description, added default='all'
• 18:4218:42, 11 April 2014 diff hist +443‎ Enable ‎ Added more examples and description of `parents` argument.

9 April 2014

• 12:3012:30, 9 April 2014 diff hist −1‎ Morph ‎ fix typo

28 February 2014

• 11:1411:14, 28 February 2014 diff hist +2,131‎ N Colorblindfriendly ‎ Added basic page for Colorblindfriendly.py script

25 February 2014

• 17:0117:01, 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.

19 February 2014

• 13:3213:32, 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
• 12:2912:29, 19 February 2014 diff hist +380‎ N Talk:Translate ‎ Questioning two statements in the Notes section current
• 12:1212:12, 19 February 2014 diff hist +4‎ m Translate ‎ →‎EXAMPLES: Added example numbers. Moved Example 1 description below its heading. current
• 12:0912:09, 19 February 2014 diff hist −94‎ Translate ‎ →‎ARGUMENTS: corrected list of arguments from 1.7.0.0 `help translate`

5 January 2014

• 15:4915:49, 5 January 2014 diff hist +1,062‎ N Geometry export mode ‎ Added basic description, example, and syntax for geometry_export_mode setting. current