User contributions for Jaredsampson

25 March 2020

• 15:4015:40, 25 March 2020 diff hist +6‎ Pml ‎ →‎Python code: Italics
• 15:3915:39, 25 March 2020 diff hist +49‎ Pml ‎ →‎Python code: add syntax highlighting
• 15:3815:38, 25 March 2020 diff hist +21‎ N Collada ‎ Create redirect current Tag: New redirect
• 15:3415:34, 25 March 2020 diff hist +36‎ Pml ‎ →‎Handy commands to include in your scripts: add <code> tags
• 15:2915:29, 25 March 2020 diff hist +17‎ N PML ‎ create redirect current Tag: New redirect
• 15:2815:28, 25 March 2020 diff hist 0‎ m Pml ‎ Jaredsampson moved page PML to Pml without leaving a redirect: Consistent with other page names
• 15:2615:26, 25 March 2020 diff hist +1,889‎ Pml ‎ Add syntax and handy commands sections
• 12:4912:49, 25 March 2020 diff hist +60‎ Pml ‎ →‎PyMOL Script
• 12:4812:48, 25 March 2020 diff hist +439‎ N Pml ‎ Created page with basic description
• 12:3912:39, 25 March 2020 diff hist +8‎ Running Scripts ‎ →‎Python or Pymol?: Add link to PML page current

2 October 2019

• 13:3813:38, 2 October 2019 diff hist +23‎ Set Color ‎ Add link to missing set_object_color command page current

6 December 2018

• 00:0700:07, 6 December 2018 diff hist +36‎ File:4gms colors.png ‎ formatting for script current
• 00:0400:04, 6 December 2018 diff hist +1,015‎ N File:4gms colors.png ‎ Prepared in response to a pymol-users thread from 11/30/2018-12/5/2018 about the appearance of transparency in a published figure. Script to reproduce: bg_color white fetch 4gms, async=0 # hemagglutinin selections select ha, chain A select l130, ha...

8 October 2018

• 13:1513:15, 8 October 2018 diff hist +184‎ Talk:MAC Install ‎ →‎Package managers: new section current
• 13:0513:05, 8 October 2018 diff hist +51‎ MAC Install ‎ →‎Pre-compiled: Make Homebrew the recommended package manager current
• 13:0113:01, 8 October 2018 diff hist −97‎ MAC Install ‎ →‎Pre-compiled: Update Homebrew info to reflect new location of PyMOL formula and no more need for flags in dependencies.

8 March 2018

• 13:1913:19, 8 March 2018 diff hist +16‎ Isomesh ‎ →‎USAGE: add units for "level" parameter

15 November 2017

• 15:2115:21, 15 November 2017 diff hist +253‎ Colorblindfriendly ‎ →‎Download the script and run locally: Add a "run from Github" example. current

26 October 2017

• 16:0816:08, 26 October 2017 diff hist +291‎ Colorblindfriendly ‎ →‎Usage: Add instructions for running as dowloaded script.
• 15:5015:50, 26 October 2017 diff hist −1‎ Colorblindfriendly ‎ →‎Usage: update code samples and use <code> instead of <tt> tags.
• 09:5109:51, 26 October 2017 diff hist −3‎ Colorblindfriendly ‎ →‎Requirements: update to reflect support for older PyMOLs
• 00:4200:42, 26 October 2017 diff hist −2‎ m Colorblindfriendly ‎ →‎Usage: fix object name for consistency
• 00:4100:41, 26 October 2017 diff hist +1,281‎ Colorblindfriendly ‎ →‎Usage: Update usage for version 0.2; Add requirements section.
• 00:1700:17, 26 October 2017 diff hist +107‎ N File:Colorblindfriendly menu.png ‎ Screenshot of the color list menu added to the OpenGL GUI by the colorblindfriendly.py script in PyMOL 2.0. current
• 00:0400:04, 26 October 2017 diff hist −35‎ Colorblindfriendly ‎ →‎Colors: show 0-255 values instead.

25 October 2017

• 22:2522:25, 25 October 2017 diff hist +116‎ Get Color Indices ‎ add reference to Get_color_index
• 22:2322:23, 25 October 2017 diff hist +141‎ Get color index ‎ Add See Also and Categories current
• 22:2122:21, 25 October 2017 diff hist +226‎ N Get color index ‎ Create page

28 July 2017

• 20:2620:26, 28 July 2017 diff hist +5‎ Selection Algebra ‎ →‎Selection Operator/Modifier Table: fix vertical line display for "or" operator

16 January 2017

• 00:1900:19, 16 January 2017 diff hist +47‎ PyMOLProbity ‎ →‎Description: add link to repository

14 January 2017

• 13:4813:48, 14 January 2017 diff hist +200‎ PyMOLProbity ‎ →‎Getting Started: Update GUI section.
• 13:4113:41, 14 January 2017 diff hist +5‎ PyMOLProbity ‎ Add screenshot.
• 13:3913:39, 14 January 2017 diff hist +247‎ N File:PyMOLProbity GUI.png ‎ Screenshot of the "Review Flips" tab of the PyMOLProbity plugin GUI, where flippable side chains in the selected object can be inspected, animated between unflipped (i.e. Reduce-output) and flipped orientations, and selected for future operations. current
• 01:5201:52, 14 January 2017 diff hist +2,538‎ N PyMOLProbity ‎ Created page.

3 October 2016

• 15:0715:07, 3 October 2016 diff hist +6‎ Save ‎ Add COLLADA (.dae) to autodetected formats. current

7 June 2016

• 15:4215:42, 7 June 2016 diff hist +8‎ m PYMOL PATH ‎ →‎Contents: close <tt> tag current
• 14:0114:01, 7 June 2016 diff hist +911‎ User:Jaredsampson ‎ Update current
• 13:3113:31, 7 June 2016 diff hist +341‎ Linux Install ‎ →‎Get latest source from SVN: Add HTTP protocol as alternative to troubleshoot sf.net SVN connection.

28 March 2016

• 01:4401:44, 28 March 2016 diff hist +124‎ Cartoon ‎ →‎Various Transparency Levels: include mention of "extract"

26 February 2016

• 02:1902:19, 26 February 2016 diff hist +19‎ COLLADA ‎ Include first version to support COLLADA.

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.