User contributions for Jaredsampson

20 February 2025

• 14:5314:53, 20 February 2025 diff hist +74 Colorblindfriendly →Introduction: Credit Okabe and Ito for color palette, update link to reflect that the J*FLY page no longer exists (using an archive.org link instead).

19 January 2023

• 19:0919:09, 19 January 2023 diff hist −11 Get Title →PYMOL API: change to get_title API (this was apparently copied from the set_title page) current
• 19:0819:08, 19 January 2023 diff hist 0 Get Title →USAGE: fix typo in command name

15 February 2022

• 21:4121:41, 15 February 2022 diff hist +2 m CGO Shapes No edit summary current

14 February 2022

• 02:5302:53, 14 February 2022 diff hist +482 N Cgo transparency Add more details to usage and arguments current
• 02:4602:46, 14 February 2022 diff hist +56 CGO Shapes Add See Also section
• 02:4102:41, 14 February 2022 diff hist +4 CGO Shapes →EXAMPLES: fix missing namespace for cgo.CONE
• 02:3402:34, 14 February 2022 diff hist +18 CGO Shapes Add Category:CGO
• 02:3302:33, 14 February 2022 diff hist +19 CGO Shapes Add category:CGO
• 02:3102:31, 14 February 2022 diff hist +569 CGO Shapes →EXAMPLES: add image for the above examples
• 02:2602:26, 14 February 2022 diff hist +53 N File:Cgo examples.jpg Assorted rendered CGO objects in PyMOL. current
• 02:2002:20, 14 February 2022 diff hist +946 CGO Shapes Add examples and CONE
• 02:0402:04, 14 February 2022 diff hist +1,340 N CGO Shapes Create page
• 01:5001:50, 14 February 2022 diff hist +625 N Load CGO Create page current

25 March 2020

• 19:4619:46, 25 March 2020 diff hist +144 Pml →Basic usage: clarify about relative paths current
• 19:4519:45, 25 March 2020 diff hist +57 Pml →PyMOL Script: fix fixed-width formatting
• 19:4219:42, 25 March 2020 diff hist +14 Pml →Basic usage: fix fixed-width formatting
• 19:4019:40, 25 March 2020 diff hist +6 Pml →Python code: Italics
• 19:3919:39, 25 March 2020 diff hist +49 Pml →Python code: add syntax highlighting
• 19:3819:38, 25 March 2020 diff hist +21 N Collada Create redirect current Tag: New redirect
• 19:3419:34, 25 March 2020 diff hist +36 Pml →Handy commands to include in your scripts: add <code> tags
• 19:2919:29, 25 March 2020 diff hist +17 N PML create redirect current Tag: New redirect
• 19:2819:28, 25 March 2020 diff hist 0 m Pml Jaredsampson moved page PML to Pml without leaving a redirect: Consistent with other page names
• 19:2619:26, 25 March 2020 diff hist +1,889 Pml Add syntax and handy commands sections
• 16:4916:49, 25 March 2020 diff hist +60 Pml →PyMOL Script
• 16:4816:48, 25 March 2020 diff hist +439 N Pml Created page with basic description
• 16:3916:39, 25 March 2020 diff hist +8 Running Scripts →Python or Pymol?: Add link to PML page current

2 October 2019

• 17:3817:38, 2 October 2019 diff hist +23 Set Color Add link to missing set_object_color command page current

6 December 2018

• 04:0704:07, 6 December 2018 diff hist +36 File:4gms colors.png formatting for script current
• 04:0404:04, 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

• 17:1517:15, 8 October 2018 diff hist +184 Talk:MAC Install →Package managers: new section current
• 17:0517:05, 8 October 2018 diff hist +51 MAC Install →Pre-compiled: Make Homebrew the recommended package manager current
• 17:0117:01, 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

• 17:1917:19, 8 March 2018 diff hist +16 Isomesh →USAGE: add units for "level" parameter

15 November 2017

• 19:2119:21, 15 November 2017 diff hist +253 Colorblindfriendly →Download the script and run locally: Add a "run from Github" example.

26 October 2017

• 20:0820:08, 26 October 2017 diff hist +291 Colorblindfriendly →Usage: Add instructions for running as dowloaded script.
• 19:5019:50, 26 October 2017 diff hist −1 Colorblindfriendly →Usage: update code samples and use <code> instead of <tt> tags.
• 13:5113:51, 26 October 2017 diff hist −3 Colorblindfriendly →Requirements: update to reflect support for older PyMOLs
• 04:4204:42, 26 October 2017 diff hist −2 m Colorblindfriendly →Usage: fix object name for consistency
• 04:4104:41, 26 October 2017 diff hist +1,281 Colorblindfriendly →Usage: Update usage for version 0.2; Add requirements section.
• 04:1704:17, 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
• 04:0404:04, 26 October 2017 diff hist −35 Colorblindfriendly →Colors: show 0-255 values instead.
• 02:2502:25, 26 October 2017 diff hist +116 Get Color Indices add reference to Get_color_index
• 02:2302:23, 26 October 2017 diff hist +141 Get color index Add See Also and Categories current
• 02:2102:21, 26 October 2017 diff hist +226 N Get color index Create page

29 July 2017

• 00:2600:26, 29 July 2017 diff hist +5 Selection Algebra →Selection Operator/Modifier Table: fix vertical line display for "or" operator

16 January 2017

• 04:1904:19, 16 January 2017 diff hist +47 PyMOLProbity →Description: add link to repository

14 January 2017

• 17:4817:48, 14 January 2017 diff hist +200 PyMOLProbity →Getting Started: Update GUI section.
• 17:4117:41, 14 January 2017 diff hist +5 PyMOLProbity Add screenshot.
• 17:3917:39, 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