Proteopedia:Openfox

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Revision as of 14:24, 6 August 2025 by Joel L. Sussman (Talk | contribs)
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Contents

Open Issues

(not in any particular order)

  • New page Template: the scenes should act on the structure currently rendered Jaime Prilusky 03:33, 29 July 2025 (UTC)
  • Mobile: When positioning horizontally (landscape mode), the phone, scrolling text, and applet should be positioned side by side. On iPad left right OK, but scrolling not working at all Jaime Prilusky 05:59, 11 June 2025 (UTC)
  • ok Journal: anonymous users (not logged-in), can not read Journal pages. --Jaime Prilusky 03:00, 30 March 2025 (UTC)
  •  ?? Mobile: The caret (^) on the left hand side of the title should collapse only the applet. Now it collapses applet plus text, leaving only the footer. Jaime Prilusky 06:04, 11 June 2025 (UTC)
  •  ?? Mobile: In the mobile view, the titles inside the scrolling text are not formatted properly, e.g. https://proteopedia.openfox.io/w/Hen_Egg-White_(HEW)_Lysozyme. Unexpectedly, when you minimize the section before the scrolling text, the Jmol window is hidden. I like that it is possible to minimize sections, though. I tried to adapt by moving the section header for the scrolling text outside of the scrolling section. --Karsten Theis 19:45, 29 March 2025 (UTC)
  • The search function result page has a full page with options before the search results. I would prefer the old order, with results on top and option below. This is the way that you want if the initial search already gives you good results. The thumbnails for the images are very cool. --Karsten Theis 19:45, 29 March 2025 (UTC)


Issues marked as solved

(might need a quick additional verification before swapping sites)

  • OK Fixed - Mobile: One sees options only for: Home, Random, Settings, Watchlist, Contributions, Log out. While on the web version pf OpenFox one sees options for: Main page, Table of Contents, Structure Index, Recent Changes, Help, Cookbook and Tools (list of several tools) --[[User:Joel L. Sussman|Joel L. Sussman] 10:30, 10 July 2025 (IL Time)
  • OK Fixed - Mutation pages working, but missing Icons on OpenFox page, please compare

https://proteopedia.openfox.io/w/Mutation:BRCA1 vs https://proteopedia.org/wiki/index.php/Mutation:BRCA1 --Jaime Prilusky 03:00, 30 March 2025 (UTC)

  • OK Fixed - Mobile: Search does not work on mobile unless you go to the home page. --Karsten Theis 19:45, 29 March 2025 (UTC)

in Proteopedia at: https://proteopedia.org/cgi-bin/morph
in OpenFox at: https://proteopedia.openfox.io/perl/morph

  • OK Fixed - ONLY the LAST button works in

https://proteopedia.openfox.io/w/Sandbox_buttons
while both buttons work in
https://proteopedia.org/wiki/index.php/Sandbox_buttons --Joel L. Sussman 10:25, 7 July 2025 (IL-Time)

  • OK Fixed - Missing 'Block Save' (blocks save page based on user and content) --Jaime Prilusky 15:43, 7 April 2025 (UTC)
  • Link [show sequence] (top left hand side) works. The replacement link hide does not. Jaime Prilusky 05:54, 11 June 2025 (UTC)
  • The link 'or create this page', appearing when searching for a non-existing page, opens a new window. This leaves the report of non-existing page open, which is confusing. Jaime Prilusky 19:00, 20 May 2025 (UTC)
  • OK Fixed - Two sets of 2 icons combined. The toolbar for editing in SAT is missing some key features in OpenFox SAT vs that in production. 20-May-2025 10:45.
  • OK Fixed -Pre-Fusion Structure section: gray box now has correct 2 buttons and they work. √
  • OK Fixed -Fusion section: gray box 1st button correct and works. Remaining 2 buttons absent -- single button "show interior cavities" is incorrect. It is absent in the section "Preventing Fusion with Drugs" where it belongs. In order for that button to work, http needs to be changed to https within the "isosurface" command in the button's HTML. Fixed √ Eric Martz 16:49, 2 June 2025 (UTC)
  • OK Fixed -Fusion section: line/spheres radio buttons are present and working. √
  • OK Fixed - due to change in the way moden MediaWiki handles PMID. On page https://proteopedia.openfox.io/w/Group:MUZIC:Titin, in section Structures - 3D structures of N-terminal part of titin or its complexes, deposited in "Protein Data Bank" none of the PMID have hyperlinks - see same page in Proteopedia where it is working. n.b. this page was created on 07:25, 16 December 2013. Joel L. Sussman 10:35, 8 June 2025 (IL-Time)
  • OK Fixed - When you edit a page, the shortcut buttons (bold, italic, ... 3D structure, scrolling text next to 3D structure) are missing. Instead, it says SAT with an SAT icon. --Karsten Theis 19:49, 29 March 2025 (UTC)
  • OK Fixed - I think all links to external URLs should open a new browser tab. For example, the link at the bottom of every page to "CC-BY-SA 3.0". Actually, this seems to be working within user-authored pages. Maybe just that "CC-BY-SA 3.0" link needs fixing? Eric Martz 18:18, 29 March 2025 (UTC) Fixed √ Eric Martz 17:39, 2 June 2025 (UTC)
  • OK Fixed - Main Page: Purple block of links at the bottom "About Contact Hot News ..." should have larger font as on the old site. These links are very important and should "jump out". Eric Martz 18:04, 29 March 2025 (UTC) Fixed √ Eric Martz 17:40, 2 June 2025 (UTC)
  • OK Fixed - the Misc has been replaced with Appearence, there one can find Advanced Options with Use advanced version of JSmol User preferences page has no Misc tab. Important for testing new JSmol releases. ("Use Java..." can be removed.) Eric Martz 17:44, 29 March 2025 (UTC) still missing Eric Martz 17:45, 2 June 2025 (UTC)
  • OK Fixed - Another example of green links being misplaced (same problem described by Karsten above) is here: https://proteopedia.openfox.io/w/Lac_repressor#DNA_Kinks -- up to the green link two leucines (Leu56) the links are correct. Then the link please click (should be with (if scene is blank, please click)) gets pushed into the section below. From that point onwards, all green links are misplaced. Eric Martz 20:34, 29 March 2025 (UTC) Fixed √ Eric Martz 18:00, 2 June 2025 (UTC)
  • OK Fixed - Fixed - is due to split of DB. When repeatedly reloading the Main Page, I get frequent errors in the row of 3 large gifs such as "Error: Image is invalid or non-existent." (under Education) or in huge font (with no image) "Proteopedia:Featured SEL/11" or "... SEL/12". Eric Martz 17:44, 2 June 2025 (UTC)
  • OK Fixed - is due to split of DB. If one clicks on Random on sidebar - for many of the pages, a structures take a very long time to load, and then finally loads with a large grey ball instead of a molecule. Joel L. Sussman 10:31, 4 June 2025 (IL-Time)
  • OK Fixed - On page https://proteopedia.openfox.io/w/6hek, structure load with a large grey ball. This is also true for https://proteopedia.openfox.io/w/Sandbox_6hek, which loads with large grey ball. However, in making a scene on this sandbox, using Load molecule 6hek in SAT, one gets a scene which shows the molecule just fine, i.e. click on green link scene_6hek to see this. This problem is virtually identical to one reported months ago. Joel L. Sussman 10:54, 4 June 2025 (IL-Time)
  • OK Fixed - on tab 'load scene', the dropdown 'Load scenes from this page' must show as a default the current page. --Jaime Prilusky 03:00, 30 March 2025 (UTC)
  • OK Fixed - on tab 'load scene', dropdown 'Scene name' and 'Version number' should have 'Choose', not selecting for the user. --Jaime Prilusky 03:00, 30 March 2025 (UTC)
  • OK Fixed - when expanded, buttons 'Save changes', 'Show preview' and 'Show changes' should be disabled. Missing yellow line: "To enable buttons below, save your scene, if desired, then hide the Scene Authoring Tools." --Jaime Prilusky 03:00, 30 March 2025 (UTC)
  • An unfortunate problem with the old site happens when there are multiple green links to animated scenes, as here:

https://proteopedia.openfox.io/w/Flaps_Morph_for_HIV_Protease If one scene is animating, clicking a green link to another animated scene fails to start the animation. Hence the need for the [Toggle Animation] button (working June 2, 2025) in OpenFox. Eric Martz 18:54, 29 March 2025 (UTC)


Issues to solve during final overall scanning

(possible a side effect of the initial database upgrade)

  • Homepage: Featured EDU/7 does not load --Karsten Theis 19:44, 29 March 2025 (UTC)


Left Aside Issues

(solve these if possible)

  • Is there a mechanism to prevent two users from editing the same page concurrently? This seems important to me, especially for collaborative student projects. Eric Martz 17:42, 29 March 2025 (UTC) Please put an answer here. Eric Martz 17:47, 2 June 2025 (UTC)
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