Proteopedia:Openfox

From Proteopedia

Current revision

Open Issues

• (1) Macros: Buttons on the examples of page https://proteopedia.openfox.io/w/Proteopedia:DIY:Macros are not working (see working version at Proteopedia:DIY:Macros. Hint: check if the directory mediawiki/mc/ exists, has content and is accessible to the browser.Jaime Prilusky 21:04, 7 August 2025 (UTC)

• (2) Jaime & Itsik need speak about this as the email portion of this page is NOT working: Special:Contact --Jaime Prilusky 16:03, 7 April 2025 (UTC)

• (3) Jaime & Itsik need speak about this one which is not working Special:SandboxReservation --Jaime Prilusky 16:09, 7 April 2025 (UTC)

• (4) 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. Please compare to Production site: https://proteopedia.org/wiki/index.php/Hen_Egg-White_(HEW%29_Lysozyme --Karsten Theis 19:45, 29 March 2025 (UTC)

• (5) If problem (5) is solved (i.e., while in landscape view, it should show left/right text/3D applet), this is not a problem and can then be ignored. The caret (^) on the left-hand side of the title should collapse only the applet. Now it collapses the applet plus text, leaving only the footer.--Jaime Prilusky

• (6) In several authored pages, scenes use a script that seems not to be properly located. (Similar issue as number 9 above) --Angel_Herraez 17:50, 12 August 2025 (UTC)
  • Scripts are trying to be retrieved from /wiki/scripts/ (Proteopedia.org) and really reside in /scripts/ (Proteopedia.Openfox)
  • Examples: Histone_acetyltransferase_1-2_Complex_(HAT1/2) , Lysine-specific_demethylase_1_(LSD-1)

• (7) Tabs inside the SAT section have tiny text titles, smaller than the standard text in the page. Also, contrast is poor (blue text on pale blue background). I vote for larger font with better color contrast. --Angel_Herraez 11:25, 13 August 2025 (UTC)

• (8) Exiting the edit page option with "cancel" link/button: This works ok, but when I have shown the SAT, then hide the SAT (no changes done), clicking on "cancel" brings the Firefox browser prompt "would you like to abandon the page?" -- this prompt should not happen; it does not in proteopedia.org.
  Additionally, if using the alternative skin (Preferences > Appearance > MinervaNeue) the "cancel" link/button is not visible, both having shown SAT or not. --Angel_Herraez 11:48, 13 August 2025 (UTC)

• (9) The script to colour the structure by Evolutionary Conservation is not doing anything, e.g. in https://proteopedia.openfox.io/w/3n9t (compare to https://proteopedia.org/w/3n9t) Console reports trying to run /wiki/scripts/consurf_prescript.spt which is not there, but in /scripts/consurf_prescript.spt (related to item #10) Same for subsequent sub-scripts invoked.

Issues marked as to be made to work by the Weizmann Team, after OpenFox becomes the production system

• Not working https://proteopedia.openfox.io/cgi-bin/latestUserLogin --Jaime Prilusky 03:00, 30 March 2025 (UTC)

• StudioManager is not working. Does the database have the table studio_access? --Jaime Prilusky 03:00, 30 March 2025 (UTC). Perl code referred to old DB , rewrite it to read new DB --Yitzhak Krumbein . Still not working: StudioManager should list current Studio pages --Jaime Prilusky 03:33, 3 April 2025 (UTC) -- I don't have access to prod Studio MGR so I can't compare Yitzhak Krumbein Just sent you a screen capture by email ---Jaime Prilusky 16:51, 3 April 2025 (UTC)

• Access restrictions not working. A Studio is a restricted access namespace where only authorized users can read/write. Now pages are open to everyone, even anonymous users, i.e. https://proteopedia.openfox.io/w/Studio:BASIL2022GV1ZBS01 --Jaime Prilusky 03:00, 30 March 2025 (UTC). Fixed --Yitzhak Krumbein

Issues marked as solved

(might need a quick additional verification before swapping sites)

• OK Fixed - Some seeded pages that use the conditionalLoad script to load the structure fail to load ('file not found', single white sphere) --Angel_Herraez 17:50, 12 August 2025 (UTC)
  • Examples: Arabidospsis_thaliana_PrRs_(pinoresinol/lariciresinol_reductases) , 1dnn , 8hbl
  • Others do work fine: 4ad0

• OK Fixed - This page Helices_in_Proteins does not load any of the 3 models. Reason: the files to be loaded into the JSmol panels are not present, e.g. the script tries /wiki/scripts/Helices_in_Proteins/3_10_helix_start/1.spt and the fix is to find it at /scripts/Helices_in_Proteins/3_10_helix_start/1.spt
  Maybe it's a manual fix since this is a special page. Angel_Herraez 17:18, 12 August 2025 (UTC)
  Same problem with Forms_of_DNA. Probably we need to fix the scenes manually so the spt and pdb files are properly found. Maybe?
• OK Fixed - 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 options 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)
  • I disagree. In my opinion, having those options at the very bottom made them go unnoticed. The list of results is often very long and not so significant. Seeing at once they can be filtered will be useful. --Angel_Herraez 11:05, 13 August 2025 (UTC)

• OK Fixed - It should be possible to see all options on the left side of the page, or on the top, as is possible on the Production system, even while NOT logged in. Specifically: Main Page; Table of Contents; Structure Index; Random; Recent Changes; Help; Cookbook. Currently, on OpenFox, it is only possible to see: Home; Random; Log In; Settings. It is also NOT possible to search.

• OK Fixed - When positioning horizontally (landscape mode), the phone, scrolling text, and applet should be positioned side by side. On iPad, left and right OK, but scrolling not working at all Jaime Prilusky 05:59, 11 June 2025 (UTC)
• OK Fixed - When I click on "edit this page", a line with icon and title for SAT appears above the textbox where content is edited. That should not be there. The correct line is also below the textbox (I did not click to open SAT) --Angel_Herraez 11:25, 13 August 2025 (UTC)
  https://proteopedia.openfox.io/wiki/index.php?title=Helices_in_Proteins&action=edit

• OK Fixed - New page Template: the scenes should act on the structure currently rendered Jaime Prilusky 03:33, 29 July 2025 (UTC)

• OK Fixed - Journal: anonymous users (not logged-in), can not read Journal pages. --Jaime Prilusky 03:00, 30 March 2025 (UTC)

• OK Fixed - Unable to read pages of Group:MUZIC https://proteopedia.openfox.io/w/Group:MUZIC when logged in with my userid. Jaime Prilusky 01:21, 12 June 2025 (UTC)

• OK Fixed - On page https://proteopedia.openfox.io/w/Group:MUZIC:Titin, Suddenly, today, I no longer can even see this page - Get message: "Special page. Permission error You do not have permission to read this page, for the following reason: You do not have permission to read this page." Joel L. Sussman 10:37, 9 June 2025 (IL-Time)

• This appears to be due to NOT all production database has been copied Page https://proteopedia.openfox.io/w/Acetylcholinesterase is not showing 3D scenes [[User:Joel L. Sussman|Joel L. Sussman] 12:15, 6 July 2025 (IL Time)

• 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 - Mobile: Page https://proteopedia.openfox.io/w/Sandbox_016_I3DC is not showing the 3D Applets. n.b. works on web browser on Mac --[[User:Joel L. Sussman|Joel L. Sussman] 10:30, 9 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)

• OK Fixed - Missing page Special:Morph --Jaime Prilusky 16:05, 7 April 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 - Interactive elements (buttons, jmol links, checkboxes) don't all work, e.g. https://proteopedia.org/wiki/index.php/Lysozyme#Ligand-bound_structures vs. https://proteopedia.openfox.io/w/Hen_Egg-White_(HEW)_Lysozyme#Ligand-bound_structures. n.b. on proteopedia production site the button is modeled extra sugars while on OpenFox it is just ring and they behave differently. This is another example like the problem just above regarding LAST button only working --Karsten Theis 19:44, 29 March 2025 (UTC)

• 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 - The 2nd instance (near very bottom of page) of the JmolButton animation off does not appear on the page: https://proteopedia.openfox.io/w/Sandbox_I3DC_005, but if one looks at the identical page on the Proteopedia production system it appears, i.e. https://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798324008210 20-May-2025 11:05.

• OK Fixed - The .mp4 movies on this page are not working: https://proteopedia.openfox.io/w/Molecular_Workbench Compare with https://proteopedia.org/wiki/index.php/Molecular_Workbench Eric Martz 21:59, 29 March 2025 (UTC) -- Fixed. Yitzhak Krumbein . Fixed √ Eric Martz 18:13, 18 May 2025 (UTC)

• OK Fixed - At https://proteopedia.openfox.io/w/SARS-CoV-2_spike_protein_fusion_transformation there is a gray box saying It will be easier to see the domains if you look at only one of the three chains:. There should be two buttons below that line of text, inside the box. They do not display. Compare with https://proteopedia.org/wiki/index.php/SARS-CoV-2_spike_protein_fusion_transformation Another gray box in the section Fusion shows none of the 3 buttons that should be within it. Two radio buttons just below the subtitle Membrane Fusion Schematic are also missing. The green link alternate pathway just above that subtitle is mispositioned farther down. Eric Martz 21:30, 29 March 2025 (UTC) All Fixed √ Eric Martz 18:02, 2 June 2025 (UTC)

• 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 - On page https://proteopedia.openfox.io/w/Forms_of_DNA, most of the buttons do NOT show, see for comparison the same page in Proteopedia: https://proteopedia.org/wiki/index.php/Forms_of_DNA. n.b. this page was created on 20:42, 24 August 2023. Joel L. Sussman 10:35, 8 June 2025 (IL-Time)

• 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 - Jmol link titles are off by one, making text unreadable (example from Lysozyme page, https://proteopedia.openfox.io/w/Hen_Egg-White_(HEW)_Lysozyme#Surface_properties) --Karsten Theis 19:45, 29 March 2025 (UTC) Appears to me to be fixed Eric Martz 17:54, 2 June 2025 (UTC)

• OK Fixed - At https://proteopedia.openfox.io/w/SARS-CoV-2_spike_protein_priming_by_furin the first BLUE link below the yellow box, SARS-CoV-2 protein S fails. Eric Martz 21:23, 29 March 2025 (UTC) Fixed √ Eric Martz 16:53, 2 June 2025 (UTC)

• OK Fixed - The buttons [Toggle Animation] and [Run alternate morph] (must be clicked after the preceding green link to work) do not work here: https://proteopedia.openfox.io/w/Lipase_lid_morph // compare with https://proteopedia.org/wiki/index.php/Lipase_lid_morph [Toggle Animation] buttons are used in dozens of pages. Eric Martz 20:43, 29 March 2025 (UTC) Fixed √ Eric Martz 16:48, 2 June 2025 (UTC)

• 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 - it was missing a closing /StructureSection. Joel fixed on the Production site and OpenFox sit [19:15, 11 June 2025 (IL) - The StructureSection/JSmol fail to load here: https://proteopedia.openfox.io/w/Proton_Channels Eric Martz 18:41, 29 March 2025 (UTC) still broken Eric Martz 17:11, 2 June 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 - Page DOI missing. Compare footer https://proteopedia.org/w/Hemoglobin vs https://proteopedia.openfox.io/w/Hemoglobin --Jaime Prilusky 03:00, 30 March 2025 (UTC)

• OK Fixed - This jumps to the correct section within the StructureSection: https://proteopedia.org/wiki/index.php/Lac_repressor#DNA_Kinks This does NOT: https://proteopedia.openfox.io/w/Lac_repressor#DNA_Kinks Eric Martz 17:57, 2 June 2025 (UTC)

• on https://proteopedia.openfox.io/w/SARS-CoV-2_spike_protein_fusion_transformation The green link An Alternate pathway is not working it yields the text in Jmol applet:
• Unrecognized file format for file https://proteopedia.openfox.io/irr ,IDOCTYPE html> <html class="client-nojs" lang=" en" dir="ltr"> <head> Joel L. Sussman 09:45, 4 June 2025 (IL time)

• OK Fixed - missing on proteopedia.openfox.io https://proteopedia.org/w/Drug_and_peptide_transport_in_humans Jaime Prilusky 15:59, 26 May 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 - is due to split of DB. On page https://proteopedia.openfox.io/w/Introduction_to_protein_structure#Turns_and_loops, structure load with a large grey ball. n.b. this may be due to the initial load command, i.e. StructureSection load='1a3n_au', which loads only the assymetric unit Joel L. Sussman 10:35, 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 - is due to split of DB. On page https://proteopedia.openfox.io/w/7o2l, no structure load, but one gets text

• OK Fixed - after loading a scene, Jmol freeze. Tried SAT on Sandbox_I3DC_001, scene Animation. Jaime Prilusky 20:28, 18 May 2025 (UTC)

• 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)

• The font used for the titles fails to distinguish zero from letter oh. This leads to serious confusion/errors. The title font in public proteopedia is not much better. This title font should be changed to one that has a line through zero to be unambiguous. Compare
  • https://proteopedia.openfox.io/w/7k0x
  • https://proteopedia.openfox.io/w/7kox
  • https://proteopedia.openfox.io/w/7v0o
  • https://proteopedia.openfox.io/w/7vo0
  • Eric Martz 17:36, 2 June 2025 (UTC)
  • And there is also the problem between number one and lowercase L.
    Maybe Atkinson Hyperlegible Font; it's SansSerif, not monospaced as most with dashed zeros are (not nice for regular text titles). Donwload web font.
    Another candidates: Go Font Finlandica GoogleFont
    Angel_Herraez 16:58, 12 August 2025 (UTC)