Proteopedia:Openfox

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==Open Issues==
==Open Issues==
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(not in any particular order)
 
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* 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)
 
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* Mobile: Page https://proteopedia.openfox.io/w/Acetylcholinesterase is not working right. n.b. works on web browser on Mac--[[User:Joel L. Sussman|Joel L. Sussman] 12:15, 6 July 2025 (IL Time)
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===A===
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* Missing page [[Special:Contact]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:03, 7 April 2025 (UTC)
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* (2) Jaime & Itsik need speak about this as the email portion of this page is NOT working: [[Special:Contact]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:03, 7 April 2025 (UTC)
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* Missing page [[Special:SandboxReservation]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:09, 7 April 2025 (UTC)
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* (3) Jaime & Itsik need speak about this one which is not working [[Special:SandboxReservation]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:09, 7 April 2025 (UTC)
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* Unable to read pages of Group:MUZIC https://proteopedia.openfox.io/w/Group:MUZIC when logged in with my userid. [[User:Jaime Prilusky|Jaime Prilusky]] 01:21, 12 June 2025 (UTC)
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* (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 --[[User:Karsten Theis|Karsten Theis]] 19:45, 29 March 2025 (UTC)
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* 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." [[User:Joel L. Sussman|Joel L. Sussman]] 10:37, 9 June 2025 (IL-Time)
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* (5) If problem (old 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.--[[User:Jaime Prilusky|Jaime Prilusky]]
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* Not working https://proteopedia.openfox.io/cgi-bin/latestUserLogin --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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* (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. --[[User:Angel Herraez|Angel_Herraez]] 11:25, 13 August 2025 (UTC)
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* Journal: anonymous users (not logged-in), can not read Journal pages. --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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* (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. [[User:Angel Herraez|Angel_Herraez]] 11:48, 13 August 2025 (UTC)
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* '''Partly Fixed -''' Mutation pages not '''Working''', '''but missing Icons on OpenFox page''', please compare
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===B===
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https://proteopedia.openfox.io/w/Mutation:BRCA1 vs https://proteopedia.org/wiki/index.php/Mutation:BRCA1
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--[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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* 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. [[User:Jaime Prilusky|Jaime Prilusky]] 06:04, 11 June 2025 (UTC)
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* (12) At 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. [[User:Eric Martz|Eric Martz]] 19:23, 12 December 2025 (UTC)
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:: This was a file not found error, due to trying to '''directly load a pdb file''' rather that a scene file; indeed, this is not done with a scene but with a jmolLink tag and a script sub-tag; the file is supposedly in a subfolder below /images/ (as per the setup of the legacy site) and maybe in this new site pdb files are located elsewhere. --[[User:Angel Herraez|Angel Herraez]] 14:42, 19 December 2025 (UTC)
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:: '''Solution:''' pdb files (posibly other files inc. images) are not located at <code>/images/ </code> but at <code>/wiki/images/ </code>. I have fixed this particular page but it might happen in other pages. <span style="color:green;">Maybe some automatic redirection could be applied, i.e. the <code>/images/</code> folder be redirected to <code>/wiki/images/</code>?</span>
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* Mobile: When positioning horizontal (landscape) the phone, scrolling text and applet should be positioned side by side. [[User:Jaime Prilusky|Jaime Prilusky]] 05:59, 11 June 2025 (UTC)
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* (14) The '''Main Page''' needs to be formatted closer to the [https://bioinformatics.org/molvis/tmp/ppda-main-page/main-old.png old production version]. Here [https://bioinformatics.org/molvis/tmp/ppda-main-page/openfox-problems.png some problems are marked]. Here is a [https://bioinformatics.org/molvis/tmp/ppda-main-page/openfox-better.png better version in openfox] (comments were inserted) but still some problems are marked.
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* 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. --[[User:Karsten Theis|Karsten Theis]] 19:45, 29 March 2025 (UTC)
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* (17) Applet '''popup window''' not working for some scenes -- [[User:Jaime Prilusky|Jaime Prilusky]] 08:33, 21 December 2025 (UTC) On page [[User:Jaime_Prilusky/Test/Simple]], popup for scene "cylinders" works fine while popup for scene "1acj with Tacrine" fails.
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: Both are working correctly for me; Firefox Win11 --[[User:Angel Herraez|Angel Herraez]] 19:05, 25 December 2025 (UTC) <span style="color:green;">Can somebody else confirm?</span>
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*[https://proteopedia.openfox.io/cgi-bin/studiomngr StudioManager] is not working. Does the database has the table studio_access? --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC). <s>Perl code referred to old DB , rewrite it to read new DB --[[User:Yitzhak Krumbein |Yitzhak Krumbein ]]</s>. Still '''not working''': [https://proteopedia.openfox.io/cgi-bin/studiomngr StudioManager] should list current Studio pages --[[User:Jaime Prilusky|Jaime Prilusky]] 03:33, 3 April 2025 (UTC) -- I don't have access to prod Studio MGR so I can't compare [[User:Yitzhak Krumbein |Yitzhak Krumbein ]] Just sent you a screen capture by email --[[User:Jaime Prilusky|Jaime Prilusky]] 16:51, 3 April 2025 (UTC)
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* (19) "Search Proteopedia" (upper right corner of page in openfox) defaults only to the Main namespace. This default will cause most user searches to fail because they won't notice and/or won't understand about '''namespaces'''. The default search should include all namespaces (but not, in my opinion, talk namespaces). [[User:Eric Martz|Eric Martz]] 16:10, 22 December 2025 (UTC)
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* 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 --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC). Fixed --[[User:Yitzhak Krumbein |Yitzhak Krumbein ]]
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===C===
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*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. --[[User:Karsten Theis|Karsten Theis]] 19:45, 29 March 2025 (UTC)
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* (21) It is helpful to have '''search hits numbered''', as they are in old Proteopedia. [[User:Eric Martz|Eric Martz]] 16:28, 22 December 2025 (UTC)
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* (22) Pages with "Workbench" in their titles should be readable only by their authors. They should have a tab "workbench" that allows the owner to enable reading and/or editing by other Users. See https://proteopedia.openfox.io/w/Proteopedia:Workbench
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** When I am logged in as Eric Martz, I can read the contents of https://proteopedia.openfox.io/w/User:Test_Account_2/Workbench <span style="color:#00b000;">Fixed √</span> --[[User:Angel Herraez|Angel Herraez]] 11:18, 29 December 2025 (UTC)
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** When I am logged in as "Test Account 2" there is no "workbench" tab there. [[User:Eric Martz|Eric Martz]] 00:08, 27 December 2025 (UTC)
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==Issues marked as solved==
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* (23) The "Request Account" form needs a number of fixes, and it did not work when I requested a new account. Please see details at https://proteopedia.org/wiki/index.php/Proteopedia:Openfox_Request_Account [[User:Eric Martz|Eric Martz]] 00:08, 27 December 2025 (UTC)
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(might need a quick additional verification before swapping sites)
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* '''OK Fixed -''' Mobile: Search does not work on mobile unless you go to the home page. --[[User:Karsten Theis|Karsten Theis]] 19:45, 29 March 2025 (UTC)
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* (24) In all my testing so far, I was using the default '''JSmol version''' 14.31.8 which is very old and obsolete. It did not occur to me to use Preferences, Appearance, Advanced JSmol version until now. I strongly recommend that the current version of JSmol 16.3.41 (or 16.3.33 as is the default in old public Proteopedia) be the default in Openfox. {{Yelspan|Otherwise, much testing will have to be redone.}} [[User:Eric Martz|Eric Martz]] 00:08, 27 December 2025 (UTC)
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* '''OK Fixed -''' Missing page [[Special:Morph]] --[[User:Jaime Prilusky|Jaime Prilusky]] 16:05, 7 April 2025 (UTC)<br>
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* (25) '''Sequence Tool help:''' In seeded pages, there is a [show sequence] link (green background) at top left hand side. Next to it there is a question mark icon. Clicking on it should open a pop-up window, but nothing happens. The target page is index.php?title=Seqtool&printable=yes
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in Proteopedia at: https://proteopedia.org/cgi-bin/morph <br>
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:: The link code is <nowiki><i id="seqtoolInfo" class="fas fa-question-circle" onclick="seqtoolInfo();" style="display: inline-block;"></i></nowiki>
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in OpenFox at: https://proteopedia.openfox.io/perl/morph
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:: The action gives an error in the browser JS console saying <nowiki>Uncaught TypeError: (intermediate value).seqtoolInfo is not a function</nowiki>
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* '''OK Fixed -''' ONLY the LAST button works in
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* (26) Seeded pages like [https://proteopedia.openfox.io/w/2ghi this one] that have evolutionary conservation data (ConSurf) include a toggle, a checkbox which right now is fully adjacent to previous and following text; space needs to be added on both sides:
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https://proteopedia.openfox.io/w/Sandbox_buttons <br>
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:: <code>Check☐to colour</code> ==> <code>Check ☐ to colour</code>
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while both buttons work in <br>
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https://proteopedia.org/wiki/index.php/Sandbox_buttons --[[User:Joel L. Sussman|Joel L. Sussman]] 10:25, 7 July 2025 (IL-Time)
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*'''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''' --[[User:Karsten Theis|Karsten Theis]] 19:44, 29 March 2025 (UTC)
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* (27) '''Main page''': The blue "i" icon (for info) overlaid at bottom-right on each of the 3 large images is displayed duplicated vertically. It seems to be CSS background-image that needs "no-repeat".
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* '''OK Fixed -''' Missing 'Block Save' (blocks save page '''based on user and content''') --[[User:Jaime Prilusky|Jaime Prilusky]] 15:43, 7 April 2025 (UTC)
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* (28) The two checkboxes "[ ] Include only Seeded (Automatic) pages - [ ] only Human created pages" '''are missing''' when searching on the search slot on the top-right corner. They only appear after searching on the 'Search results' page. [[User:Jaime Prilusky|Jaime Prilusky]] 05:16, 30 December 2025 (UTC)
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* Link [show sequence] (top left hand side) works. The replacement link '''hide''' does not. [[User:Jaime Prilusky|Jaime Prilusky]] 05:54, 11 June 2025 (UTC)
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* (29) Applet on pages in languages other than English is not working on Mobile - see [https://proteopedia.openfox.io/w/Myoglobin_(arabic) Arabic], [https://proteopedia.openfox.io/w/Hemoglobin_(Hebrew) Hebrew], [https://proteopedia.openfox.io/w/Lysozyme_(Arabic) Arabic] and [https://proteopedia.org/wiki/index.php/Lysozyme_(hebrew) Hebrew] [[User:Jaime Prilusky|Jaime Prilusky]] 06:10, 30 December 2025 (UTC)
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* 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. [[User:Jaime Prilusky|Jaime Prilusky]] 19:00, 20 May 2025 (UTC)
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* (30) When a file has multiple structures (like [https://proteopedia.openfox.io/w/1o0l here]), a toggle is displayed under the JSmol panel to play or stop animation. When the pop-up is opened (large window with a duplicate of the structure), the animation toggle icon (right-pointing triangle within a circle) is very large; its size should be adjusted as it is in the calling page.
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: <code>#animCont svg { vertical-align:bottom; width:1.3em; height:1.3em; margin-bottom:0.1em; }</code>
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: Maybe this happens because the pop-up page, JSmolPopup.htm, is not calling Proteopedia.css, or it has the wrong version of this file.
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* '''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.
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===D===
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* '''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.
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* (31) The JSmol pop-up menu in the SAT is not properly CSS formatted. Specifically, triangular arrowheads should be flushed right for each entry that has sub-menus, not left and below the entry. Compare with menu for JSmol in the page.
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* '''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 [[User:Eric Martz|Eric Martz]] 21:59, 29 March 2025 (UTC) -- Fixed. [[User:Yitzhak Krumbein |Yitzhak Krumbein ]]. <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 18:13, 18 May 2025 (UTC)
 
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* '''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. [[User:Eric Martz|Eric Martz]] 21:30, 29 March 2025 (UTC) <span style="color:#00b000;">All Fixed √</span> [[User:Eric Martz|Eric Martz]] 18:02, 2 June 2025 (UTC)
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== Issues marked as '''to be made to work by the Weizmann Team''', after OpenFox becomes the production system==
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See [[Proteopedia:Openfox/Final Setup]]
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* '''OK Fixed -'''Pre-Fusion Structure section: gray box now has correct 2 buttons and they work. √
 
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* '''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. <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 16:49, 2 June 2025 (UTC)
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== Issues marked as solved: see [[Proteopedia:Openfox/Solved]] ==
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Moved to [[Proteopedia:Openfox/Solved]]
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* '''OK Fixed -'''Fusion section: line/spheres radio buttons are present and working. √
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(Might need a quick additional verification before swapping sites)
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* '''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.''' [[User:Joel L. Sussman|Joel L. Sussman]] 10:35, 8 June 2025 (IL-Time)
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* '''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.''' [[User:Joel L. Sussman|Joel L. Sussman]] 10:35, 8 June 2025 (IL-Time)
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* '''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) --[[User:Karsten Theis|Karsten Theis]] 19:45, 29 March 2025 (UTC) <span style="color:#00b000;">Appears to me to be fixed</span> [[User:Eric Martz|Eric Martz]] 17:54, 2 June 2025 (UTC)
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* '''OK Fixed -''' At https://proteopedia.openfox.io/w/SARS-CoV-2_spike_protein_priming_by_furin the first BLUE link below the yellow box, ''<u>SARS-CoV-2 protein S</u>'' fails. [[User:Eric Martz|Eric Martz]] 21:23, 29 March 2025 (UTC) <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 16:53, 2 June 2025 (UTC)
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* '''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. [[User:Eric Martz|Eric Martz]] 20:43, 29 March 2025 (UTC) <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 16:48, 2 June 2025 (UTC)
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* '''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. --[[User:Karsten Theis|Karsten Theis]] 19:49, 29 March 2025 (UTC)
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* '''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 [[User:Eric Martz|Eric Martz]] 18:41, 29 March 2025 (UTC) <span style="color:red;">still broken</span> [[User:Eric Martz|Eric Martz]] 17:11, 2 June 2025 (UTC)
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* '''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? [[User:Eric Martz|Eric Martz]] 18:18, 29 March 2025 (UTC) <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 17:39, 2 June 2025 (UTC)
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* '''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". [[User:Eric Martz|Eric Martz]] 18:04, 29 March 2025 (UTC) <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 17:40, 2 June 2025 (UTC)
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* '''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.) [[User:Eric Martz|Eric Martz]] 17:44, 29 March 2025 (UTC) <span style="color:red;">still missing</span> [[User:Eric Martz|Eric Martz]] 17:45, 2 June 2025 (UTC)
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* '''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. [[User:Eric Martz|Eric Martz]] 20:34, 29 March 2025 (UTC) <span style="color:#00b000;">Fixed √</span> [[User:Eric Martz|Eric Martz]] 18:00, 2 June 2025 (UTC)
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* '''OK Fixed -''' Page DOI missing. Compare footer https://proteopedia.org/w/Hemoglobin vs https://proteopedia.openfox.io/w/Hemoglobin --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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* '''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 [[User:Eric Martz|Eric Martz]] 17:57, 2 June 2025 (UTC)
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* 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:
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*'''Unrecognized file format for file https://proteopedia.openfox.io/irr ,IDOCTYPE html> <html class="client-nojs" lang=" en" dir="ltr"> <head>''' [[User:Joel L. Sussman|Joel L. Sussman]] 09:45, 4 June 2025 (IL time)
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* '''OK Fixed -''' missing on proteopedia.openfox.io https://proteopedia.org/w/Drug_and_peptide_transport_in_humans [[User:Jaime Prilusky|Jaime Prilusky]] 15:59, 26 May 2025 (UTC)
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* '''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". [[User:Eric Martz|Eric Martz]] 17:44, 2 June 2025 (UTC)
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* '''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. [[User:Joel L. Sussman|Joel L. Sussman]] 10:31, 4 June 2025 (IL-Time)
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* '''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 [[User:Joel L. Sussman|Joel L. Sussman]] 10:35, 4 June 2025 (IL-Time)
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* '''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. [[User:Joel L. Sussman|Joel L. Sussman]] 10:54, 4 June 2025 (IL-Time)
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* '''OK Fixed - is due to split of DB.''' On page https://proteopedia.openfox.io/w/7o2l, no structure load, but one gets text
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* '''OK Fixed -''' after loading a scene, Jmol freeze. Tried SAT on [[Sandbox_I3DC_001]], scene Animation. [[User:Jaime Prilusky|Jaime Prilusky]] 20:28, 18 May 2025 (UTC)
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* '''OK Fixed -''' on tab 'load scene', the dropdown 'Load scenes from this page' must show as a default the current page. --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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* '''OK Fixed -''' on tab 'load scene', dropdown 'Scene name' and 'Version number' should have 'Choose', not selecting for the user. --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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* '''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." --[[User:Jaime Prilusky|Jaime Prilusky]] 03:00, 30 March 2025 (UTC)
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*An unfortunate problem with the old site happens when there are multiple green links to animated scenes, as here:
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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. [[User:Eric Martz|Eric Martz]] 18:54, 29 March 2025 (UTC)
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==Issues to solve during final overall scanning==
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(possible a side effect of the initial database upgrade)
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* Homepage: Featured EDU/7 does not load --[[User:Karsten Theis|Karsten Theis]] 19:44, 29 March 2025 (UTC)
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Line 134: Line 78:
* 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
* 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
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* https://proteopedia.openfox.io/w/7k0x
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:* https://proteopedia.openfox.io/w/7k0x
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* https://proteopedia.openfox.io/w/7kox
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:* https://proteopedia.openfox.io/w/7kox
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* https://proteopedia.openfox.io/w/7v0o
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:* https://proteopedia.openfox.io/w/7v0o
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* https://proteopedia.openfox.io/w/7vo0
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:* https://proteopedia.openfox.io/w/7vo0
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* [[User:Eric Martz|Eric Martz]] 17:36, 2 June 2025 (UTC)
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:* [[User:Eric Martz|Eric Martz]] 17:36, 2 June 2025 (UTC)
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:* And there is also the problem between number one and lowercase L.
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:Maybe [https://www.BrailleInstitute.org/freefont/ Atkinson Hyperlegible Font]; it's SansSerif, not monospaced as most with dashed zeros are (not nice for regular text titles). [https://github.com/googlefonts/atkinson-hyperlegible Donwload web font]. <br>Another candidates: [https://www.fontsquirrel.com/fonts/go Go Font] [https://fonts.google.com/specimen/Finlandica?preview.text=abc%20oO0%20l1 Finlandica GoogleFont] <br> [[User:Angel Herraez|Angel_Herraez]] 16:58, 12 August 2025 (UTC)
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: Current font is better, but not very good: [[Image:Linux Libertine sample.png]]--[[User:Angel Herraez|Angel Herraez]] 11:58, 30 December 2025 (UTC)

Current revision

Contents

Open Issues

A

  • (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)
  • (5) If problem (old 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
  • (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. Angel_Herraez 11:48, 13 August 2025 (UTC)

B

This was a file not found error, due to trying to directly load a pdb file rather that a scene file; indeed, this is not done with a scene but with a jmolLink tag and a script sub-tag; the file is supposedly in a subfolder below /images/ (as per the setup of the legacy site) and maybe in this new site pdb files are located elsewhere. --Angel Herraez 14:42, 19 December 2025 (UTC)
Solution: pdb files (posibly other files inc. images) are not located at /images/ but at /wiki/images/ . I have fixed this particular page but it might happen in other pages. Maybe some automatic redirection could be applied, i.e. the /images/ folder be redirected to /wiki/images/?
  • (17) Applet popup window not working for some scenes -- Jaime Prilusky 08:33, 21 December 2025 (UTC) On page User:Jaime_Prilusky/Test/Simple, popup for scene "cylinders" works fine while popup for scene "1acj with Tacrine" fails.
Both are working correctly for me; Firefox Win11 --Angel Herraez 19:05, 25 December 2025 (UTC) Can somebody else confirm?
  • (19) "Search Proteopedia" (upper right corner of page in openfox) defaults only to the Main namespace. This default will cause most user searches to fail because they won't notice and/or won't understand about namespaces. The default search should include all namespaces (but not, in my opinion, talk namespaces). Eric Martz 16:10, 22 December 2025 (UTC)

C

  • (21) It is helpful to have search hits numbered, as they are in old Proteopedia. Eric Martz 16:28, 22 December 2025 (UTC)
  • (24) In all my testing so far, I was using the default JSmol version 14.31.8 which is very old and obsolete. It did not occur to me to use Preferences, Appearance, Advanced JSmol version until now. I strongly recommend that the current version of JSmol 16.3.41 (or 16.3.33 as is the default in old public Proteopedia) be the default in Openfox. Otherwise, much testing will have to be redone. Eric Martz 00:08, 27 December 2025 (UTC)
  • (25) Sequence Tool help: In seeded pages, there is a [show sequence] link (green background) at top left hand side. Next to it there is a question mark icon. Clicking on it should open a pop-up window, but nothing happens. The target page is index.php?title=Seqtool&printable=yes
The link code is <i id="seqtoolInfo" class="fas fa-question-circle" onclick="seqtoolInfo();" style="display: inline-block;"></i>
The action gives an error in the browser JS console saying Uncaught TypeError: (intermediate value).seqtoolInfo is not a function
  • (26) Seeded pages like this one that have evolutionary conservation data (ConSurf) include a toggle, a checkbox which right now is fully adjacent to previous and following text; space needs to be added on both sides:
Check☐to colour ==> Check ☐ to colour
  • (27) Main page: The blue "i" icon (for info) overlaid at bottom-right on each of the 3 large images is displayed duplicated vertically. It seems to be CSS background-image that needs "no-repeat".
  • (28) The two checkboxes "[ ] Include only Seeded (Automatic) pages - [ ] only Human created pages" are missing when searching on the search slot on the top-right corner. They only appear after searching on the 'Search results' page. Jaime Prilusky 05:16, 30 December 2025 (UTC)
  • (30) When a file has multiple structures (like here), a toggle is displayed under the JSmol panel to play or stop animation. When the pop-up is opened (large window with a duplicate of the structure), the animation toggle icon (right-pointing triangle within a circle) is very large; its size should be adjusted as it is in the calling page.
#animCont svg { vertical-align:bottom; width:1.3em; height:1.3em; margin-bottom:0.1em; }
Maybe this happens because the pop-up page, JSmolPopup.htm, is not calling Proteopedia.css, or it has the wrong version of this file.

D

  • (31) The JSmol pop-up menu in the SAT is not properly CSS formatted. Specifically, triangular arrowheads should be flushed right for each entry that has sub-menus, not left and below the entry. Compare with menu for JSmol in the page.


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

See Proteopedia:Openfox/Final Setup


Issues marked as solved: see Proteopedia:Openfox/Solved

Moved to Proteopedia:Openfox/Solved

(Might need a quick additional verification before swapping sites)


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
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)
Current font is better, but not very good: Image:Linux Libertine sample.png--Angel Herraez 11:58, 30 December 2025 (UTC)
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