Proteopedia:Wishlist

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This is the page to list features you wish Proteopedia had. As Proteopedia grows and develops, we will try to implement the best and most appropriate ideas.

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Contents

Wishlist for Outside the Molecular Scene Authoring Tools (SAT)

Items Awaiting Solutions

  • Make the printable version of pages more useful. Currently, when the page contains a scrollable structuresection, printing the printable version truncates the text not in the scrolling box (on Firefox and Chrome, e.g.). Also, the links are removed. For a PDF version of the article, it would be nice to retain the links, and to remove the scrollable structure section (maybe replacing the Jmol window by a white box labeled "interactive 3D content would appear on the live page here"). --Karsten Theis 14:32, 6 February 2021 (UTC)
  • Prevent use of coordinates with unknown source --Karsten Theis 13:51, 28 August 2019 (UTC)
    • Incorporate a remark into PDB when copying an uploaded file to getfrozenstructure
    • Incorporate a remark into PDB when returning a morph from the pymol morph server
    • Urge users to incorporate source information and their name into PDB headers before they upload
  • Change the default rendering for nucleic acids to use set cartoonSteps true or similar. --Angel_Herraez 11:57, 30 January 2018 (UTC) See also below, wishlist for SAT
    • Not easy, since it needs load =xxxx/dssr to retrieve the information --Angel_Herraez 17:37, 22 March 2018 (UTC)
  • In the login redirect page, add some useful links. --Angel_Herraez 11:57, 30 January 2018 (UTC)
  • In the home page --Angel_Herraez 11:57, 30 January 2018 (UTC)
    • add some stats and their application (?)
    • add links to I3DC / journals
    • animated image of journal banners
  • In I3DC, each graphic journal banner should be linked to the main journal website.
  • Beside the 'biological assembly' radio button, add a help/info icon to explain 'probable biological unit'. --Angel_Herraez 16:40, 20 July 2018 (UTC)
  • A form for reserving a block of Sandbox Reserved NN pages would be a great help to educators who have their students create content in sandbox pages. Eric Martz 21:24, 31 January 2010 (IST) (after discussion with Jaime Prilusky) A mechanism now exists for creating a block of Sandbox Reserved pages. Contact Image:Contact-email.png to arrange this. The Special:SandboxReservation form needs to be linked into all relevant pages.
  • Popup for scripted animations: a popup mechanism where the author of the page can specify an uploaded script to be played in the popup window. This would allow complex scripted animations to be played in a large (resizable) Jmol window. An example of such a scripted animation is at the "Play Animation" button at User:Eric_Martz/Molecular_Playground/HIVDrug. Eric Martz 20:33, 16 November 2009 (IST)
  • Molprobity could be added under About this structure in the auto-seeded pages. Eric Martz plans to write a short explanation to accompany a link. Eric Martz 20:00, 13 April 2008 (IDT)
  • Sequence and structure-related entries could be linked to every entry. Currently, at 2ic8, I can click the link to PDBSum, and there click a mysterious plus button, which gives me a list of sequence-related entries. However, I must then enter each one by hand into Proteopedia. It would be great if this list, already linked, were at the bottom of every PDB-code-titled page. OCA already does sequence-based searching. All we need is a structure-based search as well for "structure neighbors". Eric Martz 04:30, 26 April 2008 (IDT)
  • Quiz improvements in the emailed report (see Help:Quiz): (Eric Martz 21:29, 31 January 2010 (IST))
    • Include the full URL of the page containing the quiz.
    • In addition to the summary score, the score for each question, with questions identified by number and the text of the question.
    • Change the subject of the report email message to the student's name, and the summary score.
  • Automatic Animations: A mechanism to create a button that generates, in Jmol, an animation made from all the green links on the page (or a subset of them from a checkbox list?). Thanks to Lynmarie Thompson for this suggestion. Eric Martz 19:06, 11 November 2009 (IST) See partial solution below.
  • To encourage authors to follow Proteopedia:Policy regarding links to Wikipedia, automatically detect wikipedia during every preview/save and refer the author to Proteopedia:Policy. Emartz 02:10, 16 March 2008 (IST)
  • Tabulate characteristics of PDB codes on Category pages (in this order): PDB code, resolution, year, title, authors (ideally first and last author names like "Harel/Sussman" for 2ace), number of chains in the asymmetric unit, and ligand abbreviations. 2ace would look like this:
2ace2.50A1996NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA Harel/SussmanChains=1ACH
Topic pages should be listed first, before PDB code pages, and without any additional characteristics.
  • Support two Jmols side by side, for comparisons. (this is already possible, but not possible to sync them yet: see 2b8n --Eran Hodis 22:23, 5 April 2008 (IDT))
    • Synchronize mouse-directed rotations and zooms (this now works amazingly well, see Chapter 4 in the Demo Tutorial at http://bioinformatics.org/jmol-tutorials -- where by the way you can also see "toggle quality" working very clearly -- my links are labeled "smoother rotation" and "smoother graphics" to the lower left of Jmol).
    • Provide a mechanism for one green link that sends separate scripts to each Jmol simultaneously. Maybe not necessary? Just use two green links? What is cool is to start with scenes that align the two molecules. Then they stay aligned as you rotate/zoom with the mouse (provided spin is left off at the beginning -- when it is on, one molecule tends to lag behind the other).
  • Add a 'quality' parameter to the applet tag to enable the quality level of the 3D model to be set on loading. Greg Black 21:41, 2 February 2009 (IST) Any strong reasons to do this? Quality affects speed, and so it should be a decision of the user. Angel Herraez 08:43, 17 June 2017 (UTC)

Items Solved

  • SOLVED: Shorten the Related Entries List: In a seeded page, e.g. 1h6m, when there are more than 30 related entries, make the division scrollable at 5 lines, instead of letting it push other important sections out of view. Jaime Prilusky 20:11, 18 November 2020 (UTC)
  • SOLVED: For a PDB-code titled page with an X-ray structure, initially the resolution is shown. But after a couple of seconds, it is replaced with the radio buttons for asymmetric unit vs. biological assembly. It would be great if the resolution would also remain visible.(reminded by Eric Martz) Jaime Prilusky 03:24, 4 June 2018 (UTC) This is now fixed --Angel_Herraez 19:37, 16 October 2018 (UTC)
  • SOLVED: Make it possible to filter a search for either seeded pages or authored pages. --Angel_Herraez 16:40, 20 July 2018 (UTC). Checkboxes under Search page allows to search only for Seeded or Human authored pages. Jaime Prilusky 11:24, 22 July 2018 (UTC)
  • SOLVED: Automatically front, center, and size ligands and sites when their green links are clicked. That is, the molecule should rotate to put the selected entity in front of its center of mass, the selected entity should become the center of rotation/zoom, and the molecule should be zoomed (up or down) to make the selected entity fill e.g. 75% of the Jmol diameter.
I believe this is implemented. However, two issues could be improved: (a) When there are several ligands with same name, the focus act on their center, which is not too helpful. It would be better to focus on just the first one. (b) If the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script. Angel_Herraez 09:05, 17 June 2017 (UTC).
Both (a) and (b) are fixed now (the first group in the first chain is selected for focus). Angel_Herraez 12:07, 5 September 2017 (UTC)
  • SOLVED IN PART: Automatic Animations: A mechanism to create a button that generates, in Jmol, an animation made from all the green links on the page (or a subset of them from a checkbox list?). Thanks to Lynmarie Thompson for this suggestion. Eric Martz 19:06, 11 November 2009 (IST)
SOLUTION: Each JSmol panel has a button that any user can click to produce an animate image on that scene (one at a time). Also, for seeded pages such animation will be displayed in the page initially, in place of the model. Angel Herraez 08:41, 17 June 2017 (UTC)
  • SOLVED: On a seeded page, if viewing the full model, then switching between Biological Assembly and Asymmetric Unit should display the full model too. --Angel_Herraez 11:06, 24 June 2017 (UTC)
  • SOLVED: Biological units (from RCSB) should be the default initial scenes, with a view of the asymmetric unit optional, as agreed in discussion. Eric Martz plans to provide a mock-up of an advanced page that would have views from EBI PQS, EBI PISA, and RCSB biological units, with brief explanations of each.
SOLUTION: Default in seeded pages is the preferred assembly, i.e. biological assembly, from PDBe (but stored in Proteopedia server). If not available, the classical PDB entry will be displayed, which should be asymmetric unit. Below the JSmol the type of currently displayed model is identified and, if both are available, there are radio buttons to switch between them. Angel Herraez 08:35, 17 June 2017 (UTC)
  • SOLVED: Searching for a plural should find the singular match, and vice versa. For example: I searched for "histocompatibility antigens" and did not find the page "Category: Histocompatibility antigen". Searching for "histocompatibility antigen" did find this page. Emartz 19:00, 8 March 2008 (IST) In contrast, searching for "theoretical model" does find Theoretical models. Eric Martz 20:42, 16 November 2009 (IST) This appears to have been solved. See the examples at Help:Searching#Advantages_of_the_wiki_search_box. Eric Martz 00:55, 9 November 2011 (IST)
  • SOLVED: Searching for a term should find a redirect titled with that term. For example, I searched for "supplementary materials" but failed to find Proteopedia:Workbench. So I created a page titled Supplementary materials and redirected it to Proteopedia:Workbench. However, when I search for "Supplementary materials", the results page still says "No page title matches", despite the statement above that on the same search results page "You searched for supplementary materials" showing the link in blue (which would be in red if there was no such page)! Eric Martz 04:05, 19 December 2009 (IST) SOLUTION: The solution may have been present all along but difficult to notice. After you complete the search, scroll to the bottom of the page, where you will find checkboxes for the domains/namespaces included in the search by default. If you are logged in, the default is what you set in my preferences. The last checkbox is List redirects. It is unchecked by default and this cannot be changed in my preferences. Check it and rerun the search. Now Article Title Matches include redirect pages. Example: Searching for CRABP finds zero title matches, but after you check the List redirects box, there are five title matches. Eric Martz 23:44, 8 November 2011 (IST)
  • SOLVED: Ability to display a page with a specified version of Jmol, e.g. using a query parameter in the page URL, would enable safe testing of new features and new versions of Jmol before the entire database is upgraded to a new version of Jmol. Eric Martz 21:24, 31 January 2010 (IST) (after discussion with Jaime Prilusky) A mechanism now exists for requesting a specific Jmol version when displaying a Proteopedia page. Contact Image:Contact-email.png to arrange this. Jaime Prilusky 07:32, 14 March 2010 (IST)
  • SOLVED: There is now a link to FirstGlance underneath the molecule for every automatically seeded page. In every article titled with a single PDB id code, a link to (for a random case) "Explore 2ace" that goes to FirstGlance in Jmol. The link syntax is http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace.
  • SOLVED: Accept uploaded PDB filenames with spaces: When entering the name of an uploaded PDB file in the SAT's slot from uploaded file, the filename should be accepted with embedded spaces, which should automatically be converted to underscores. Currently, use of spaces produces a red "file not found" exception message in Jmol. Eric Martz 00:38, 16 December 2009 (IST). Jaime Prilusky 05:40, 16 December 2009 (IST) Done. Tested with 1ea5_rot.pdb -- Fix confirmed with "Hivpi binding simulation.pdb.gz" Eric Martz 20:56, 17 December 2009 (IST)
  • SOLVED: Long ligand names should be broken onto two lines so they are readable. An example is NDP at 3inm. Eric Martz 23:20, 11 December 2009 (IST). Implemented a close enough solution Jaime Prilusky 07:39, 13 December 2009 (IST)
  • SOLVED: Coloring by evolutionary conservation, based on the ConSurfDB server, is now offered on every page that is titled with a PDB code.
  • SOLVED: All models in NMR ensembles (and the 118 multiple-model X-ray entries) should be the initial view in auto-seeded pages. Eric Martz plans to provide the script for this.
  • SOLVED: Green links are now bold by default. A user-settable preference to make all green links bold or underlined (when not touched with the mouse) (I prefer underlined, with bold onMouseover) because in Windows browsers, the font is very thin, and the green color is hard to see. It is hard to scan a paragraph and find the green links. Also 9% of males are colorblind. Emartz 19:51, 9 March 2008 (IST)
Fortunately, full color blindness isn't as common as 9% but I agree underlining wold be the best to catch them all. --Ralf Stephan 10:54, 15 February 2009 (IST)
  • SOLVED: Have selenomethionine (MSE) treated as any other amino acid in the (Jmol) default settings - User:Morten Grøftehauge- June 1, 2008. I agree that it is very strange to have MSE treated as a ligand! Fixing this is far more important than adding new display options, like 2 jmols, so I'm moving this up. - User:Kevin Karplus -18 Aug 2008. MSE and other Non-Standard_Residue are now properly identified in the Structure block. See 2ab5 - Jaime Prilusky 10:24, 19 August 2008 (IDT)
  • SOLVED:Mechanism to spawn (open) a child window containing only Jmol with the current scene. Advantages: the child window can be resized, thereby resizing Jmol; the child window can be kept in view while the text in the parent Proteopedia window is scrolled. It should be possible to have green links work on both the Jmol on the Proteopedia page, and the child Jmol. Emartz 00:06, 17 March 2008 (IST). Implemented automatically generated button to spawn a popup window - Jaime Prilusky 10:16, 19 August 2008 (IDT)
  • SOLVED: (March 2, 2008): Quality (antialiasing) chosen by the user with "toggle quality" should remain in effect for all green links within that page. Imagine that you're projecting scenes to a class. Currently, with every new scene, you have to click "toggle quality" again to get high quality.
  • DISREGARDED: Several standard scenes, such as those in FirstGlance in Jmol, could be provided in a pull-down menu on the auto-seeded pages. It could be one more row in the table below Jmol. Eric Martz plans to provide the scripts and HTML color keys for these. Eric Martz 19:54, 13 April 2008 (IDT) Update: I am no longer in favor of this. Since FirstGlance in Jmol provides these, I see little advantage to the proposed redundancy, with the disadvantage of maintaining two similar systems. Eric Martz 22:34, 6 January 2011 (IST)

Wishlist for Inside the Molecular Scene Authoring Tools (SAT)

Items Awaiting Solutions (SAT)

  • Improve and simplify the transition options (proposal). --Karsten Theis 13:47, 28 August 2019 (UTC)
  • Add some links to useful sites. --Angel_Herraez 11:47, 30 January 2018 (UTC)
  • Add a picking option for dragging labels (set picking label) and instructions (may require shift+drag; double-click to set the label). --Angel_Herraez 11:47, 30 January 2018 (UTC)
  • Add an "advanced" tab. --Angel_Herraez 11:47, 30 January 2018 (UTC)
    • links to tutorials
    • validation with clashes {*}.radius = {*}.property_clashes.all
    • validation with density load =xxxx/val; {*}.radius = {*}.property_rsrz.all
    • display domains load =xxxx/dom; show domains;
    • contacts script for ligands (surface, rainbow, hotspots as in PDBe)
  • Rendering style for nucleic acids (DSSR): set cartoonSteps true --Angel_Herraez 11:47, 30 January 2018 (UTC)
  • Add hints to transition options, with better explanation, animated demos... --Angel_Herraez 11:47, 30 January 2018 (UTC)
  • Advanced load option for large assemblies e.g. viruses: load filter "bychain" -- one dummy atom per chain. --Angel_Herraez 11:57, 30 January 2018 (UTC)
  • cystine should be added to the protein residues list under groups in the selection dialog. cys (cysteine + cystine) can already be selected in limit to residue types. After adding cystine, one could, for example, select cys, then remove cystine from selection, leaving cysteine selected. Eric Martz 03:38, 19 April 2011 (IDT) This will have to wait until the version of Jmol within Proteopedia is upgraded. "Cystine" is defined in Jmol 12.2 but not in 11.8. Eric Martz 23:33, 18 January 2012 (IST)
  • Color keys displayed beneath Jmol, changing as needed with each green link. For example "alpha helix" and "beta strand" colored in the standard Jmol secondary colors. The standard keys should be pre-built and callable by name, perhaps by a parameter in the <scene ...> tag. Emartz 01:59, 19 March 2008 (IST) This is a really good idea! I've had to go to other sites to figure out what things stand for and was actually wondering if there was a way to make a key, but I guess not right now. Emily Forschler 03:14, 6 June 2008 (IDT) A color key mechanism is being implemented. See Gramicidin_Channel_in_Lipid_Bilayer for examples of resulting color keys. If you wish to be a beta tester for new capabilities, contact Image:Contact-email.png.
  • In Colors, ability to make a surface translucent. Eric Martz 22:31, 6 January 2011 (IST)
  • In Colors, ability to apply "color translucent -1" to the selected atoms. This works much better than positive integers for e.g. spacefill. Also, for cartoon, it would be useful if the coils were made a higher translucency than the ribbons in order to match better. Eric Martz 21:43, 5 February 2011 (IST)

Items Solved (SAT)

  • Report the number of atoms selected, below Jmol. Update report with each change in number selected. Eric Martz 22:06, 13 January 2011 (IST) SOLVED: Jaime Prilusky 10:42, 19 November 2020 (UTC)
  • Allow to load any scene on the page, independently of their origin --Jaime Prilusky 12:21, 3 September 2020 (UTC) SOLVED: Jaime Prilusky 10:41, 19 November 2020 (UTC)
  • Load scenes when the provided name is a REDIRECT page --Jaime Prilusky 12:21, 3 September 2020 (UTC) SOLVED: Jaime Prilusky 10:41, 19 November 2020 (UTC)
  • In Selection, within distance of selected, add option to expand selection to include entire residues containing any selected atoms. The Jmol command is "select within(group, selected)". Eric Martz 20:40, 21 March 2010 (IST) SOLVED:
  • In Representations, change set representation to replace representation and add add to representation and remove from representation. This allows, for example, the (sidechains + alpha carbons) of selected residues to be rendered as ball and stick (add representation) without erasing a backbone trace for those alpha carbons. Eric Martz 22:10, 25 January 2011 (IST) SOLVED: Jaime Prilusky 04:57, 11 October 2020 (UTC)
  • In Representations, include a dialog for slabbing. Eric Martz 21:45, 5 February 2011 (IST) SOLVED: Jaime Prilusky 03:42, 11 October 2020 (UTC)
  • Under the Save Scene tab add an option to spin about the z-axis in stead of the y-axis. Karl Oberholser 18:16, 26 January 2011 (IST) SOLVED: Jaime Prilusky 10:19, 10 October 2020 (UTC)
  • Under the Save Scene tab spin selection add an option for a rocking motion rather than a full 360 degree rotation. Karl Oberholser 16:35, 31 January 2011 (IST) SOLVED: Jaime Prilusky 10:19, 10 October 2020 (UTC)
  • Under the Load Molecule tab add an option to append a molecule. Karl Oberholser 17:50, 26 January 2011 (IST) SOLVED: Jaime Prilusky 09:38, 10 October 2020 (UTC)
  • SOLVED: When a scene is open for editing, it should remember the transition options that were used for it. --Angel_Herraez 11:56, 5 September 2017 (UTC). Implemented --Angel_Herraez 12:34, 17 October 2018 (UTC)
  • SOLVED: Review the correct functioning of scene transitions. Angel_Herraez 14:18, 19 June 2017 (UTC) Jaime Prilusky 11:39, 17 October 2018 (UTC)
  • SOLVED: When loading a scene in the SAT, show the caption so it becomes possible to edit it rather than rewrite it. When clicking on a new green link, overwrite the old caption even if the new scene has an empty caption. --Karsten Theis 15:04, 13 October 2018 (UTC) Jaime Prilusky 11:34, 17 October 2018 (UTC)
  • SOLVED: Add capability to the SAT for creating scenes of biological assemblies. Verify match between model used by the applet tag and that used by the SAT (maybe getLatestStructure vs. getFrozenStructure). Angel_Herraez 14:18, 19 June 2017 (UTC) Jaime Prilusky 11:34, 17 October 2018 (UTC)
In the applet tag, now it is possible to indicate if to load Asymmetric Unit or Biological Assembly (i.e. load=2ace_au load=2ace_ba). So the same mechanism could be used in the SAT, if we add a pair of radio buttons beside the "PDB code" slot. Need to take care of default and maybe what to do if the particular file does not exist. Angel_Herraez 11:06, 20 August 2017 (UTC)
  • SOLVED: Create a "reset" button for scene authoring tools, in particular the representations tab. Or an "undo" button. Something to allow the image to be returned to normal after experimenting with different representations without reloading. Emily Forschler 00:07, 6 June 2008 (IDT)
Undo/redo buttons implemented --Eran Hodis 20:47, 17 March 2010 (IST)
  • SOLVED: In the SAT, select groups within: In the SAT, Selection dialog, section "select within distance", change "select atoms within" to "select [ ]groups/[ ]atoms within". For groups, first select atoms within, then "select within(groups, selected)". Eric Martz 20:51, 7 December 2009 (IST)
  • SOLVED: Boldface labels option in the Scene Authoring Tool. Probably just a checkbox, and should be checked by default, since normal labels are hard to see. Eric Martz 23:05, 6 February 2010 (IST)
  • SOLVED: Popup in the SAT. This would allow small details to be seen more clearly, and show whether spinning is too jerky when Jmol is larger. Eric Martz 23:16, 7 December 2009 (IST). Please report side effects Jaime Prilusky 07:58, 13 December 2009 (IST)
  • SOLVED: When saving a scene (in the "save scene" dialog), a radio button to choose between "force spinning on", "force spinning off", "inherit spinning set by the user with 'toggle spinning'". (inherit spinning not implemented on purpose --Eran Hodis 22:23, 5 April 2008 (IDT))
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