Proteopedia:Wishlist: Difference between revisions
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===Items Awaiting Solutions=== | ===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"). --[[User:Karsten Theis|Karsten Theis]] 14:32, 6 February 2021 (UTC) | |||
* Prevent use of coordinates with unknown source --[[User:Karsten Theis|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 <code>set cartoonSteps true</code> or similar. --[[User:Angel Herraez|Angel_Herraez]] 11:57, 30 January 2018 (UTC) | * Change the default rendering for nucleic acids to use <code>set cartoonSteps true</code> or similar. --[[User:Angel Herraez|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 --[[User:Angel Herraez|Angel_Herraez]] 17:37, 22 March 2018 (UTC) | ** Not easy, since it needs load =xxxx/dssr to retrieve the information --[[User:Angel Herraez|Angel_Herraez]] 17:37, 22 March 2018 (UTC) | ||
* In the login redirect page, add some useful links. --[[User:Angel Herraez|Angel_Herraez]] 11:57, 30 January 2018 (UTC) | * In the login redirect page, add some useful links. --[[User:Angel Herraez|Angel_Herraez]] 11:57, 30 January 2018 (UTC) | ||
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** add links to I3DC / journals | ** add links to I3DC / journals | ||
** animated image of journal banners | ** animated image of journal banners | ||
* In [[I3DC]], each graphic journal banner should be linked to the main journal website. | * 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'. --[[User:Angel Herraez|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 [[Sandboxes|sandbox pages]]. [[User:Eric Martz|Eric Martz]] 21:24, 31 January 2010 (IST) (after discussion with Jaime Prilusky) <span style="color:brown;">A mechanism now exists for creating a block of ''Sandbox Reserved'' pages. Contact {{Template:Contact}} to arrange this.</span> The [[Special:SandboxReservation]] form needs to be linked into all relevant pages. | * '''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 [[Sandboxes|sandbox pages]]. [[User:Eric Martz|Eric Martz]] 21:24, 31 January 2010 (IST) (after discussion with Jaime Prilusky) <span style="color:brown;">A mechanism now exists for creating a block of ''Sandbox Reserved'' pages. Contact {{Template:Contact}} to arrange this.</span> 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]]. [[User:Eric Martz|Eric Martz]] 20:33, 16 November 2009 (IST) | * '''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]]. [[User:Eric Martz|Eric Martz]] 20:33, 16 November 2009 (IST) | ||
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===Items Solved=== | ===Items Solved=== | ||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''Shorten the <i>Related Entries</i> 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. [[User:Jaime Prilusky|Jaime Prilusky]] 20:11, 18 November 2020 (UTC) | |||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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 [[User:Eric Martz|Eric Martz]]) [[User:Jaime Prilusky|Jaime Prilusky]] 03:24, 4 June 2018 (UTC) This is now fixed --[[User:Angel Herraez|Angel_Herraez]] 19:37, 16 October 2018 (UTC) | |||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> Make it possible to filter a search for either seeded pages or authored pages. --[[User:Angel Herraez|Angel_Herraez]] 16:40, 20 July 2018 (UTC). Checkboxes under Search page allows to search only for Seeded or Human authored pages. [[User:Jaime Prilusky|Jaime Prilusky]] 11:24, 22 July 2018 (UTC) | |||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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. | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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. | ||
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===Items Awaiting Solutions (SAT)=== | ===Items Awaiting Solutions (SAT)=== | ||
* Improve and simplify the transition options ([[User:Karsten_Theis/transition_proposal|proposal]]). --[[User:Karsten Theis|Karsten Theis]] 13:47, 28 August 2019 (UTC) | |||
* Add some links to useful sites. --[[User:Angel Herraez|Angel_Herraez]] 11:47, 30 January 2018 (UTC) | * Add some links to useful sites. --[[User:Angel Herraez|Angel_Herraez]] 11:47, 30 January 2018 (UTC) | ||
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** links to tutorials | ** links to tutorials | ||
** validation with clashes <code>{*}.radius = {*}.property_clashes.all</code> | ** validation with clashes <code>{*}.radius = {*}.property_clashes.all</code> | ||
** validation with density <code>load = | ** validation with density <code>load =xxxx/val; {*}.radius = {*}.property_rsrz.all</code> | ||
** display domains <code>load = | *** tip: https://chemapps.stolaf.edu/jmol/jsmol/validation.htm | ||
** display domains <code>load =xxxx/dom; show domains;</code> | |||
** contacts script for ligands (surface, rainbow, hotspots as in PDBe) | ** contacts script for ligands (surface, rainbow, hotspots as in PDBe) | ||
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* Advanced load option for large assemblies e.g. viruses: <code>load filter "bychain"</code> -- one dummy atom per chain. --[[User:Angel Herraez|Angel_Herraez]] 11:57, 30 January 2018 (UTC) | * Advanced load option for large assemblies e.g. viruses: <code>load filter "bychain"</code> -- one dummy atom per chain. --[[User:Angel Herraez|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. [[User:Eric Martz|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. [[User:Eric Martz|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. [[User:Emartz|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. [[User:Emily Forschler|Emily Forschler]] 03:14, 6 June 2008 (IDT) <span style="color:brown;">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 {{Template:Contact}}.</span> | |||
* In Colors, ability to make a '''surface''' translucent. [[User:Eric Martz|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. [[User:Eric Martz|Eric Martz]] 21:43, 5 February 2011 (IST) | |||
* | * A better '''color picker''' for the [[SAT|Scene Authoring Tool]]. See [http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/JmolColorPicker/Test%20VSColorPicker.html these demos], and ''colorpicker'' discussion on the jmol-users list. | ||
===Items Solved (SAT)=== | |||
* | * Report the number of atoms selected, below Jmol. Update report with each change in number selected. [[User:Eric Martz|Eric Martz]] 22:06, 13 January 2011 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|Jaime Prilusky]] 10:42, 19 November 2020 (UTC) | ||
* | * Allow to load any scene on the page, independently of their origin --[[User:Jaime Prilusky|Jaime Prilusky]] 12:21, 3 September 2020 (UTC) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|Jaime Prilusky]] 10:41, 19 November 2020 (UTC) | ||
* | * Load scenes when the provided name is a REDIRECT page --[[User:Jaime Prilusky|Jaime Prilusky]] 12:21, 3 September 2020 (UTC) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|Jaime Prilusky]] 10:41, 19 November 2020 (UTC) | ||
* In | * 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)". [[User:Eric Martz|Eric Martz]] 20:40, 21 March 2010 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> | ||
* In Representations, | * 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. [[User:Eric Martz|Eric Martz]] 22:10, 25 January 2011 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|Jaime Prilusky]] 04:57, 11 October 2020 (UTC) | ||
* In | * In Representations, include a dialog for '''slabbing'''. [[User:Eric Martz|Eric Martz]] 21:45, 5 February 2011 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|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. [[User:Karl Oberholser|Karl Oberholser]] 18:16, 26 January 2011 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|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. [[User:Karl Oberholser|Karl Oberholser]] 16:35, 31 January 2011 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|Jaime Prilusky]] 10:19, 10 October 2020 (UTC) | ||
* | * Under the Load Molecule tab add an option to append a molecule. [[User:Karl Oberholser|Karl Oberholser]] 17:50, 26 January 2011 (IST) <span style="background-color:yellow;color:green">'''SOLVED:'''</span> [[User:Jaime Prilusky|Jaime Prilusky]] 09:38, 10 October 2020 (UTC) | ||
* | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> When a scene is open for editing, it should remember the transition options that were used for it. --[[User:Angel Herraez|Angel_Herraez]] 11:56, 5 September 2017 (UTC). Implemented --[[User:Angel Herraez|Angel_Herraez]] 12:34, 17 October 2018 (UTC) | ||
* | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> Review the correct functioning of scene transitions. [[User:Angel Herraez|Angel_Herraez]] 14:18, 19 June 2017 (UTC) [[User:Jaime Prilusky|Jaime Prilusky]] 11:39, 17 October 2018 (UTC) | ||
* | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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. --[[User:Karsten Theis|Karsten Theis]] 15:04, 13 October 2018 (UTC) [[User:Jaime Prilusky|Jaime Prilusky]] 11:34, 17 October 2018 (UTC) | ||
=== | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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). [[User:Angel Herraez|Angel_Herraez]] 14:18, 19 June 2017 (UTC) [[User:Jaime Prilusky|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. [[User:Angel Herraez|Angel_Herraez]] 11:06, 20 August 2017 (UTC) | |||
*<span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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. [[User:Emily Forschler|Emily Forschler]] 00:07, 6 June 2008 (IDT) | *<span style="background-color:yellow;color:green">'''SOLVED:'''</span> 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. [[User:Emily Forschler|Emily Forschler]] 00:07, 6 June 2008 (IDT) | ||