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) | * 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 copying an uploaded file to getfrozenstructure | ||
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* '''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> 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) | ||
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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) | * 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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** validation with clashes <code>{*}.radius = {*}.property_clashes.all</code> | ** validation with clashes <code>{*}.radius = {*}.property_clashes.all</code> | ||
** validation with density <code>load =xxxx/val; {*}.radius = {*}.property_rsrz.all</code> | ** validation with density <code>load =xxxx/val; {*}.radius = {*}.property_rsrz.all</code> | ||
*** tip: https://chemapps.stolaf.edu/jmol/jsmol/validation.htm | |||
** display domains <code>load =xxxx/dom; show domains;</code> | ** 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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* 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) | * 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. | * 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)=== | ===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 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 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> | ||