Proteopedia:Wishlist: Difference between revisions
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* 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. | ||
* '''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) < | * '''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. | ||
* '''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. (This can be done with overflow: auto; in the style for the division.) | * '''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. (This can be done with overflow: auto; in the style for the division.) | ||
*< | *<span style="color:808080">'''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. [[User:Eric Martz|Eric Martz]] 19:54, 13 April 2008 (IDT)</span> '''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. [[User:Eric Martz|Eric Martz]] 22:34, 6 January 2011 (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) | * '''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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* '''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: | * '''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: | ||
<table border=1 cellpadding= | <table border=1 cellpadding=3 cellspacing=0 style="margin-left:3ex;"><tr><td> | ||
2ace</td><td>2.50A</td><td>1996</td><td>NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA</td><td> Harel/Sussman</td><td>Chains=1</td><td>ACH | 2ace</td><td>2.50A</td><td>1996</td><td>NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA</td><td> Harel/Sussman</td><td>Chains=1</td><td>ACH | ||
</td></tr></table> | </td></tr></table> | ||
Topic pages should be listed first, before PDB code pages, and without any additional characteristics. | :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]]'' --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT)) | * Support '''two Jmols side by side''', for comparisons. (''this is already possible, but not possible to sync them yet: see [[2b8n]]'' --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT)) | ||
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** 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). | ** 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. [[User:Greg Black|Greg Black]] 21:41, 2 February 2009 (IST) <span style="color:brown">Any strong reasons to do this? Quality affects speed, and so it should be a decision of the user. [[User:Angel Herraez|Angel_Herraez]] 08:43, 17 June 2017 (UTC) | * Add a 'quality' parameter to the applet tag to enable the quality level of the 3D model to be set on loading. [[User:Greg Black|Greg Black]] 21:41, 2 February 2009 (IST) <span style="color:brown">Any strong reasons to do this? Quality affects speed, and so it should be a decision of the user.</span> [[User:Angel Herraez|Angel_Herraez]] 08:43, 17 June 2017 (UTC) | ||
===Items Solved=== | ===Items Solved=== | ||
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:<span style="color:brown;">'''SOLUTION:'''</span> 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. [[User:Angel Herraez|Angel_Herraez]] 08:35, 17 June 2017 (UTC) | :<span style="color:brown;">'''SOLUTION:'''</span> 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. [[User:Angel Herraez|Angel_Herraez]] 08:35, 17 June 2017 (UTC) | ||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''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. [[User:Emartz|Emartz]] 19:00, 8 March 2008 (IST) In contrast, searching for "theoretical model" does find [[Theoretical models]]. [[User:Eric Martz|Eric Martz]] 20:42, 16 November 2009 (IST) < | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''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. [[User:Emartz|Emartz]] 19:00, 8 March 2008 (IST) In contrast, searching for "theoretical model" does find [[Theoretical models]]. [[User:Eric Martz|Eric Martz]] 20:42, 16 November 2009 (IST) <span style="color:brown;">This appears to have been solved. See the examples at [[Help:Searching#Advantages_of_the_wiki_search_box]].</span> [[User:Eric Martz|Eric Martz]] 00:55, 9 November 2011 (IST) | ||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''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)! [[User:Eric Martz|Eric Martz]] 04:05, 19 December 2009 (IST) < | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''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)! [[User:Eric Martz|Eric Martz]] 04:05, 19 December 2009 (IST) <span style="color:brown;">'''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.</span> [[User:Eric Martz|Eric Martz]] 23:44, 8 November 2011 (IST) | ||
* <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''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. [[User:Eric Martz|Eric Martz]] 21:24, 31 January 2010 (IST) (after discussion with Jaime Prilusky) < | * <span style="background-color:yellow;color:green">'''SOLVED:'''</span> '''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. [[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 requesting a specific Jmol version when displaying a Proteopedia page. Contact {{Template:Contact}} to arrange this.</span> [[User:Jaime Prilusky|Jaime Prilusky]] 07:32, 14 March 2010 (IST) | ||
*<span style="background-color:yellow;color:green">'''SOLVED:'''</span>'' 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 http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace]. | *<span style="background-color:yellow;color:green">'''SOLVED:'''</span>'' 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 http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace]. | ||
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* '''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) | * '''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) < | * '''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 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) | * 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) | ||