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 include the best and most appropriate ideas.

If you want to report a problem in an existing feature, please do so at Proteopedia:Problems.

When adding a suggestion, please identify yourself by adding ~~~~ at the end. This is wikitext that is converted into your name and the date.

This list has the most important items at the top.

  • 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.
  • 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)
  • 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)
  • 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.
  • ConSurf coloring can be provided as discussed with Nir Ben-Tal and Elana Erez. This could be one of the standard scenes on the proposed menu of standard scenes.
  • 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)
  • 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.
  • 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)
  • 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)
  • 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)
  • 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))
  • 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.

  • 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)
  • 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.
  • 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.
  • 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).
  • Have selenomethionine (MSE) treated as any other amino acid in the (Jmol) default settings - User:Morten Grøftehauge- June 1, 2008
  • 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)

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, Eric Martz, Emily Forschler, Kevin Karplus, Jaime Prilusky, Greg Black, Ralf Stephan, Karl Oberholser, Angel Herraez, Karsten Theis
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