Proteopedia:Wishlist: Difference between revisions
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moved up MSE bug |
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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. | ||
*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 | |||
* 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. [[User:Emartz|Emartz]] 00:06, 17 March 2008 (IST) | * 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. [[User:Emartz|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. | * 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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** '''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). | ** '''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). | ** 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). | ||
*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) | *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) | ||