Proteopedia:Wishlist: Difference between revisions

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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 Suggestions from [[User:Emartz | Eric Martz]], highest priority at the top:
-# 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].
+* 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].
-# 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)
+* '''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)
-# 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. [[User:Emartz|Emartz]] 19:51, 9 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 &lt;scene ...&gt; tag. [[User:Emartz|Emartz]] 01:59, 19 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]]. [[User:Emartz|Emartz]] 02:10, 16 March 2008 (IST)
+* 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. [[User:Emartz|Emartz]] 19:51, 9 March 2008 (IST)
-# 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'".
+* 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]]. [[User:Emartz|Emartz]] 02:10, 16 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)
+* 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'".
-# Support two Jmols side by side, for comparisons.
+* 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)
-## 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).
+* Support '''two Jmols side by side''', for comparisons.
-## 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).
+** '''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).
 The following suggestions have been implemented. They remain listed here for the historical record.