2010/10/28 Angel Herráez <angel.herr...@uah.es>
> Dear developers,
>
> 1.
> As a result of my sessions with students, there is a recurrent topic that
> has appeared in
> previous years, and maybe now is the time to tackle it:
> Using the applet and popup menu, one can color by chain, but there is no
> way to select
> chains other than from the command line. Also, the default chain colors are
> often too subtle
> and similar. So I think it would be really useful for general nonexpert
> users to be able to
> select a chain from a list, in the same way one can select residues of a
> certain amino acid, or
> all atoms of a certain element, or hetero groups from a list too.
> I can manage the addition in the popup menu, but I need guidance or help in
> how the
> computed menus are programmed.
> I've looked in org/jmol/popup and see that
> updateElementsComputedMenu() depends on elementsPresentBitSet
> updateHeteroComputedMenu() depends on htHetero
> but have been unable to pursue this further. Is there a similar variable
> for chains, or that
> infrastructure will need to be implemented anew?
>
The enabling/disabling of options depends upon the name of the menu item in
the resource. For example, PDB indicates that a file must be a PDB or MMCIF
file with residues (other than just UNK) for that item to be enabled.
But don't we have
Set Picking...select chain
on the menu?
>
> 2.
> I would like to add menu subentries that allow to make use of the new
> commands for
> calculating protein secondary structure. This I know how to do, I think, as
> it is just a popup
> menu entry mapping to a command.
> My plan is
> Style > Structures > Calculate by DSSP | Calculate by Ramachandran
> at the end, after "trace" and a separator.
> Opinions are welcome.
>
>
This one's a bit tricky -- no doubt you also want "Original" there along
with "using DSSP" I might need to hard-code that in, but if you look at
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm that now has
that option in JavaScript. It involves setting a Jmol variable "isDSSP" (or
perhaps an atom property, if more than one structure is allowed, as would be
the case for a popup-menu item) and then checking that. Otherwise, you would
have to save the structure every time a file is loaded. That's not as
efficient. Sounds like I need to do that.....
>
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
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