select <whatever>
show sequence
If in JavaScript:
var x = JmolScriptWait("show sequence")
2009/12/14 Angel Herráez <[email protected]>
> El 14 Dec 2009 a las 16:12, Vincent Le Guilloux escribió:
>
> > I think I have what I want with that. I didn't saw that within could
> > be combined like that... I really need a full day to make my hands on
> > Jmol scripting :)
>
> If you can do it in just one day, we'll give you a medal ;-)
>
>
> > What I need exactly on that, is to allow the user to hide several
> > sub-systems: predicted active sites in my case. For each active site,
> > I've a checkbox that allow the user to display and hide it.
>
> Yes. You can use hide but in combination. That's better than using
> cpk off; wireframe off;
>
>
> > So for now, I simply use this script to hide a given pocket:
> >
> > select pocket# ; cpk off ; wireframe off; isosurface surf# off ;
>
> select pocket# ; hide hidden,selected
>
> or just
>
> hide hidden,pocket#
>
> (I'm not sure if the isosurfaces will be affected by hide)
>
>
> > and the following to display it again:
> >
> > select pocket# ;cpk 1.5 ; wireframe on ; for displaying.
>
> display displayed, pocket#
>
>
> > Just a last question:
> > Is it possible to retrieve residue names / ID for the current selected
> residue
> > (in order to display them in a text area) ? That is, the user click on
> > a button associated with a pocket, and I retrieve amino acid names and
> > IDs from Jmol and display it as text in the text area... As far as I
> > know it's not, but just in case...
>
> It is possible, but not totally straightforward.
> Main problem is that you could retrieve the info for all atoms in the
> set, but that's not easily converted into a simple human-readable
> list of residues (each residue will have a variable nr. of atoms).
>
> Say, if you are doing
>
> define pocket1 amino and within(group, within(5.0, STP2) );
> display displayed, pocket1;
>
> pocketData = {pocket1}.group
> //and then put that 'pocketData' Jmol variable into your textarea
>
> (That's just an approximation; you'll have to sort out the details;
> the place to read is
> http://chemapps.stolaf.edu/jmol/docs/#atomproperties
>
>
>
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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
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