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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