Re: [Jmol-users] residue highlighting

[Angel H. <ang...@ua...>]

Hello Helix 

I see you have much to learn about Jmol ;-)
Well, that's what the list is for.

First and most important, as you have already perceived, ANY ACTION IN Jmol AFFECTS 
ONLY THE CURRENTLY SELECTED PART OF THE MODEL

> a) Suppose I want to select more than one residue and through a checkbox can I select multiple 
> residues and display them in spacefill?

No problem. The syntax is e.g.  
	select Ala125, Ala165, His136
commas or the OR keyword can be used.
In order to use checkboxes (see Jmol.js manual in the web), you apply each command to 
each checkbox, e.g.:
	jmolCheckbox("Ala125", "define temp selected; select Ala125; spacefill on; select 
temp", "define temp selected; select Ala125; spacefill off; select temp")

The "define temp" is there so that you don't chenge the previous selection state; I hope you 
can follow the logic.


> b) While I was trying to change some of the applets features like cartoon, backbone etc.., i 
> noticed that the structure changes were only taking place in the selected residue and not in the 
> protein chain, means suppose I only want to change the protein representation and not the 
> selected residue(which is in spacefill), how this can be done, because the changes are taking 
> place in selected residue and not in the protein chain?

Yes, as I said above, this is how Jmol works. You first select, then change rendering.

> c) Could it be possible to display text in the applet itself, I want to display the residue number and 
> three digit code in the applet.

Static text in the applet is done with "echo" command. You can also attach text to atoms 
using "label".


> Thanks once again for your time and suggestion.

You are welcome.