Re: [Jmol-users] select&delete atoms / save settings

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

Hi, Naomi, and welcome to Jmol world

> I'm a Jmol newbie and was wondering if it is possible to pick/select 
> random atoms by clicking on them with the mouse. 

Yes, this is possible. Use
	set picking select	(see note below)
It is cummulative (goes on adding successive atoms to the selection).
(Probably you will need "select none" before)

It is helpful to also use "set display selected" to see what's going 
on (marks the selected atoms with an orange halo)

> Furthermore I would like 
> to delete selected atoms (permanently in the input file), but I don't kn=
ow 
> how.

Jmol cannot write/save files, so you cannot alter the input file 
(fortunately, I would say) nor save to a new file.

> I checked the Mouse tutorial which has a short section on selecting atom=
s, 

You are right; it deals with mouse actions, but mouse clicking 
actions are not documented there. Look at 
http://www.stolaf.edu/academics/chemapps/jmol/docs/
or, directly, at
http://www.stolaf.edu/academics/chemapps/jmol/docs/#setpicking

Oh, I now see "set picking select" is not listed there (Bob, maybe 
you should add it?). It is a Chime command; I just checked it is also 
understood by Jmol, seemingly as a synonym to "set picking atom".

> but I didn't get much out of it. I also had a look at the Interactive 
> Script Documentation and tried the 'set picking' command using the scrip=
ts 
> console. But this doesn't seem to select atoms.

Clicking with the mouse pointer does select the atoms, after the "set 
picking" command. If you want to select by script, you use "select" 
command with the atom IDs.

> And one last question: How can I save settings like switched on labels a=
nd 
> their positions, background colour, etc. permanently? 

As far as I know, you cannot do that (though I might be wrong). If 
you use the applet, you can set whatever you want in a script and run 
it whenever you load a molecule.

> Sorry for these rather basic questions.

Not at all. That's why this list exists.
=B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7=
 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7
 Dr. Angel Herraez
 Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
 E-28871 Alcala de Henares  (Madrid), Spain
 fax: +34-91 885 45 85