Re: [Jmol-users] Picking groups (elements or equivalent sites)]

[<ha...@st...>]

> ha...@st... said:
>> Alan Hewat wrote:
>>>What would be great would be to have additional picking commands: "set
> picking ELEMENT"  (select all atoms of that element)
>
>> easy.
>
> That would already be very helpful. I would then click on any Aluminum
> atom for example and so select all (visible) aluminum atoms.

This won't be just the visible ones, though. You can add that designation
when you process the selection. So whatever your JavaScript is going to do,
you would add "and visible" to that. OK? Or we could institute something like

  set pickingVisibleOnly

that would restrict the picking groups, etc. to only those atoms that are
visible.

>
>>>"set picking SITE" (select all symmetry related atoms for
>>>that particular site)
>
>> hmm. That might be a challenge. How exactly do you define "site"?
>
> With "set picking SITE" I would like to click on a particular aluminum
> atom eg Al2 as listed in the CIF file, and so select all (visible) Al2
> atoms but not Al1 or Al3.

so, for example, we have:

loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Si   0.46970   0.00000   0.00000
O   0.41350   0.26690   0.11910

"site 1" is Si, "site 2" is O, right? And then when we apply symmetry (in
this case) all the Si are "site 1" and all the O are "site 2". Yes? If so,
this will require a new atom field "site" I think. We should probably then
also add the label field %S for "site"


>
>> Are you referring to the selection halo that works with "set display
> selected"?
>
> No. I mean those atoms that are visible after a restrict command like:
> load \"y12367.cif\" {3 3 3};restrict cell={2 2 2};
>
> I don't want atoms from the invisible cells, that are only there to allow
> construction of complete octahedra.

I'm wondering if we also need a select option for element. Maybe just

  within(element, selected)

for example. "within" sounds a bit strange, but it is already in place and
will work. That way the user doesn't necessarily have to use the mouse to
effect this element-based selection, and multiple elements can be selected
at the same time. Similarly:

 within(site, selected)

would select all of the same site.

It's great to have you thinking about this, Alan.

Bob


>
> Alan.
> _____________________________________________________________
> Dr Alan Hewat, ILL Grenoble, FRANCE <he...@il...>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm
> _____________________________________________________________
>
>
>
>
> _____________________________________________________________
> Dr Alan Hewat, ILL Grenoble, FRANCE <he...@il...>fax+33.476.20.76.48
> +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm
> _____________________________________________________________
>
>
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