Re: [Jmol-users] Some isosurface scripts broken with recent Jmol updates?

[Alan H. <he...@il...>]

Bob has immediately corrected this problem with isosurfaces for large
numbers of invisible atoms in 11.9.33_dev. It works perfectly. Many
thanks.

Now I have an associated question :-) Why is the qualifier "VISIBLE"
imposed for "set picking SELECT" with SITE and ELEMENT ? I understand that
you don't normally want to draw selection halos around invisible atoms,
but sometimes when you select a site, you do want the selection to apply
to ALL equivalent sites, even those that are invisible.

Why ? In ICSD I select sites that I want to exclude from the construction
of isosurfaces and label them with a property. For example, I want to
exclude extraneous atoms occupying sites in zeolite channels so that I can
draw the channel isosurface. But I don't know how to select the equivalent
invisible sites, and this results in isosurfaces limited by those
invisible occupied sites.

A simple extension might be: "set picking SELECT SITE ALL" which would
preserve the "VISIBLE" implied by "set picking SELECT SITE". (But perhaps
there is an existing alternative to achieve that?)

To avoid selection halos being drawn around invisible atoms, you could
allow an explicit VISIBLE qualifier i.e. "selectionHalos ON VISIBLE".

The point is that sometimes you want to select even the invisible atom
sites, but would prefer only the visible atom selection to be hallowed.

Alan.

Alan Hewat said:
> I'm coming back to this because I think I understand why isosurface
> scripts that work with Jmol 11.8.18 no longer work with 11.9....
>
> For inorganic structures including zeolites with cavities we construct
> polyhedra by including atoms from neighbouring unit cells, hiding these
> many additional atoms in the display. Specifically we have e.g.
> jmolApplet(600,'load "tmp/fiz.cif?69767" { 3 3 3 };restrict cell={ 2 2
> 2};..
>
> Version 11.8.18 apparently knew to ignore the surrounding hidden cells
> when drawing isosurfaces - or at least it worked fine with such
> constructs.
>
> Version 11.9... apparently tries to construct isosurfaces with all the
> extra hidden atoms - or at least it just freezes the drawing with whatever
> activity it is engaged in - I couldn't wait long enough for it to finish.
>
> Isosurfaces work with Jmol 11.9... if I replace the opening statement by:
> jmolApplet(600,'load "tmp/fiz.cif?69767" { 1 1 1 };...
>
> But obviously I need the original construct in order to construct all the
> polyhedra :-)
>
> Alan.
>
> On Wed, Feb 10, 2010 at 3:50 AM, Alan Hewat <he...@ill.fr> wrote:
>>
>> Is it possible that some isosurface scripts have been broken with recent
>> Jmol updates ? For example the isosurface POCKET, INTERIOR... scripts for
>> the Zeolite-LTA example seem to freeze Jmol version 11.9.27_dev loaded
>> with page http://chemapps.stolaf.edu/jmol/docs/examples-11/new2.htm
>>
>> The same isosurface POCKET, INTERIOR... instructions do work for the
>> Zeolite-LTA structure with Jmol 11.8.7 used by ICSD (FIZ) and Jmol
>> 11.2.7 used by the zeolite atlas on
>> http://izasc.ethz.ch/fmi/xsl/IZA-SC/ftc_3d.php so its not my computer or
>> Java installation (I also tried a different machine).
>>
>> Alan
> ______________________________________________
> Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
> <Alan.Hewat@NeutronOptics.com> +33.476.98.41.68
>       http://www.NeutronOptics.com/hewat
> ______________________________________________
>
>


______________________________________________
Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
<Alan.Hewat@NeutronOptics.com> +33.476.98.41.68
      http://www.NeutronOptics.com/hewat
______________________________________________