> Now I have an associated question :-) Why is the qualifier "VISIBLE"
> imposed for "set picking SELECT" with SITE and ELEMENT ?
Hmm. Looking back, it was I myself who asked 2.5 years ago for "set
picking SELECT" to be restricted to "VISIBLE" :-) Sorry, I didn't foresee
the need to select invisible atoms then.
Alan
Alan Hewat said:
> 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 <[email protected]> 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
<[email protected]> +33.476.98.41.68
http://www.NeutronOptics.com/hewat
______________________________________________
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