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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