I have added the "AREA" keyword to the isosurface command. No idea how you
would calculate the volume...
This can be along with the creation of the surface or just by itself:
isosurface mysurface area sasurface
isosurface area
or with an ID
isosurface myiso area
isosurface otheriso area
The variable "isosurfaceArea" is set to this number, in case one wants to
manipulate that further.
Be aware that this may not be a particularly accurate measure of the true
"molecular surface area" of a molecule, but it is the accurate measure of
the sum of all triangles in the surface model.
see http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
On Wed, Feb 11, 2009 at 9:18 PM, Yi Mao <[email protected]> wrote:
> I was using jmol to generate surface based on gaussian output. The
> guassian output is in *.cube format.
>
> I use the option below to to view the isosurface at different values
> of density.
> "isosurface cutoff density_number "cubefilename"
>
> I am interested in computing the volume and surface areas of these
> isosurfaces that are displayed by jmol. So my question is, is there a
> way to generate the date file for these isosurfaces by jmol?
>
> Thanks!
>
> Regards,
> Yi
>
> Yi Mao
> Department of Mathematics
> Michigan State University
> East Lansing, MI 48824
>
>
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