On Tue, Mar 19, 2013 at 10:19 AM, Alexander Rose <
alexander.r...@weirdbyte.de> wrote:
> Hi,
>
> Jmol hangs after isosurface area/volume calculation is requested for
> solvent/molecular isosurfaces.
>
>
> load =1crn;
> isosurface select {*} molecular;
> isosurface area; # hangs in 13.1.13 but works in 13.0.13
>
>
> load =1crn;
> isosurface select {*} sasurface;
> isosurface area; # works in 13.0.13 and 13.1.13
>
>
Yes, I see it. Fixed. http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>
>
> I also have a question regarding the actual calculation of area/volume.
> The calculation is done in jvxl.data.MeshData.calculateVolumeOrArea(). For
> the area calculation it is just a matter of summing up the triangle areas.
> For the volume the signed area of tetrahedrons (triangle as the base and
> origin as the tip) is summed. Is this correct so far? I wonder what happens
> if volume/area are calculated for an open isosurface e.g. with a hole
> somewhere. The are is certainly unaffected but what is the volume supposed
> to be. Does someone know the effect open isosurfaces have on the algorithm
> used for volume calculation?
>
A hole (meaning an incomplete surface, not a donut-topology surface) will
result in the volume being a meaningless number.
>
>
>
> Best
> Alexander
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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