On Tue, Mar 19, 2013 at 10:19 AM, Alexander Rose <alexander.rose@weirdbyte.de> wrote:

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.



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Robert M. Hanson
Larson-Anderson Professor of Chemistry
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St. Olaf College
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