Two issues there.
1) SASURFACE and SOLVENT automatically exclude water. For small molecules
or to not exclude water, use:
isosurface vdw 1.4
or
set solventProbe 1.4; isosurface molecular
2) That's a bug when the number of vertices is 0. That's fixed, but for now
just don't do that.
Bob
On Sat, Jun 23, 2012 at 8:27 AM, Daniel Aioanei <[email protected]> wrote:
> I'm not able to compute the sasurface of a water (H2O) molecule:
>
> $ isosurface test sasurface 1.4
> test created with cutoff=0.0; isosurface count: 0
> $ show isosurface
> $
>
> After the above commands, I cannot see any surface drawn, and in fact
> after issuing the "show isosurface" command, it's not possible any
> more to rotate the molecule in the GUI. With other (larger) molecules
> the above procedure works as expected.
>
> Interestingly, if I create a "molecular" surface instead, still no
> surface is drawn, the molecule can still be rotated and the console
> output looks like this:
>
> $ isosurface test molecular
> test created with cutoff=0.0; isosurface count: 1
> $ show isosurface
> <?xml version="1.0"?>
> <jvxl version="2.2" jmolVersion="Jmol 12.3.32_dev 2012-06-20 18:17"
> xmlns="http://jmol.org/jvxl_schema";
> xmlns:cml="http://www.xml-cml.org/schema";>
> ...
> </jvxlEdgeData>
> <jvxlInvalidatedVertexData bsEncoding="base90+35" count="736"
> len="736"> -#}3+ </jvxlInvalidatedVertexData>
> </jvxlSurfaceData>
> </jvxlSurface>
> </jvxlSurfaceSet>
> </jvxl>
>
> I encountered the above behaviour on a very recent jmol codebase
> checked out from svn (jmol revision 17324) with Java 7u[4-5] on Mac OS
> X and Fedora Linux.
>
>
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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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