On Sat, Jun 30, 2012 at 12:36 PM, Daniel Aioanei <[email protected]> wrote:
> What is the relationship between the isosurface of a set of atoms and
> that of a subset of the atoms? I kind of expected that the latter be a
> subset of the former one, but that doesn't seem to be the case.
> Indeed, by selecting only some atoms, in fact none of the triangles I
> get appear in the isosurface of the full molecule. For comparing two
> triangles I compare the vertex positions and values, sorted in a
> canonical order, so that two triangles with permuted vertices are
> still considered equal.
>
>
The isosurface routine will select a grid that spans the set of atoms. So
if there are fewer atoms, the grid will be different.
> What I need is to get the potential-mapped sasurface partitioned by
> groups of atoms. If I select one group of atoms at a time and compute
> their sasurface, will that correctly cover the whole molecule? Is
> there any guarantee that 1) the group sasurfaces do not overlap (as
> long as the groups constitute a valid "partition" of the molecule,
> i.e., they do not overlap and together they contain all atoms of the
> molecule), and 2) considering them together will result in a surface
> covering the full molecule, without any "cracks"?
>
>
I think you need to work with the surface as a whole. If necessary, you can
create two identical isosurfaces -- they will have identical vertex arrays.
Then at least on one, you could do this:
set isosurfacepropertySmoothing false
isosurface s1 SASURFACE MAP PROPERTY atomindex
Now the values for that surface give you the atom index for the properties
of the other isosurface. Although, when I do that I'm seeing a very thin
band for one of my atoms that should be attributable to two others. Not
sure what's going on there....
Bob
>
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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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