Hi Bob,
I tried it with the released 12.1.30 and to me it still looks like there are
points in $isosurfaceObject[] which are not on a surface or a cavity. The image
(http://dl.dropbox.com/u/3778149/3dqb_surface-points2.jpg) shows part of a cut
(via slab plane ...) through an molecular surface (isosurface molecular). I
drew all vertices as green points: "var vertex = $isosurfaceObject[i]; draw ID
@{"fooV"+i} CIRCLE @vertex COLOR darkred DIAMETER 0.1;". In the right part of
the image there are a lot of green points just sitting on the surface as
expected. But in the left you see more green dots hovering somewhere but not on
any surface.
Besides all this I should state my real goal. I want to calculate weather an
atom/point is inside of an isosurface (or on specific fragment, e.g. cavity)
and in which if there are more then one. As far as I know this is currently not
possible with Jmol. So I want to export (or to have access within Jmol to) the
Jmol calculated surfaces. When I would have the vertices and even better the
faces too, I could try to calculate weather a point is inside of a polyhedron
defined those vertices and faces. The output of "write MESH ..." has tag
'jvxlTriangleData' and a tag 'jvxlVertexData' which might be the faces and
vertices!? However I have no clue how to decode the data inside those tags. Any
help appreciated!
Best
Alexander
complete code:
load "=3dqb"
isosurface id "s2" select {protein} ignore {not protein} molecular;
slab plane {resno=298} {resno=166} {resno=88}; slab on;
var len = getProperty("shapeInfo.isosurface",1,"vertexCount");
for (var i=1; i<=len; i++){
var vertex = $s2[i];
var nvertex = $s2[i+1];
draw ID @{"fooV"+i} CIRCLE @vertex COLOR darkgreen DIAMETER 0.1;
}
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