On Fri, Jan 14, 2011 at 8:27 AM, Alexander Rose <[email protected]
> wrote:
> 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.
Yes, that would be right. They are flagged as "not part of the surface" but
they are not removed from the list. Right now you won't be able to use
$isosurfaceObject[] for working with the points, I think.
> 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.
>
No doubt.
>
> 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!
>
>
I think just writing the data as VRML will serve you best. It's a simple
list of vertexes and triangles, and only the surface will be there. Pretty
tricky figuring out if a point is within a convoluted surface or not.
>
> 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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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