Alex,
On Sun, Dec 19, 2010 at 6:04 AM, Alexander Rose <[email protected]
> wrote:
> Hi,
>
> (using 12.1.25)
>
> I've been working with the 'isosurface cavity' command and got a couple of
> questions regarding it.
>
> load "=3KDC"
>
> This produces a fragmented isosurface:
> isosurface id "foo" select {protein} ignore {not protein} cavity 1.2 5;
>
> Here I am interested in binding cavity
> isosurface id "foo" set 9;
>
> As a side note: Using a higher resolution I get more and larger cavities
> which look more convincing to me:
> isosurface id "foo" select {protein} ignore {not protein} resolution 2
> cavity 1.2 5;
> Maybe the default resolution should be higher?
>
> I think you just have to experiment.
> Once I issued isosurface id "foo" set 9; I do not know how to display all
> cavities again. I can issue 'set 1' to get fragment 1 though.
>
> I want to get the volume of the displayed fragment 'isosurface id "foo"
> volume' but this works only the first time, when I display another fragment
> the volume does not change.
>
> that's a bug. Fixed for Jmol 12.0.26 and 12.1.27.
> When all fragments are displayed (before using 'set 9') and I issue
> 'isosurface id "foo" volume' (isosurface id "foo" area) I get the summed
> volume contrary to what is stated in the documentation "*If the surface is
> fragmented, the result is an array; otherwise it is a decimal number.*"
>
> Is there a way to get the number of fragments in a isosurface?
>
>
with this fix, just issue
isosurface set 0 volume
$ load 1crn.pdb
$ isosurface cavity
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
$ isosurface volume
isosurfaceVolume = 286.5688
$ isosurface set 0 volume
isosurfaceVolume = [8.390304267406464, 20.143751442432404,
11.703342812756697, 35.84804334227616, 32.73594017808015, 76.77707885671407,
91.71226038233483, 9.258056499995291]
$ print isosurfaceVolume
8.390304267406464
20.143751442432404
11.703342812756697
35.84804334227616
32.73594017808015
76.77707885671407
91.71226038233483
9.258056499995291
$ print isosurfaceVolume.sum
286.5688
> It would also be very nice if 'getProperty "shapeInfo.isosurface['foo']"'
> would work.
>
>
That array is numerical. If you only have one isosurface, just use:
getProperty shapeInfo.isosurface[1]
You should be able to see the correspondence between isosurface name and
number using
isosurface list
> Is there a way color the fragments differently - other then 'isosurface
> colorscheme "sets" cavity'?
>
>
no, just that way.
> A powerful feature would be some access to the marching cube gridpoints so
> one could do something like:
> mgp = getProperty "shapeInfo.isosurface[1].gridpoints"
> display WITHIN(5, @mgp)
>
>
The gridpoints are cleared from memory after use, and in many cases they are
"streamed" so as never to accumulate. But do you perhaps mean the vertices
of the triangles that make up the surface? You do have access to those
points:
print $isosurface1[1]
This displays the coordinate of the first point in the triangulation. The
total number of vertices can be obtained using
Var x = getProperty("shapeinfo.isosurface",1,"vertexCount")
Added to Jmol 12.1.27 also now is:
Var x = $isosurface1.length
This reports a point such as {1.0, 2.0, 4650.0} that indicates (x) the
number associated with this isosurface, (y) the total number of isosurfaces,
and (z) the total number of vertices.
>
>
> Best
> Alexander
>
>
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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
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it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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