From: Axel Kohlmeyer (
Date: Thu May 04 2006 - 07:01:39 CDT

On Thu, 4 May 2006, Prof. Y. U. Sasidhar wrote:

> I have a set of x y z data. I want to see these points in 3D to locate
> regions where the points are more dense etc. I am also interested in iso
> surface plots of point density. Can this be done in VMD ?

you can probably do this by a some smart scripting.
first you have to do a histogram on a regular grid
(equally spaced in x-,y-, and z-direction) and then
you can try to display iso-surfaces of that data.
this can be best done with some external program, but
of course since VMD embeds the full tcl and python
language interpreter, you could use those as programming
languages as well. see e.g.:
which computes a 2d-histogram.

do you need to display a molecule along this data?
then you can either dump the histogram into a .cube or .dx
file and load it into the molecule (so you don't have to
do the analysis over and over again, each time you want
to look at it, or just add it to the molecule as volumetric
data set, see e.g.:

otherwise it would probably better to use a more specialized
program for that kind of analysis like OpenDX:


Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.