VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 24 2002 - 09:51:44 CST

Dear Reinhard,
  The since the volumetric data rendering features in VMD are very
new, we decided not to build-in any file readers yet. Instead, we made
an easy-to-use Tcl interface for attaching volumetric data to a molecule,
so that anyone could write their own volumetric data file loader for
themselves, with the eventual goal of having more of this functionality
built into the core of VMD. The "potsel" script in the VMD script library
takes a VMD atom selection, sends it to Delphi for processing, and
then reads Delphi's electrostatic grid output file and loads it back
into VMD for display. This script while somewhat complicated, is a
decent practical example of how one uses the "mol volume" Tcl command
in VMD.
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsel/

This is the line from the script that actually attaches the volumetric
data to the active molecule:

mol volume top "SOD Potl Delphi/Insight, (1 unit)=(kT/2000e)=(25.6/2000mV) " [list $xOrigin $yOrigin $zOrigin] $xVec $yVec $zVec $igrid $igrid $igrid $valList

The mol volume command takes a text string describing the data set,
an {x y z} vector for the origin (bottom lower left of data set),
three axis-side-length vectors (vectors each point in the "x", "y",
and "z" directions for the data's local xyz coordinate system, but instead
of being unit length, they are the length of the x, y, z side of the
parallelpiped.), the number of samples in each x,y,z dimension, and
the last parameter is a Tcl list containing the actual grid of scalar values
organized with the X dimension changing fastest, then Y, then Z...

If you have any questions about writing a volume loader script using
the mol volume feature, please let us know, and we will be happy
to help you get it going.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 24, 2002 at 04:02:33PM +0100, Reinhard Klement wrote:
> Dear VMD-L,
> perhaps I was missing a message on this list, in the release notes or
> the Users Guide. I cannot find any informations about the file formats
> for volumetric data which can be read into VMD to generate slices and
> iso surfaces. Can anyone point me to a source of information about this
> topic?
>
> Thank you in advance
>
> Reinhard Klement
>
> --
> Reinhard Klement
> Max-Planck-Institut für biophysikalische Chemie
> Abteilung Molekulare Biologie
> Am Fassberg 11
> D-37077 Göttingen
>
> GERMANY
>
> phone:
> +49 551 201 1389
> fax:
> +49 551 201 1467
>
> e-mail: rklemen_at_gwdg.de or reinhard.klement_at_mpi-bpc.mpg.de
>
> Web:
> http://www.mpibpc.gwdg.de/abteilungen/060 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078