VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 29 2003 - 13:51:23 CST

Dear Rui,
  Hmm, strangely the 'mol volume' command is missing from the
docs. Perhaps it got deleted by mistake during the editing for VMD 1.8.
I'll fix this immediately.

In any case, the command allows you to attach a volumetric data set
to a molecule. Two scripts in the script library basically illustrate
it in actual use, they are here:
 http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readcube/
 http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readedm/

The command is as follows:
  mol volume top
    "name of data set"
    $originVector
    $xaxisVector $yaxisVector $zaxisVector
    $xsize $ysize $zsize
    $zmap

Notes:
 - "top" could be any molecule ID.

 - The name of the data set is just a string, and this is the string
   that will be displayed in the graphics->representations form when you
   go to use the Isosurface or VolumeSlice representations with the data.

 - originvector, and the x/y/zaxisVector parameters are all Tcl lists.
   See the scripts above for examples of how to create lists etc.
 
 - The $x/y/zsize parameters are single numbers indicating the
   number of data points along each dimension of the volumetric data set.

 - $zmap is a flat list of all of the data points, stored with the X
   dimension varying most quickly, followed by the Y dimension, followed
   by the Z dimension. So, the data is stored in the list in this order:
    x0y0z0 x1y0z0 x0y1z0 x1y1z0 x0y0z1 .....

Let me know if you need more help using it.

If you are thinking of writing a file loader for some volumetric data file,
VMD 1.8 also supports file plugins for volumetric data, so that option may
be the best if you have large data sets to load.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 29, 2003 at 04:17:30PM -0000, J. Rui Rodrigues wrote:
> Hi,
> I cannot find any information regarding the "mol volume" command referred in
> the user guide at
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node66.html
> How does it works?
> Thanks,
> Rui Rodrigues
>
>
> 

-- 
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              
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