VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 31 2002 - 15:36:29 CST

Dear Francesco and VMD-L,
  There are at least two or three approaches to loading the "cube" files
you describe. I'll list all of them below:
  1) write a "cube" file reader in Tcl, load the data from the file, and
     use the "mol volume" Tcl commands to add the cube data to a molecule
     in VMD. Once loaded, use the "VolumeSlice" and "Isosurface" reps to
     view the new data. (best method)

  2) write a "cube" file reader in Tcl, load the data from the file, and
     use the data to apply colors to the molecule, displayed using one of
     the existing VMD reps.

  3) write a "cube" file reader in Tcl, load the data from the file, and
     use the VMD "draw" or the more complicated "graphics" commands to
     render the data within VMD.

  4) write a "cube" file reader in Tcl, load the data from the file, and
     write out a Raster3D or Grasp surface file, and load the file into
     VMD.

There are some examples of techniques 1) and number 2) here, done
for the program Delphi:
  http://www.ks.uiuc.edu/Research/vmd/script_library/volumetric.html

Let us know if you have questions about using the "mol volume" command
or the volumetric data display features.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 25, 2002 at 02:01:41PM +0100, Francesco Gervasio wrote:
> Dear all,
>
> I was wondering if anyone tryed to draw Gaussian "cube" files with vmd.
> A "cube" file is a 3 D grid of electron density values from which one
> normally,
> given a cutoff value, plots an electron density surface.
> I immagine that the best way to visualize such a surface is to convert
> the "cube"
> file to a Raster3D format and load that in VMD.
> Any suggestion/program to do that?
>
> Thank you,
>
> Francesco Gervasio
> gervasio_at_chim.unifi.it 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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