VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 22 2002 - 11:34:29 CDT

Dear Vlad,
  Have you changed the isosurface rep from the default "box" mode that
shows the volume's bounding box to the isosurface display mode?
Since I don't know which version you're using I can't tell you exactly
which control to toggle, but you need to do this in order to see your
isosurface. Also, you'll need to select an appropriate isovalue
for you data in order to see a good surface. I can tell you more
but I've got to run now.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 22, 2002 at 05:58:09PM +0200, Vlad Cojocaru wrote:
> dear VMD users,
> I am trying to read some cube files with VMD. I downloaded the script
> from the library and after I loaded the pdb and then read the cube file
> I got the following:
>
> topLabel = >Calculation of electrostatic
> potential <
> Second line = >SCF Total Density<
> Number of atoms: 18
> Origin: -5.88309354688 -5.33054332797 -3.45521941652
> xgrid and vectorX: 74 11.8640319211 0.0 0.0
> ygrid and vectorY: 66 0.0 10.5814338755 0.0
> zgrid and vectorZ: 44 0.0 0.0 7.05428925036
> Length of list is 214896, wanted total= 214896
> Info) Added volume data, name=Gaussian cube
>
>
> Could somebody give me some advices how should I proceed? I tried to
> create new repr. using Isosurface and VolumeSlice but I do not know how
> to set the parameters for retrieving the electrostatic potential
> representation for my molecule.
> Thanks a lot in advance for any advice,
> Best regards,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>
> 

-- 
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