VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Jun 14 2000 - 14:37:01 CDT

Hi,

The problem with VMD asking for a pair of files for GRASP was a bug in
version 1.4. The problem was fixed in VMD 1.5, available from our web site.

VMD's support for GRASP is admittedly far from complete, but if you're
willing to work with it, there are a few things you can do. First,
to load a grasp molecule in a different color, you have to set the variable
vmd_grasp_color in the text console, for example,

  set vmd_grasp_color 4

will cause the next grasp molecule to be yellow. The number can be anything
from 0 to 15.

If you need to move the molecules around relative to each other, you can
fix all but one of the molecules using the Molecule dialogue box, the
rotate and translate the unfixed molecule.

Hope this helps,

Justin

>
> We are having some trouble getting the output of GRASP loaded into VMD.
>
> GRASP has a variety of outputs after it has generated a surface. It can
> create a
> surface as a series of points in PDB format, but this looks hideous and
> is fairly useless as
> the surface information has been lost.
>
> The VMD file dialogue has GRASP files listed , but it asks for a file
> pair and GRASP only generates single
> files (as far as I can tell.) I can get a GRASP surface file to display
> in VMD by selecting
> some arbitrary second file. The surface is displayed, but I am not sure
> about centering
> or other features (we are trying to stack several surface images and
> they need to be centered
> on the same point.) Also, VMD appears to treat the surfaces as objects
> and I am unable to get
> get each loaded surface to display in a different color.
>
> Any help in this would be appreciated.
>
> Thanks,
>
> A.
>
>
> --
> Andrew Hall
> hall_at_estradiol.cbr.tulane.edu
> Center for Bioenvironmental Research
> Tulane University/Xavier University
> 

-- 
Justin Gullingsrud         3111 Beckman Institute
H: (217) 384-4220
W: (217) 244-8946          The time of purification is at hand...