VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 01 2007 - 11:16:38 CST

Ivana,

On Thu, Feb 01, 2007 at 09:28:20AM -0500, ivana adamovic wrote:
> Dear John,
>
> Thanks a lot John!
> I have tried your suggestions, but things are still not working ...
> Here is the summary:
> ------------------------------------------
> 1. To run example file:
> ....
> >to load the examples as if you had started them from the command line:
> > cd /your/home/directory/Desktop/1kdx
> > play 1kdx.vmd
>
> It shows up now, but the whole surface is just white. Is it something
> about parameters, or something else that needs to be set up?

If your card doesn't support 3-D texturing, that's the problem.
Check that you're video card lists "3-D" in the "Textures" message when it
starts up, e.g.:
  Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)

Otherwise, if your video card does have 3-D textures, the problem is most
likely that the color scale data range isn't set correctly (graphical
representations window, trajectory tab). It should be set to a range
such as -8 to 8, for example.

> -----------------------------------
> 2. To read CHARMM el. potential file I have upgraded to VMD 1.8.5 and
> did following (two different things):
>
> 2.a) I have assumed that the proper extension for el. potential is dx
> (reading examples). Is that so?

NO. The CHARMM PBEQ module emits it's own density map format, and so
you need to add the new CHARMM PBEQ plugin to your VMD installation in order
to be able to load the file. You can either run one of the new test versions
of VMD 1.8.6, or add the VMD 1.8.5 plugin update 1 to your system in order
to directly load the CHARMM PBEQ maps into VMD.

The PBEQ files are independent fo the PDB/PSF/DCD, so you only
really need to load the other files if you want to view
the structure colored by potential. For basic testing you should
be able to load CHARMM PBEQ map all by itself and display isosurfaces
with it, etc.

Let me know whether your machine is reporting that it has 3-D texturing
or not, and we'll proceed from there.

  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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