VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 20 2004 - 17:49:01 CDT

Dinesh,
  The problem is that VMD expects the units to be in Angstroms, and
your file is using some other units. The problem isn't actually XYZ
specific, but rather is a failure in the automatic bond determination
code. Apparently our bond determination code has a weakness in that it
can't cope with having 32,000 atoms within a cubic Angstrom. In any
case, you're going to want to fix those atom coordinates. Your coordinates
currently appear to be some sort of fractional cell coordinates rather
than any physical units, since they range from exactly 0,0,0 to
0.97, 0.97, 0.97....

If you fix the coordinates I'd expect your problem to go away.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 20, 2004 at 12:40:39AM -0700, pinisetty dinesh wrote:
> Respected Dr.John,
> I am attaching the file in xyz format with
> 32,000 atoms.It is FCC structure with 32,000 atoms.
> Thanking you,
> Dinesh.
>
>
>
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-- 
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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