VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 15 2011 - 11:21:02 CDT

Hi,
  This is usually caused by problems with the interpretation of the
coordinate units in the files being loaded. Is it possible that you've
got your atomic coordinates in units of nanometers, but have saved them
to a file format (e.g. PDB) that expects Angstroms?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 15, 2011 at 12:09:51PM -0400, Moeed wrote:
> Hello all,
>
> I have a problem visualizing my structure in vmd. Once I load structure
> and trajectory files file I see some artificial bonds connecting all atoms
> while there is no bond between them. Has anyone any ideas why this is
> happening?
>
> Thank you, 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078