VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Feb 22 2007 - 23:44:37 CST

On Thu, Feb 22, 2007 at 10:11:27PM -0600, Hai-Jun Su wrote:
> Hi, everyone
>
> The attached two pdb file are the exactly the same. However when I
> load them into VMD, their tube or ribbon image is slightly different.
> Could anybody tell me what is wrong. Thanks.

They are not quite the same file, as diff says they're different... :-)

The important difference is that the elements are listed in column 81 in
dyn2HIU.pdb, but they should be in columns 77-78, according to the PDB
format. This means that VMD doesn't have that information, and in this
particular case it makes a difference.

If you fix that, both files render the same image.

Cheers,
Leo 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign