VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 07 2005 - 16:10:41 CST

Patrick,
  There's not presently a way of doing this.
VMD currently completely ignores atom indices specified
in various file formats, including PDB. This allows
VMD to read illegally formatted PDB files (which are commonly
used for performing large MD simulations and other things).
(think of the old XPLOR convention of writing alphanumerics for
 atomids beyond a certain range, etc)
It also makes VMD robust when reading PDB files that include
hand-edited text where multiple atoms might have the same index,
or where the file has a large gap in the atom index sequence.

I could definitely see adding a new selection keyword to allow selection
by the index values from the original file, though the responsbility
of watching out for the items I list above would then be on the shoulders
of the user. I don't have time to mess with this for VMD 1.8.3, but that
might be worth doing for a subsequent revision.

  John

On Fri, Jan 07, 2005 at 04:47:00PM +0100, pl wrote:
> Hi all,
>
> I'd like to change the default index of atoms that
> start at 0 in vmd to 1 in order to match exactly
> the atom number of a pdb file. Is there a way to
> change that default?
>
> Thanks
>
> --
> ------------------------------------------------------------------
> | Patrick LADAM | |
> | Laboratoire CSSB | THE BIG BANG THEORY: |
> | UFR SMBH | |
> | 74 rue Marcel Cachin | In the begining there was |
> | 93017 Bobigny CEDEX | nothing at all. |
> | >>> NEW e-mail: <<< | |
> | ladam_at_smbh.smbh.univ-paris13.fr | Then, it exploded... |
> | Tel: 01 48 38 77 26 / 76 85 | |
> | Fax: 01 48 38 77 77 | |
> ------------------------------------------------------------------
>
> 

-- 
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