VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 04 2006 - 00:06:25 CDT

Hi,
  I'm not sure what your script looks like, but no, DCD files don't
explicitly store atom indices, they are implicit monotonically increasing
numbers... You can select atoms by their index like this:
  set sel [atomselect top "index 0 to 50"]

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 03, 2006 at 10:15:19PM -0400, Jeffrey A Tibbitt wrote:
>
> Dear VMD Community,
>
> I'm working on a script to convert a dcd trajectory to a pdb trajectory,
> but got stuck when trying to access the atom number. Do dcd files even
> contain atom number? If not, how would one loop through all atoms in a
> frame? But if so, how can a selection be set (below) to a specific
> atomnumber?
>
> set sel [atomselect top atomnumber 1]
>
> Jeff Tibbitt
> jtibbitt_at_odu.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