From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 26 2004 - 17:51:03 CDT

Jim,
  If you can't load an "unwrapped" version of your trajectory data,
then deleting bonds greater than some sane value seems like an expedient
way of dealing with the problem. An alternative would be to write a Tcl
script that correctly unwraps your atom coordinates so that bonded atoms
don't end up on opposite sides of the periodic cell. If anyone else already
has a script for this, please feel free to chime in.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 26, 2004 at 03:19:02PM -0400, Jim Shepherd wrote:
> I am trying to use VMD to display a polymer network in which molecules
> exit one face of the periodic box and re-enters on the opposite face.
> The structure and atoms locations are being imported from PSF and PDB
> files and all of the atoms are within the periodic box. When displaying
> the molecules in VMD, the bonds connecting atoms that would be on
> opposite sides of the periodic box are drawn across the box (the
> displayed bond length is equal to the PB size minus the actual bond
> length). I have searched the mailing list archives, read the user
> manual and FAQ, and searched google without finding any definite
> solutions.
>
> I tried using the dynamic bond drawing method, but it frequently draws
> bonds between adjacent, non-bonded atoms. It looks like I may be able
> to delete these bods by using scripts, but I am not sure what the best
> approach would be. Should I use the atomselect command to find all the
> bonds and then remove bonds that are longer than some threshold?
>
> -Jim Shepherd

-- 
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