VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 25 2001 - 13:39:35 CDT

Dear Mauricio,
  The default lengths used in the distance-based bond
search in VMD aren't currently controllable by the user, however this
suggestion is a good one (and one made by others previously) that we
intend to improve when time allows. The immediate solution to your problem
would be to:
  1) use a structure file such as a PSF file, or use conect2psf to create one
     if you're working with a PDB that has conect records.
or
  2) use Tcl or Python scripts to allow you to interactively add or delete
     bonds.

We intend to improve these mechanisms substantially, but our development
time is already maxed out with other activities, so it may be a while still.
(I have a large backlog of good things VMD should be doing that we haven't
 had time to implement yet)

Thanks for using VMD!
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 24, 2001 at 01:40:17PM -0500, Mauricio Carrillo Tripp wrote:
> Hi,
> Is there a way to define the bond length?
> I have a structure where two atoms are bonded,
> but vmd finds them too far away to each other and
> doesn't draw the bond. I looked in the manual, but
> couldn't find anything...
>
> thank you
>
> Mauricio C Tripp
> Biophysics Dept
> CCF-UNAM
> Mexico 

-- 
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