VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 29 2008 - 14:04:44 CST

Hi,
  You can use the "$sel getbonds" and "$set setbonds" commands to directly
alter the bonds for groups of atoms in VMD from your own scripts. Besides
this, you could generate structure files that have explicit bond information,
and you can also edit bonds graphically using the Mouse->add/remove bonds
menu item.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 25, 2008 at 08:48:52AM +0100, massimo camarda wrote:
> Hello,
> I'm trying to display bonds only between specific types of atoms. ie. I
> would like to show (using the dynamic bond representation or the "within"
> command) the bonds between Carbon and Silicon BUT NOT between Silicon and
> Silicon.
> I can set a cutoff but this works for all the atoms represented, so it shows
> all the bonds.
> Is there a way to specify it in VMD?
> The other way to solve the problem would be to specify the bonds one by one,
> can you tell me a site where a can read some information about the format of
> the file (I use ".xyz" a format that does not specify the bonds) to use.
> Thank you
> Massimo 

-- 
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