From: John Stone (
Date: Tue Aug 29 2006 - 12:58:40 CDT

  Yes, VMD and most other visualization tools determine bonds
using distance-based bond determination methods (though often with
additional criteria). If you get one bad bond that you'd like to fix,
an easy way to correct this is to use the Mouse->Add/Remove Bonds menu in VMD.
(then pick the two atoms where there's a bond that shouldn't be, or
 where a bond is missing...)

  John Stone

On Tue, Aug 29, 2006 at 10:44:58AM -0700, Sandra Bennun Serrano wrote:
> Hello,
> I just installed VMD to visualize a molecule, because I found that in
> Rasmol this molecule shows bonds where there are not, I though it was
> related with visualization, in VMD this problem almost disapear but still I
> can see like a bond where there is not, I wonder or would like to know
> which is the criteria for the program to show atoms bonded, or atoms not
> bonded,I have the pdb and conf.gro files for my molecule. How can I have
> the correct visualization of the molecule?
> Since in those files we only provided the coordinates, how does the program
> know that the is bonding or not, is there a distance criterium?.
> Thanks,
> Sandra

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