From: John Stone (
Date: Tue Dec 27 2022 - 10:10:24 CST

  VMD uses a distance based bond determination heuristic when you
load files that don't otherwise provide explicit bond connectivity
information. The best way to resolve this kind of problem is to use
a file format that actually specifies bond connectivity. Since you
didn't state what file format you used, my assumption is that it was
something like PDB that lacks this information.

  John Stone

On Wed, Dec 21, 2022 at 04:49:48PM -0300, I. Camps wrote:
> Hello, all,
> I have three systems (three carbon nanotubes with different chiralities)
> that, when visualized in VMD, some bonds are broken, looking as if the
> structure has holes.
> Visualizing the same structures in other softwares like Maestro, Jmol,
> Avogadro and Chimera, the structures look right: all bonds are drawn and
> there are no holes.
> Is there any place in VMD where we can manually change the threshold bond
> parameters to "fix" this issue?
> Thanks in advance.
> Camps

Research Affiliate, NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801