VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 29 2011 - 12:41:50 CDT

On Wed, Jun 29, 2011 at 12:57 PM, Joseph Bylund <joseph.bylund_at_gmail.com> wrote:
> Dear all,
> First is there somewhere an explanation of displaying bond orders in VMD?

i don't know for sure, but here is a quick lowdown.

bond order is only shown for a very small number
of representations, e.g. Bonds, in a (to me) unusual
way as multiple concentric cylinders.

very few file formats provide bond order information.

> If not: Is there a way to display bond order in vmd when reading PDB files?
>  Is this necessarily determined by "CONECT" records or distance search?  Is
> there a way to toggle which is used?

VMD doesn't set bond order, you have to set it from script.
you can do this via the atomselect command, which has
a get/set bondorder option.

cheers,
    axel.

> Thanks for any help,
> -Joe
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.