VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Fri Jul 08 2005 - 02:58:31 CDT

Hi Chris,

Try using an atomselect and playing with the getbonds/setbonds options.

Jerome

On Thursday 07 July 2005 18:30, Chang, Christopher wrote:
> Hi,
>
> I work with transition metal complexes, and the automatic bond detection
> does not create visible bonds for coordinate covalent metal-ligand bonds,
> which are longer than the thresholds. I use VMD to (among other things)
> visualize intermediate structures in optimizations, which are generally
> easiest to output as XYZ files, i.e. no connectivity information. There
> doesn't seem to be a means to save or create user-drawn bonds into a VMD
> state file--I've tried to see what happens when drawing bonds using
> "logfile console", but this just reports "label add Atoms 0/x" whether the
> mouse is in add/remove Bonds mode or not.
>
> Is there a scripting command in VMD to toggle on add/remove bonds mode,
> such that a subsequent series of "label add Atoms 0/X" commands could be
> issued to automatically create user-defined bonds? Or better yet, just to
> define bonds directly without creating a PSF file?
>
> Thanks,
>
> Chris
>
> Christopher H. Chang, Ph.D.
> Research Associate
> National Renewable Energy Laboratory
> 1617 Cole Blvd., Mail Stop 1608
> Golden, CO 80401
> Phone (303) 275-3751
> Fax (303) 275-4007 

-- 
Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 87
http://www.edam.uhp-nancy.fr/