VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_theochem.ruhr-uni-bochum.de)
Date: Fri Jul 08 2005 - 03:26:15 CDT

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
>
>
>
>
Hey Chris,

I am also working with TM and overcome the problem you mentioned by just
using "dynamic bonds" representation and a proper selection of atoms to
display the bonds I want. With "dynamic bonds" you can tune the cutoff
distance parameter for the bond (check the user's guide).

Eddi 

-- 
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Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
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