VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed Feb 16 2005 - 06:09:46 CST

On Wed, 16 Feb 2005, Adrian Koh wrote:

AK> Dear all,

dear adrian,

AK> I have with me the xyz-coordinates of a list of atoms in the .xyz
AK> format. I'd like to add bonds between some atoms, how can this be
AK> done? I've attached a sample file for your reference.

you can either do this interactively, via the checking the
Mouse->Add/Remove Bonds button and then clicking on atoms,
or you can create a selection and use the 'set bonds' subcommand
to define bonds.

stupid example:

set sel [atomselect 0 "index 0 1 2"]
$sel setbonds {{1 2} {0 2} {0 1}}

will draw a bond between atoms 0 and 1,
1 and 2, and 0 and 2.

regards,
        axel.

AK>
AK> Thanks!
AK>
AK>
AK> Adrian.
AK> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.