From: Axel Kohlmeyer (
Date: Mon Apr 25 2005 - 08:47:20 CDT

On Mon, 25 Apr 2005, haider abbas wrote:

HA> Dear all vmd user,
HA> i am using molecular visualization program "vmd-1.8.2"
HA> and "rasmol".
HA> when i visualize the same file with vmd and rasmol,vmd
HA> screen shows less number of bonds in comparison with
HA> rasmol. That is some bonds are missing between the
HA> atoms in vmd visualizer screen while it is present in
HA> rasmol screen. Somebody please help me to overcome
HA> this problem.

vmd and rasmol probably have different algorithms or
parameters to determine, what is a bond and what not.
with VMD you can either explicitely set bonds via the
script interface, but that can become complicated for
large molecule.

alternatively you can use the 'Dynamica Bonds' representation
in combination with VDW (using a small radius like 0.1 or 0.2)
to get something similar to the cpk visualization. or just use
a very small bond diameter for something that is close to
the lines representation. with Dynamic Bonds you can explicitely
specify the bonding distance. also you can have several Dynamic Bond
representations on top of each other for different subsets of
your molecule, if you need different bondlengths.

see the VMD manual for more details.

        axel kohlmeyer.

HA> i will really appreciate.
HA> Haider Abbas
HA> Department of Physics
HA> Jamia Millia Islamia University
HA> New Delhi
HA> India
HA> ________________________________________________________________________
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Dr. Axel Kohlmeyer   e-mail:
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
If you make something idiot-proof, the universe creates a better idiot.