VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed Oct 13 2004 - 00:46:39 CDT

>>> "BH" == Bret Hess <Hess> writes:

BH> In work on CdSe nanoclusters with ligands, the C-H, C-C bonds
BH> are fine, but no Cd, or Se bonds show. How do I get VMD to show them?

bret,

if you don't provide the bonding information with a .psf file or
similar, VMD tries to guess bonds. the list of radii used for that
is (currently) very limited. also 'Cd' will be recognized as 'C'.
there are two ways, to add additional bonds.

1) you can add a 'Dynamic Bonds' representation to your visualization,
where you can set the distance cutoff manually.
you may have to use a selection to avoid adding too many bonds
elsewhere.

2) you can create selections and then use the get/set bonds command
to add a list of bonding atoms indices to each atom in the selection.
it is a bit more complicated, but this way you can set any bond you
want.

regards,
        axel. 

--
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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/
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If you make something idiot-proof, the universe creates a better idiot.