From: Axel Kohlmeyer (
Date: Tue Apr 13 2004 - 11:27:30 CDT

>>> "LV" == Lubos Vrbka <> writes:

LV> hi,


>> I am having the same problem with visualizing boehmite. John Stone and
>> others provided help for the problem in some messages below. I just shut of
>> all the bonds and then added back the ones I wanted. I hope that helps.
LV> thanks, but what do you mean by "shutting all the bonds and adding them
LV> back"? is there any info how to do that? which questions on vmd-l should
LV> i have look at?

LV> i saw your "too many bonds error" question on vmd-l - this could be
LV> connected, but there was no answer...

there are two ways to 'fix' the bonds.
a) use the dynamic bonds representation in combination with
   a VDW repesentation.
b) set the bonds 'manually'. check out the documentation of
   the atomselect command. e.g. you do a

set sel [atomselect 0 {name O}]


$sel getbonds

will give you a list of bonding partners for each oxygen atom.
with the corresponding

$sel setbonds <list of list of atom indices>.

you'll set the oxygen half of the bonds. now you have to do the
other half as well.

LV> there's one more question arising... if you turn periodic images of the
LV> unit cell on - is there any way how to force vmd to draw bonds between
LV> the periodic images, i.e. in my case to connect the whole zeolite framework?

vmd does not do that automatically (yet?). but how about adding replica
of one layer of atoms_outside_ of the box so that you'll be able
to set/get the bonds. if you set the box size correctly, the periodic
images overlap perfectly with the additional atoms/bonds.


LV> regards,

LV> --
LV> Lubos
LV> _@_"

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.