VMD-L Mailing List
From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Apr 13 2004 - 11:27:30 CDT
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>>> "LV" == Lubos Vrbka <shnek_at_tiscali.cz> writes:
LV> hi,
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}]
then
$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.
axel.
LV> regards,
LV> --
LV> Lubos
LV> _@_"
-- ======================================================================= 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.
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