VMD-L Mailing List

From: Kooser, Ara S (askoose_at_sandia.gov)
Date: Tue Apr 13 2004 - 09:42:10 CDT

Hello,

   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.

Ara Kooser

-----Original Message-----
From: Lubos Vrbka [mailto:shnek_at_tiscali.cz]
Sent: Tuesday, April 13, 2004 8:02 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: xyz aluminium connectivity questions

hi vmd'ers,

i'm trying to visualize zeolite structure with some of the silicon atoms
replaced by aluminiums. the problem is, that vmd doesn't always connect
aluminium to all 4 neighbouring oxygens (sometimes it doesn't connect it
at all).

i can see many error messages "MolAtom xy: Exceeded maximum number of
bonds (8)" in the vmd console window - is this somehow related?

the problem also could be that i have "core" and "shell" representations
of oxygen atoms that lay very close to each other...

another question - when i have sequence of xyz files - is vmd
recalculatind bond structure for every step or is it using its first
guess for all frames? if it is the latter case - is there any way how to
change this behaviour?

i can send you the structure if it would help you, just let me know if
you need it.

thanks for your help, 

-- 
Lubos
_@_"