VMD-L Mailing List

From: Kooser, Ara S (askoose_at_sandia.gov)
Date: Tue Apr 13 2004 - 10:14:28 CDT

Hello,

   I haven't tried to connect periodic images. I am not sure if that will
work.
   John Stone wrote a script to turn the bonds off. With my boehmite I
removed the bonds Then to show connectivity between Al and O of the
substrate I created a representation using "(name ao) or (name oh)" and
selected "DynamicBonds". I do this for each atom type I want connected. I
then created another representation using all and CPK to show the spheres. I
am in the process of writing scripts and a tutorial for geochemistry
visualization in VMD. I should have a rough draft in 2-3 weeks.

Ara Kooser

-----Original Message-----
From: Lubos Vrbka [mailto:shnek_at_tiscali.cz]
Sent: Tuesday, April 13, 2004 9:00 AM
To: Kooser, Ara S
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: xyz aluminium connectivity questions

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.
thanks, but what do you mean by "shutting all the bonds and adding them
back"? is there any info how to do that? which questions on vmd-l should
i have look at?

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

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

regards, 

-- 
Lubos
_@_"