VMD-L Mailing List

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Tue Apr 13 2004 - 10:29:07 CDT

hi,

> I haven't tried to connect periodic images. I am not sure if that will
> work.
let's wait what will other people say... :)

> 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.
is it possible to download the script somewhere?

you are talking about dynamic bond stuff, i.e. bonds between substrate
and zeolite matrix (this answers one of my questions about
"recalculating bonds". i see this can be used also for the zeolite
matrix itself, but - what is the difference between al and si? (vmd
doesn't connect al to framework oxygens whereas silicons are connected ok)

some tutorial would be really great :)

regards, 

-- 
Lubos
_@_"