From: massimo camarda (
Date: Mon Feb 25 2008 - 01:48:52 CST

I'm trying to display bonds only between specific types of atoms. ie. I
would like to show (using the dynamic bond representation or the "within"
command) the bonds between Carbon and Silicon BUT NOT between Silicon and
I can set a cutoff but this works for all the atoms represented, so it shows
all the bonds.
Is there a way to specify it in VMD?
The other way to solve the problem would be to specify the bonds one by one,
can you tell me a site where a can read some information about the format of
the file (I use ".xyz" a format that does not specify the bonds) to use.
Thank you