VMD-L Mailing List

From: Sandra Bennun Serrano (sbennun_at_ucdavis.edu)
Date: Tue Aug 29 2006 - 12:44:58 CDT

Hello,
I just installed VMD to visualize a molecule, because I found that in
Rasmol this molecule shows bonds where there are not, I though it was
related with visualization, in VMD this problem almost disapear but still I
can see like a bond where there is not, I wonder or would like to know
which is the criteria for the program to show atoms bonded, or atoms not
bonded,I have the pdb and conf.gro files for my molecule. How can I have
the correct visualization of the molecule?
Since in those files we only provided the coordinates, how does the program
know that the is bonding or not, is there a distance criterium?.
Thanks,
Sandra