From: Nima Nouri (nouri.f.nima_at_gmail.com)
Date: Fri Jan 21 2011 - 01:01:23 CST

Hi pascal

On Fri, Jan 21, 2011 at 1:17 AM, pascal boulet <
pascal.boulet_at_univ-provence.fr> wrote:

> Dear all,
>
> I have a periodic structure of a solid compound. I calculated the ELF
> and stored it in a cube file to visualize the function with VMD.
>
> The atoms I am interested in are located at the boudary of the unit cell
> and I would like to draw a bond between two atoms located in two
> different cells. When I do it the bond appears inside the "original"
> unit cell and not across the cell boundary. Is there a way to enforce
> the bond across the boundary?
>
>
You should use a combination of pbc wrap/unwrap/join commands.
>From the things you have mentioned I think you shoudl first draw your bond
and then use the join command.
lets say you have a atom named C. and you want to bring all of the molecules
containing C atom to the side which the C atom is located in. (You don't
want it to be splitted by the PBC)

pbc join res -ref "name C" -now

A more general help and the command lists of PBC plugin is available in:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

> Thanks for your help,
> Pascal
>
> --
> Dr. pascal Boulet, computational chemist
> University of Aix-Marseille I
> Laboratoire Chimie Provence, UMR 6264
> Group of Theoretical Chemistry
> Avenue Normandie-Niemen
> 13397 Marseille Cedex 20
> France
> **********
> Tel. (+33) (0)491.63.71.17
> Fax. (+33) (0)491.63.71.11
> **********
> http://www.lc-provence.fr
> https://sites.google.com/a/univ-provence.fr/pb-comput-chem
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>

-- 
 Best Regards
N.Nouri
Ph.D Student
Department of Mechanical Engineering
Isfahan University of Technology
Isfahan, Iran
gpiutmd.webs.com