From: Axel Kohlmeyer (
Date: Wed Feb 20 2013 - 09:34:47 CST

On Wed, Feb 20, 2013 at 3:31 PM, <> wrote:
> Dear VMD users/developers
> May I ask how to save the coordinates (to xyz file) of a periodic system
> plus added periodic images by x,y or z axis. I have an ion that is near
> the boundary of the system and some of its coordination shell molecules
> are from the neighbouring cell so I want to save the file with all
> coordinationg molecules.

you cannot directly. since the periodic display is done after the
fact, i.e. the graphical objects are replicated, not the coordinate

however, the topotools plugin (bundled with VMD) contains a function
that allows to do an explicit replication (i.e. it creates a new
molecule) from the console. please have a look at:


> Thank you in advance.
> Stefan Kolev, PhD student
> -----------------------------------------
> Интернет от MSAT Cable

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.