VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Dec 22 2012 - 09:50:51 CST

On Wed, Dec 19, 2012 at 6:58 AM, anyy zsj <zsjanyy_at_gmail.com> wrote:
> Hello:
> Here I ask you for how to get the coordinate of periodic images. In
> my case, I want to show some atoms of the original structure and some
> other atoms from its periodic images. I used the periodic images in
> the representation and make a selection by something like this: x>2
> and x<5. However, the selection is only applied to the original
> structure. So is there an easy way to achieve this? Thank you.

periodic display in VMD is achieved by replicating the
representation, not the coordinates. the only way to apply
different selections to the original and the images is to
overlay multiple representations and have in one only
the "self" part visible and in the others only the desired
periodic image and not the self representation. the selection
has to always be applied to the coordinates in the principal
image. another alternative is to replicate the coordinates
either externally or via some tcl scripting and then work
with the resulting supercell.

cheers,
     axel.

>
>
>
> Shijun Zhao 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.