From: Ashar Malik (
Date: Sat Apr 28 2018 - 08:12:45 CDT

> I want to exclude a cubic structure from the center

Make use of selections like this:

x < 6 and x > 3

These can be used with x, y or z coordinates. Best way would be to centre
the system at origin (0,0,0) and then split the lengths equally between +x
and -x and so on.


a pyramidal one

This can be tricky (I think). You will need to some geometrical
expressions which you will solve to work out number of atoms within your
Pyramidal region.
A way to avoid this would be to load a pyramidal arrangement of (any) atoms
and use "within" to select atoms from your structure which occupy the same
space --- this is a rough sketch of what you should be doing.
Rectangular/Cubic/sphrical shapes are easy to work out. I don't think I can
thing of anything to use directly for Pyramid-based selections which is why
I am suggesting the above two methods. Perhaps you can wait and someone
else may reply, otherwise try my suggestions and if they don't work right
back and I think I will be able to work out something.

On Sat, Apr 28, 2018 at 10:29 PM, Doaa Saayed <> wrote:

> Dear All,
> I have a 3 D Si substrate and I want to exclude a cubic structure from the
> center for the first project and a pyramidal one for the 2nd.
> please guide me for doing this..
> thanks in advance
> --