This script takes a 3D periodic structure and slices it in the X, Y or Z direction thus enabling you to look at the internal atom positions.

This script was inspired by work presented at the EUGM by Prof. Dieter Hofmann at GKSS. His team regularly use this approach to look at packing of polymers in cells.

There are a variety of slicing options such as slicing by atom coordinates only or preserving molecules that cut across slice boundaries.

When the slices are created, they are placed into a collection document. You can choose whether to display them as a square or just leave them in the original cell view.

A final option is to color by cluster. This calculates close contacts with a defined cut-off radius and then colors the molecules by the number of close contacts. This gives you some idea of the size of the clusters.

Modules: Materials Visualizer
Materials Studio Version: 5.0 (but should work with 4.x - not tested)

Note that you will need to rotate the structure if you use the "square" view to get the slices in the correct order. You can Label the Physical System by Name and use the names to help orient the structure.

Cheers

Stephen