The boundbox object can do this. You can set it to whatever size you want and place it wherever you want, and then you can use

select within(boundbox)

On Thu, Dec 29, 2011 at 1:16 AM, Anasuya Dighe <> wrote:

How do i put an entire protein molecule inside a cube/grid with x-axis spanning
till the
largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis
spanning till the largest z-coordinate?

Once i do this, can i divide the larger cube(i.e. the one holding the entire
protein) into smaller ones of lesser dimensions? Say, 2A x 2A x 2A?

Once i generate these smaller cubes, is there a way via Jmol, by which i can
navigate through the protein molecule, (smaller)cube by (smaller)cube?
As in, can Jmol be used to tell me which residues are lying in which (smaller)
cube and so on?

I am aware that it is possible to integrate objects like spheres and grids into
Jmol, but i dont know how to address the following problem and visualise the

Please let me know.
 - Anasuya

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