Add axes and transparent example grid box; how to get molecule coordinates

[shamsaraj]

This commit improves the functionality of gridbox.py by adding visual axes, a transparent example box, and instructions for obtaining molecular coordinates in PyMOL.

[JarrettSJohnson]

Thank you for your contribution. I tried it out and it looks probably as intended, but the newly added functionality should probably be within the gridbox function itself, not when the script is ran. You can probably add axes as an argument (as you have alluded to at the end of the script) and run the rest of the logic if it's true.