I think the examples are just to show of the power of the application. You don't have to load enzyme structures into it.
Going back a bit...
There was a nice and easy application for MacOS you can use comfortably under shapeshifter. Chem3D I think it was called and was designed to work alongside ChemDraw (used for skeletal structure drawing etc.) but ran happily as a stand alone.
I used my amiga to run shapeshifter for many such apps that I needed at the time. It could import a bunch of standard structure formats and had various visualisation options (including output to eps for printing, which was handy) and could do some basic operations including conformational energy minimisation - provided you have the patience to wait for it ;-)
