CrystalMaker lets you work with multiple windows, so it is easy to compare multiple structures: just load each structure into its own window, and then arrange the windows to compare them (e.g., use the Window > Tile command.
Alternatively, you can compare multiple structures in the same window, CrystalMaker provides two ways of doing this:
Sequentially, using Animation
Directly, by shift-clicking on individual structure thumbnails to make them all visible. (Note that you can Lock one or more structures, which then lets you rotate or move the other visible structures relative to the locked ones; to lock a structure, move the mouse over to the right-hand side of the thumbnail's title, so the little padlock icon appears, then click this).
See Also