You can move the origin for a crystal structure by using the Transform > Unit Cell > Move Origin" command. You can specify the fractional coordinates of a point, and CrystalMaker will move the origin to that point.
Tip: If you want to move the origin to a particular atom, simply select that atom (e.g., by clicking on it with the Arrow tool), then choose the Move Origin command. The fractional coordinates of your selected atom will appear in the dialog.