In PyMOL, all the molecules on display can be moved by pressing the middle mouse button and dragging. But, what if you want to move only one molecule among the multiple molecules being displayed?
To do this, first choose Mouse > 3 Button Editing. Now hold down the Shift key and click anywhere on the desired molecule using the middle mouse button and drag to move it. Only the selected molecule is moved and the rest remain as they are.
Tried with: PyMOL 1.4.1 and Ubuntu 12.04 LTS