Rotate or translate the selection

First make your selection.

Next rotate, translate or zoom as usual, but start with the mouse in the selection. So if you click and drag the selection, ONLY the selection will be rotated or translated. If you click and drag anywhere else the whole molecule will be rotated or translated (actually, only your viewpoint).

If you 'zoom' the selection you are really moving the selected objects perpendicular to the screen (in or out the screen).