The X axis is horizontal in the plane of the screen, the Y axis is vertical in the plane of the screen, and the Z axis is perpendicular to the plane of the screen. By default, using a three-button mouse (although fewer buttons can be workable), structures are:
Selection of atoms and bonds from the graphics window is also called picking. During picking (by default, Ctrl-left mouse button), the cursor looks like a pointing hand.
Models that have been deactivated for motion cannot be translated or rotated with the mouse or commands.
The mouse button assignments can be changed in the Mouse preferences.
Note that holding the Shift key down will reduce the speed (mouse sensitivity) of manipulations in the main window and Side View by a factor of 10.
Finally, if Show atomspec balloon is set to true in the General preferences, placing the cursor close to an atom or bond will cause the corresponding label information to appear and remain until the cursor is moved away.
On a Mac with a one-button mouse, buttons 2 and 3 can be emulated with the option and apple (clover) keys, respectively. For example, mouse action with the option key pressed performs XY-translation (assuming default Mouse preference settings).
A two-button mouse is also workable. If the right button of a two-button mouse is not already performing XY-translation, use the Mouse preferences to reassign XY-translation to button 3. The right button of a two-button mouse should then work for XY-translation, leaving the left button for rotation (the default). Scaling can be performed with the Side View and/or the command scale instead of with the mouse.