The primary means of controlling the view is via the mouse. Motions are accomplished by pushing mouse buttons and moving the mouse. The left mouse button controls rotations in the X and Y directions. When the left mouse button is held down, left and right movement of the mouse rotates around the Y axis, while up and down movement rotates around the X axis. The middle mouse button, by default, controls the scale and Z rotations. In this case, left and right motion rotates around the Z axis, while up and down motion zooms the image in and out, respectively. The binding of the middle mouse button may be changed by the ``Mouse Binding'' menu, described in §6.11.3. The right mouse button pops up the macro menu, (See §6.10 for details). Translations of the molecule may be accomplished by pushing both the left and middle mouse buttons. Here, left/right motion corresponds to translations along the X axis, while up/down motions correspond to translations along the Y axis. Note that the mouse sensitivity may be set with the Control Panel under the ``File'' menu (§6.1.8).
The left and middle mouse buttons are also used to ``pick'' objects on the screen. For instance, placing the cursor over a bond and clicking the left mouse button will select that atom and display the identity of that atom. The middle mouse button picks only surface vertices, while the left button can not be used to pick vertices. The pick functionality will be discussed in further detail in §6.9.
The cursor in the graphics window will change to indicate the current mode of motion. Here's a table summarizing the motion modes and their associated cursors:
| Mouse controls | |||
| Button(s) | Motion | Action | Cursor |
| 1 | None | picking | cross-hair |
| 1 | Up-Down | X-rotation | cross-hair |
| 1 | Left-Right | Y-rotation | cross-hair |
| Default binding (always used if shift, control or alt is pressed) | |||
| 1 | Up-Down | X-rotation | cross-hair |
| 1 | Left-Right | Y-rotation | cross-hair |
| 2 | Up-Down | scale | sizing icon |
| 2 | Left-Right | Z-rotation | curved arrows |
| Z translation binding | |||
| 2 | Up-Down | Z-translation | double arrow |
| Stereo binding | |||
| 2 | Up-Down | stereo separation | dot |
| 2 | Left-Right | stereo twist | dot |
| Light position binding | |||
| 2 | any | Light Position | dot |
| 1&2 | Up-Down | Y-translation | quad arrows |
| 1&2 | Left-Right | X-translation | quad arrows |
| 3 | None | Macro menu popup | - |
Note that it's possible to attach mouse motion to objects other than the main view. You may, for instance, attach the mouse to a subset of atoms and rotate that subset independent of the rest of the molecule. When the cursor is attached in this manner, you can always press and hold shift, alt, or control before any mouse buttons to temporarily re-attach the mouse to the global view. See §6.8 for details on attaching mouse motion to a subset.