| Rotate | click LEFT and DRAG MOUSE |
| Translate | click RIGHT and DRAG MOUSE |
| Zoom | ROTATE MOUSE WHEEL |
| Add Atom (or Carbon ring) | click appropriate menu button, e.g. 'N', move cursor over focus atom and click LEFT, then move cursor onto the canvas, hold down 'shift' key and click LEFT |
| Move Atom | move cursor over atom, hold down 'shift' key, click LEFT and DRAG MOUSE |
| Delete Atom or Bond | click 'Del' menu button, move cursor over atom or bond and click LEFT |
| Link Atoms | click 'Link' menu button, move cursor over 1st atom and click LEFT, then move cursor over 2nd atom and click LEFT |
| Change Atom Details | move cursor over atom and double-click LEFT |
| Change Bond Type | move cursor over bond and double-click LEFT |
| Change Ligand Id | move cursor over ligand id label and double-click LEFT |
| Choose Different Atom | to choose an atom from the periodic table, click the down-arrow menu button to bring up the table, then click the appropriate atom; alternatively, choose 'Periodic Table ...' from the 'Options' menu |
| Toggle Checkboxes | to toggle the checkboxes in the menu bar you can use these key shortcuts: 'a' to toggle Atom Id's, 's' to toggle Hydrogens and 'd' to toggle Charges |
| Shortcut to Carbon | click RIGHT to set the atom type to Carbon |