| Rotate | click KEYPAD BUTTON and DRAG KEYPAD |
| Translate | click KEYPAD BUTTON, hold down 'ctrl' key and DRAG KEYPAD |
| Zoom | click KEYPAD BUTTON, hold down 'alt' key and DRAG KEYPAD up-and-down (Note: KEYPAD must be clicked before 'alt' on Linux) |
| Add Atom (or Carbon ring) | click appropriate menu button, e.g. 'N', move cursor over focus atom and click KEYPAD BUTTON, then move cursor onto the canvas, hold down 'shift' key and click KEYPAD BUTTON |
| Move Atom | move cursor over atom, hold down 'shift' key, click KEYPAD BUTTON and DRAG KEYPAD |
| Delete Atom or Bond | click 'Del' menu button, move cursor over atom or bond and click KEYPAD BUTTON |
| Link Atoms | click 'Link' menu button, move cursor over 1st atom and click KEYPAD BUTTON, then move cursor over 2nd atom and click KEYPAD BUTTON |
| Change Atom Details | move cursor over atom and double-click KEYPAD BUTTON |
| Change Bond Type | move cursor over bond and double-click KEYPAD BUTTON |
| Change Ligand Id | move cursor over ligand id label and double-click KEYPAD BUTTON |
| 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 key 'q' to set the atom type to Carbon |