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Quick Guide to JChemPaint

Drawing molecules

Upon start, you will be presented with an empty working space, or canvas. (If you already drawn a molecule and want to start anew, choose the menu Edit > New.)

  1. In the beginning, all atoms you add will be carbons; don't worry, it is better to change them into another element once you have them drawn.
  2. If the molecule contains rings, it is generally better to start with them.
  3. Then, draw the chains, one bond at a time: click on button (if not already selected) and then on the atom where you want the new atom to be linked. To bond two existing atoms, click on the first one and, without releasing the mouse button, drag to the second atom.
  4. To convert a single bond into double or triple, click on the single bond using the tool. You can also use and to add stereochemical information to an existing bond.
  5. To modify the chemical element of an existing atom, click on one of the buttons C H O N P S etc. and then click on the atom(s) whose identity you want to change.


toolbarPositioning the mouse pointer over each button in the toolbar* you will see a floating tooltip with its function.
(* in the JCP panel, not here)