To measure distances, double click on the structure. Now, as you touch other parts of the structure, the distances will be shown on a pink line. Double click to fix the distance report in black.
For easier measurements, turn on the spacefill representation (a requirement for accuracy when surfaces are displayed). To cancel without fixing a distance report, simply move the mouse outside of the Jmol rectangle. To remove an already fixed report, double click on each of the two atoms again. To remove all distance reports, click the Reset button to refresh the molecular view.