The Jmol Applet

Jmol is an Applet for displaying chemical structures. The Applet will allow you to manipulate the structure by rotation, translation and zooming in and out. You can also measure distances, angles and torsion angles between atoms. There are no "plugins" required. Please note, the speed at which the structure displays is dependent on the speed of downloading the applet, and the size of the structure file, some of which can be very large.


Jmol display of caffeine

Mouse Features*

left button middle button right button
Open Jmol menu Ctrl + click
or click on 'Jmol' logo 		click
Rotate around X,Y drag
Move along X,Y (= translate) Shift + double-click and drag double-click and drag Ctrl + drag
Rotate around Z Shift + drag horizontally drag horizontally Shift + drag horizontally
Zoom in / out Shift + drag vertically drag vertically
or use mouse wheel
Slab not implemented
Reset and centre Shift + double-click double-click

* in all cases be sure to click away from the molecule.
Note: On a single-button mouse, Alt + drag may be equivalent to drag with middle button

How to make measurements:

  • Distance (2 atoms):
    1. double-click on the starting atom
    2. to fix a distance measurement, double-click on second atom

  • Angle (3 atoms):
    1. double-click on the starting atom
    2. click on the second atom (central atom in angle)
    3. to fix an angle measurement, double-click on third atom

  • Torsion angle or dihedral (4 atoms)
    1. double-click on the starting atom
    2. click on the second atom
    3. click on the third atom
    4. to fix a dihedral angle measurement, double-click on fourth atom

  • In all cases:
    • move pointer over destination atom in order to see measurement results without leaving a permanent measurement
    • move outside the window in order to cancel the measurement
    • make the same measurement again in order to delete the measurement

    My thanks to Angel Herraez, the author of the Jmol Mouse Manual
Default Atom Colors

R Spinney