Biomolecules Module:
Jmol Tutorial

Jmol is a free open source applet developed by the people at www.jmol.org for the interactive display of molecules in web browsers. No plugins are necessary in order to view molecules with Jmol; the only requirement is a web browser that supports Java and has both Java and Javascript enabled. You can check if your browser is set up correctly by visiting Jmol's browser check page.

The table lists several things you can do with Jmol to manipulate a molecular structure. Each line of the table lists an action you can perform to the structure and the mouse and keyboard buttons you should push to perform that action. Instructions in red refer to clicks you make with your mouse; instructions in blue refer to buttons on the keyboard you hold down while clicking and moving the mouse. Use the structure of ATP at the right to practice (table taken from the Chime and RasMol home page at the University of Massachusetts).

Atoms in molecular structures are often colored according to the following scheme: carbon, gray; oxygen, red; nitrogen, blue; hydrogen, white; phosphorus, orange.

* The X and Y axes are left-right and up-down on your screen, respectively. The Z axis is perpendicular to your computer screen.

** The Slab Mode option must be activated in the Jmol script before this option can be used. Think of the slab as a plane parallel to your computer screen. Anything on the other side of the slab plane from you can be seen. The Slab Plane option moves the slab plane closer or further away from you when you move the mouse up or down.

***Opening the Jmol menu only requires a right mouse click (Windows) or held mouse click (Macintosh). The menu gives a multitude of options to manipulate the display which are best learned by practice. Trying the options in the Color and Display submenus will provide the most striking changes to the display.

For more information on how to use Jmol, try the Jmol homepage.