Molecular Coordinate Files
(Optional)

Below you can view and manipulate some of the molecules we are studying. (Your computer must have Java. Also, you may need to click a security bar at the top to let the script run.)

The program used to represent the molecules is JMole, which is one of several that make use of information in molecular coordinate files to draw representations of molecules. The data in these files is obtained mainly from x-ray crystalography.

Once a molecular coordinate file below is open, move the mouse pointer over the molecule and use the left mouse button to rotate molecule. Use the right mouse button to see menu for changing the style of representation. {MAC users: hold down mouse button to see menu.} For example, try the spacefill representation. Also, with the shift key depressed, use the left mouse button to zoom.

Select one of the molecules on the right:

Turn spacefill representation

Turn ribbon representation

Turn wireframe representation

In ribbon, change color of hydrophobic amino acids

Here is an example of how you can change the representation. Select hemoglobin above. Turn off the spacefill representation and turn on the wireframe representation. Now use the right mouse button to display menu. Under "SELECT" choose "hetero" and then "ligand". Now go to "STYLE" choose "scheme" and the "cpk spacefill". You will now see the heme prosthetic groups with the atoms shown as spheres, while the protein is shown in the wireframe representation.

Here is another example: Select hexokinase above with the spacefill turned on. Use the right mouse button to display menu. Under "SELECT" choose "hetero" and then "ligand". Now go to "COLOR " choose "atoms" and then "green". You will now see the green glucose molecule nestled into the catalytic site. With the shift key depressed, use the mouse to zoom in on the glucose. Note how precisely it fits into the site.

National Protein Data Bank at Brookhaven National Laboratory has files for thousands of proteins. Use one of the "search" tools to find a protein of interest. You can view the protein at the site via JMole