Program: TutorialOur PDB TutorialConnolly functionAtomic Density functionPDB
We start with a description of what this program does. We take in a protein name, from which we get a pdb file, which thousands may be found at The Protein Databank (note that we use the same name as the Protein Databank, such as "1aew" or "1crn"). The pdb file provides a lot of information about a protein, but most importantly to our program, it contains centers and radii of the atoms comprising the protein. This information is then transformed into a screen image. For information on how to use The Protein Databank, follow the link to Our PDB Tutorial.
To use the program, follow any link to the Program page. On this page you will find a box which allows you to enter a protein name.
Once you have entered the protein name, a new page will open in which you will be asked to confirm the name of the protein. After clicking submit, you see the protein, in all its glory. The image may be adjusted using a mouse in several ways. Clicking and holding the left mouse button while moving the mouse rotates the protein. Clicking and holding the right mouse button while moving the mouse translates the protein. Clicking and holding the mouse wheel while moving the mouse zooms in and out. If you do not have a mouse wheel or right mouse button, then clicking and holding the mouse button while holding the alt key allows zoom and clicking and holding the mouse button while holding ctrl allows translation.
On the page with the protein, you will also be asked to enter the number of isolines present. This will add lines around the protein, indicating where the Atomic Density function takes on certain values. This is similar to a topographical map, where a line is drawn through places of the same elevation. To see a new protein, just close the page and start over from the top of the page. Our contact information can be found on the Meet the Team page, so send any questions.
Note: You need Java3d to run this program. Go to the Java Sun page to download Java3d.
