Third Exercise

Jmol, a Java-based molecular graphics program built on the code for the old classic Rasmol, has been installed on the Modeling Center machines. The executable is located at /usr/local/Jmol/Jmol.jar. It requires the Jave Runtime Environment (jre), which is installed in /usr/java.

Jmol can read and display structures presented both in PDB (protein DataBank) format and as Cartesian coordinates. The format of Cartesian files is simple: the first line contains the total number of atoms. The second line is blank. Each succeeding line contains an atomic symbol and the three Cartesians for that atom. It is relatively easy to use your text editor to convert the Cartesians output by any of our programs to this format.

There are two ways to access Jmol.

• Use your text editor to create a file called, for example, RunJmol

• The first line should start with a #, and describe what the file is meant to do; the # makes the line a comment, ignored by the computer

• Then skip a line and write:

  (path to jre) -jar (path to Jmol)

• On the three newer machines the jre path is /usr/java/jre1.6.0_20/bin/java; on the older machines it is/usr/java/jre1.5.0_22/bin/java

• Jmol, of course, is in /usr/local/Jmol

• Save the file and make it executable: chmod a+x RunJmol

• Then type ./RunJmol and the program should start. (The ./ tells Linux to look in the current directory for RunJmol.)

• On the newer machines, for example, the line should read:

  /usr/java/jre1.6.0_20/bin/java -jar /usr/local/Jmol/Jmol.jar

Or, you can put an alias in your .bashrc file aliasing Jmol to a line like the above. Now

• Openone of your .pcm files from the PCModel exercises, and save it in .pdb format.

• Examine the .pcm and .pdb files; what iinformation is contained in each?

• Now display the structure in Jmol (use the .pdb file) and save a picture of the display. Transfer the image to your laptop or desktop.

• Paste the image into a Word document and email me the Word document.