A Tutorial for
Using Jmol to Do Molecular Modeling

Before You Can Get Started

Obtaining Jmol

Before you can get started with learning how use Jmol, you must first obtain a copy of the program, along with a file containing the atomic coordinates of a molecule that wish to view with Jmol.

After download the download file and extracting it you should endup with a folder called "Jmol-x.x.x", where x.x.x is the version number. the version that will be used in this tutorial is "Jmol-10.3.1". There are a number of files in the the folder, most of which are used to serve webpages containing Jmol applets. To run Jmol as a standalone application, the only file you need is "Jmol.jar":

For this tutorial, we will copy the "Jmol.jar" application file to a separate folder in which we will also place the structure files for the molecules that we wish to look at with Jmol. Placing the structure files in the same folder as the "Jmol.jar" application will make them easier to find and open.

Obtaining Structure Files

We will now obtain a structure file that we can work with with Jmol. The best source of structure files for biological macromolecules is the Protein Data Bank, which is a Federally supported database that is hosted by Rutger University and is managed by the Research Collabratory for Structural Bioinformatics (RCSB). The RCSB is a collaboration between Rutgers University, the University of California-San Diego and the University of Wisconsin-Madison.

The Protein Data Bank website currently contains close to 40, 000 structure files along with a wealth of information on structural biology and bioinformatics. The website has an animated tutorial that introduces the viewer to some the features of the new interface for the Protein Data Bank.

Now that you are an expert with using the Protein Data Bank website:

Human erythrocyte pyruvate kinase is an oligomeric protein containing four identical subunit. The second (middle) domain for each subunit is decribed as having a TIM barrel topology. Just out of curiosity, before leaving the PDB website determine:

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Before you get started

Creating models