What do molecular modeling programs do?
Molecular modeling programs visually render molecules in 3D from an array of spatial
coordinates stored in a standard file type (ex: .pdb). These files are created when structures of
macromolecules have been resolved via crystallography or NMR. These coordinate files are then
submitted to a database (e.g. Protein Data Bank) or further processed by advanced applications.
As you become familiar with PDB files (and other coordinate file types), it is important to note that
very little structural information is contained within these files. The atoms are labeled and x,y,z
coordinates are supplied, but it usually up to the modeling program (and the user) to decide how
render the bonds, surfaces, and other stylized representations of the molecules.
There are many different molecular viewing programs, and what differentiates them is the way in
which they interpret, process and display the features of a macromolecule. Some programs also
offer tool sets to manipulate and save modified structures. Still others are used to animate or
perform advanced computations involved in single-molecule kinetics.
Many of these programs run as “standalone” applications that are downloaded and installed on
your computer. However, this means that the molecular coordinate file must also be present
locally. This is inconvenient for those wanting to share a large repository of information or for
those who wish to use molecular viewing for educational purposes. This is Jmol’s specialty.
What is Jmol?
Jmol is a free, open source molecule viewer for students, educators, and researchers in
chemistry and biochemistry. Jmol is a successor to such legacy products as XMol, Rasmol, and
the Chime plugin.
Because Jmol’s core rendering engine was written in Java, it is cross-platform, running on
Windows, Mac OS X, and Linux/Unix systems. However, v1.4.2 (or higher) of Sun Java must be
installed. See below for installation instructions.
The class will use the JmolApplet implementation for structure-based homework. The applet is
generally stored on a remote web server (e.g. Protein Data Bank) and downloaded whenever a
user visits a web page that integrates Jmol. At this point in time, the applet is unsigned or
“untrusted”, meaning that it runs in a protected environment and cannot affect your machine.
The Jmol application is an optional download from the Jmol development web site. It is a Java-
based “wrapper” around the Jmol rendering engine that can be run locally from the desktop.
How do I install Jmol?:
Step 1: Make sure that the latest version of Sun Java is installed on your operating system.
The easiest way to check is to visit http://www.java.com, click on the link to “download the latest
Java software”, and follow the instructions. If you already have the latest version, the installation
will terminate. If not, make sure that you install Java, including extensions for the browser(s) you
plan on using to view molecules.
Step 2: Visit http://www.jmol.org to test your Java installation and the Jmol applet.
If the main graphic on the front page is displayed, installation was successful. That’s it!
Remember, Jmol doesn’t actually exist on your machine as an application, so there is nothing
else to install or configure.
