Jmol: Viewing Molecules with Java

Let's dig back into some chemistry software to see what kind of work you can do on your Linux machine. Specifically, let's look at Jmol, a Java application that is available as both a desktop application and a web-based applet.

You can use Jmol to help analyze the results you get from other software packages that actually calculate the chemical effects you are researching. It can read in dozens of different file formats, and you can use it to visualize everything from small molecules to huge macromolecules, like proteins. You also can visualize crystals and orbitals. You even can visualize animated events, such as chemical reactions and molecular vibrations.

Most Linux distributions should have Jmol available within their package management repositories. For example, you can install it on Debian-based distributions with this command:


sudo apt-get install jmol

If you want to use the latest and greatest version, download it from the main project website. The download comes as a simple zip file containing everything you need to run Jmol. You also will need to install a Java virtual machine in order to run Jmol.

If you installed Jmol from the package manager, you probably will have a script available that will make running Jmol easier. If you install it from the binary zip file, you will need to run it manually by calling Java and using the JAR file as a command-line option.

When you first start Jmol, you'll see a blank screen, ready for input. Across the top is a series of icons allowing for easy access to the key functions available within Jmol. If you already have data files to analyze, you can use them. Otherwise, you may need some sample files in order to play with the functionality available.

Figure 1. When you first start Jmol, you get a blank workspace ready for your work.

The binary distribution doesn't include any sample files in order to save on download bandwidth; however, several sample data files are available from the main website. You can get the entire set by downloading a snapshot of the source files. In the examples for the rest of this article, I'm using several of the sample data files available from the source snapshot download.

The simplest example is just to load a data file and see what it looks like. Figure 2 shows what you get when you load the sample file Jmol-datafiles/gaussian/phenylnitrine.g94.out.

Figure 2. The basic display you get when you load a molecule is a ball and stick display.

The data display is an interactive one. Using your mouse, you can click and drag the molecule to rotate it around to see all of the details.

The Display menu item provides a number of options to play with the molecule. The Atom menu item allows you to change how much of the van der Waals force field to show. The Bond menu item shows how thick to make the bonds between atoms. With these two options, you can tailor the display so that the appropriate amount of detail is shown. The Label menu item allows you to add either symbols, names or atomic numbers to the atoms within the molecule.

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Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.