Jmol: Viewing Molecules with Java

You also can use scripts interactively by clicking the File→Script Editor menu item. This pops up a new window where you can write your script, check its syntax and then run it within Jmol. This provides a huge amount of power, allowing you to get the exact type of analysis you need.

Figure 6. Jmol provides a full scripting language to help automate your analysis steps.

Once you've done your analysis, several output options are available. The File→Export menu item gives you four options. You can select Export Image to save a static image in one of several image file formats.

Because Jmol also operates as a Java applet, you can select Export to Web Page to generate a web page that you then can use within your own website to share your research results.

If you want a higher-resolution image of a molecule, you can select Render in POV-Ray to use the POV-Ray external program to render a high quality 3D image.

The last export option is Write State, which saves the current workspace so that you can reload it later and continue your analysis. There also is an extra output option under Tools→Gaussian that pops up another window. Here you can set several options for a Gaussian input file that you can then use to run further simulations of your molecule.

Figure 7. You can use Jmol to generate Gaussian input files based on your analysis.

With these tools, you easily can share your research results with others and build on the work you are doing.


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.