Jmol: Viewing Molecules with Java

Near the bottom of the Display menu, there is a check box for whether hydrogen atoms are displayed within the display of the molecule.

While I'm talking about how to affect the display of the molecule, I should mention that the View menu item provides a number of presets on how to line up the molecule. So, with a single click, you can view the molecule along any of its axes.

Jmol also can display animations of events, along with static images. The animations subdirectory contains several examples that you can play with. When you load it up, you start with a static image of the molecule as before.

Figure 3. When you load an animation, it starts with a static image of your molecule.

Within the icon bar at the top of the window, there are a series of buttons at the far right-hand side that allow you to step through the frames of the animation frame by frame. If you want to see the full animation, there's set of options under the Tools→Animate menu item. Here, you can go through the animation once, or you can put it on a loop.

You can even use a mode called Palindrome that goes forward through the animation and then backward. That way, you need to calculate only one half of the motion, yet you still are able to visualize the entire range of the motion.

Several more analysis tools are available. Clicking the Tools→Spectra→JSpecView menu item pops up a new window. Under the File menu item, you'll find options to add extra files, or do H1 or C13 simulations. You can select Tools→Measurements to measure the distance between atoms within your molecule, and you can set the units used for those measurements with the Tools→Distance Units menu item. You actually can edit the molecule after it is loaded too.

Figure 4. JSpecView is an extra tool available for looking at the spectra of molecules.

If you click the icon button with the hover-over description "Open the model kit", you'll get a small set of drop-down items on the top left side of the display window. It allows you to delete atoms, move bonds around or even change the atom species at specific locations.

Figure 5. Jmol also lets you edit molecules.

If you have some type of analysis that you need to repeat several times, Jmol supports the addition of macros. Macros are just simple text files that contain a set of Jmol instructions. If you save them in the ~/.jmol/macros directory, Jmol will pick them up and provide them within the Macros menu item.

The language for the macros is the same used for Jmol's scripting capabilities. This scripting language is based on of RasMol, with some minor changes. There is a full language reference available here.

______________________

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.