Molecular coordinate files and the JSmol applet are provided to assist students in visualizing chemical structures and symmetry. Relevant examples from lecture and the problem sets will be made available via links at left when the topics are discussed in lecture.
JSmol Requirements and Instructions
The JSmol applet will load automatically and run on any modern browser that is JavaScript-enabled and supports the HTML5 canvas element. For security or convenience, JavaScript may be turned off by default on your browser of choice; to run the JSmol applet, JavaScript must be enabled, typically via a browser preference setting. The JSmol applet runs smoothly in Chrome and Safari, is okay on Firefox, but is "unworkably slow" on Internet Explorer according to the JSmol Wiki. The poor performance of the JavaScript engine on Internet Explorer is likely only a concern for large macromolecular structures and should not be an issue for our purposes.
The operation of JSmol is largely self-evident, and documentation is available. Note that a full set of program controls is accessible within the applet by (1) clicking on the "JSmol" tag at the lower right-hand corner of the applet window, (2) ctrl-clicking the main (left) mouse button, or (3) clicking the secondary (right) mouse button.
Other Options
Alternatively, all coordinate files can be downloaded for viewing outside the browser on any program that can read Protein Data Bank (.pdb) coordinate files. A number of free-of-charge program options exist, including the standalone Jmol applet (Jmol.jar; requires Java 1.4), Mercury, and Vesta. The last two programs are sophisticated, modern visualization packages that are available for all major OS's (Windows, Mac, Linux). For further practice, additional molecular coordinate files in a variety of formats (.pdb, .xyz, and others) can be readily obtained by web-searching for desired molecules.