Terry M. Gray
Computer Support Scientist
Molecules are three-dimensional objects. The chemical properties of substances are often critically dependent upon these three-dimensional shapes. Three-dimensional structure is an especially important consideration when the properties involve interactions with other substances. Examples are the interaction of chiral compounds with chiral columns and the binding of ligands to macromolecules. The biological role of nearly every biochemical depends on its three-dimensional structure.
Despite the importance of the three-dimensional structure to chemistry and biochemistry, it is often neglected in teaching, and, consequently, in the students' grasp of the principles involved. This is due in part to teaching methodologies involving two-dimensional and static representations of molecular structure: textbook/overhead transparency pictures, blackboard/overhead transparency drawings, testing based on easily memorized (but not necessarily intuitively grasped) word descriptions of structure, etc.
With the rise of molecular computer graphics and the near ubiquity of personal computers, it is now possible to remedy this deficiency. I will describe three molecular visualization programs MDL Chemscape Chime, RasMol, MAGE. On the World Wide Web there are resources for each of these programs that have been developed by other chemistry and biochemistry instructors for use in lecture rooms equipped with display capabilities or for interactive homework/labwork. In the Department of Chemistry at Colorado State University the two main lecture rooms (A101, A103) are equipped with such display capabilities. We also have a LCD projector on a cart that is available for the smaller classrooms and seminar rooms.
Because of the wealth of resources available on the WWW, it is not necessary that the instructor become a custom developer of these resources. However, such development is not difficult once the initial hurdle of learning new software is passed. Many instructors will want to custom build some of these teaching tools once they see their usefulness.
Chime is a plugin for web browsers. It works with recent versions of Netscape Navigator and Microsoft Internet Explorer. It is availble on the Macintosh, Silicon Graphics, and Windows versions of those browsers. During installation it is placed in the Plugin Folder of your browser. Plugins give your browser the ability to display other file types than the usual HTML and graphics that are built-in to each browser. For example, if you have the Chime plugin installed and you encounter a protein data base (PDB) formatted file, your browser recognizes the PDB file format as belonging to Chime. Chime is activated and the molecular structure is displayed in the browser window. (Without Chime, PDB files would simply be displayed as a text file of the three-dimensional coordinates.) Chime recognizes other coordinate files such as MDL mol files, xyz files, and RasMol script (spt) files. Not only can you display these structures but you can also interact with them:
A detailed description of Chime, instructions for downloading, sample files, and more can be found at the MDL free software site for Chime.
If you install Chime, you should be able to visualize web pages that have embedded molecular structures, for example, the Chemistry Department's Chime page that has a spinning vitamin B12 molecule or the Computer Support Page that has a smaller and not spinning vitamin B12 molecule. If you have not installed Chime or have not installed it correctly, you will see a broken image icon where the embedded Chime images would be. Here are the coordinates of bacteriophage T4 lysozyme. If you click on that link and have Chime installed correctly, you should see the molecular structure of that protein. If not, you should see the text of the coordinate file. Alternatively, if you prefer organic chemistry to biochemistry, try this structure of caffeine.
While Chime was developed for web browsers surfing the web, it is not necessary to be on the internet to use Chime. Chime turns your web browser into a molecular viewer of files on your hard drive. This is important for use in lectures since most of the time you won't want to be dependent on the network during your lecture--the network may be down, you may not be able to connect to the site of interest, network traffic may be high so you file transfer times will be high. In other words, it is usually prudent to have everything you need on your own computer. Web browsers allow you to do just that. You can open a file on your own computer in your browser. For example in Netscape Navigator 4 (Netscape Communicator) you can use the File, Open, Open Page in Navigator... command. A dialog box comes up that allows you to find any file on your computer to view in the web browser. If that file is an HTML file, it will display like a normal web page. If that file is a file that is interpretable by Chime, the plugin will fire up and the molecular structure will display. You can also drag the file into the browser window and it displays as a molecular structure. If you want to experiment with this, try the following:
One very interesting application of Chime is with Rasmol scripts in Chime. Here you can display "movies" of successive molecular structures with scripted rotations, zoom, display mode changes, colors, etc. Several of these have been developed by Eric Marz, an immunoligist at University of Massachusetts. Here is an example (again, this will only be displayed if you have installed Chime correctly). This is a 10 minute lecture demo on DNA structure and protein-DNA interactions.