| Mage is a graphics program especially well suited for visualizing three-dimensional structures of proteins and other macromolecules. The program was developed by Robert M. Weiss, David C. Richardson and Jane Richardson of Duke University (1) and is free and user-friendly. It is an important tool for biochemists and finds many applications in biochemistry courses. We utilize Mage to create interactive instructional graphics of potential use in a wider range of undergraduate chemistry courses, and present some of those applications here.
Mage is straightforward to download from the Web and comes equipped with a rich but simple vocabulary for constructing associated data files, plus an appealing palette of working colors. The data files use plain text scripts and are called kinemages. Names of kinemage files are identified by a .kin extension and are easily created or modified using any text editor. Simple generation of kinemage files and subsequent attractive interactive displays make Mage our program of choice for developing instructional graphics. Many diagrams prepared at chalkboard or on overhead slide can be organized in terms of points, lines, spheres and labels. Such constructions usually can be incorporated into a kinemage, and the resulting interactive 3-D display is more clear and impressive than the most carefully hand-drawn original. Furthermore, recent offering of an associated Mage applet allows direct and quick viewing of kinemage files from any Java-capable Web page and considerably expands its scope of utilization. The applet includes a help menu (keyboard activated using the "h" key) showing an extensive list of key-strokes for real-time control of line width, background color (white/black), perspective, monoview or stereoview (both wall- and cross-eyed), plus other options.
Spatial concepts in chemistry courses are among the more challenging topics for many of our students, and we have invested in elaborate models and created "masterful" overhead slides to help illustrate such features. The Internet has opened an additional avenue of communication for students and teachers so lecture notes, homework problems, and previous exams are available to many students from a class Web site.
Our first look at Mage quickly motivated us to use it as a graphics tool for illustrating spatial chemical concepts, and we soon began posting Mage files on our class Web site. But, in order to use these files students were asked to download the executable Mage program from the Mage home page. Only a few did so; downloading and transfer of files is perceived to be a complicated task by many students, although emailing and printing of Web pages are not. However, thanks to the Mage applet, students can now view interactive Mage displays simply by clicking on an associated Web page link; no other action is required. The applet makes instructional Mage files available for immediate viewing—click on the link and Mage starts right up. Interactive lecture graphics are delivered quickly from any Java-capable browser directly to each student's computer. Even computer-shy students now have direct access to lecture graphics.
We find MAGE especially useful for illustrating features about VSEPR models, permanent dipole moments, model crystal structures, radius ratios, hybridization, molecular stereochemistries, symmetries, and determining reducible representations of vibrational modes. Mage applet examples for all of these illustrations are presented here. They are set-up to run as a browser-activated Web page and provide the same real-time interactive Mage applet graphics displays as used in our classrooms. Kinemage files are not very large. All files on this JCE WebWare site only require about 200 kb of storage.
We actively seek ways to increase our library of molecular kinemage files in order to take advantage of this seemingly transparent graphics interface. For example, a Mage feature furnishes the length between any two objects selected by mouse-click, so bond distance measurements (and comparisons) are accessible in class. Consequently, kinemage molecular graphics files are used often in advanced inorganic chemistry classes to illustrate bonding and stereochemical concepts.
However, such files come in a variety of formats and some changes are required to make them work with the Mage applet. Kinemage files can be derived from several common file formats and students contribute to this process as part of a class project. They obtain atomic coordinates for assigned structures from original literature sources and generate a text file of the coordinates. Later, we meet to review their data and discuss some aspects of running selected graphics programs, space groups, asymmetric units and molecular symmetries. Together we prepare (with student as keyboard operator) a kinemage file from their information, and they leave with a printed copy of unit cell contents and a working Mage file for their molecule. These brief meetings result in greater student awareness about actual magnitudes of bond distances and angles, and their relation to textbook geometries.
The project is described in more detain in the accompanying documentation. The documentation also presents some Mage programming basics and outlines the design of several instructional Mage files.
Figure 1. A screenshot from Mage. A Tool for Developing Interactive Instructional Graphics.
Literature Cited
- Richardson, D. C.; Richardson, J. S. Prot. Sci.1992, 1, 3
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