The Mage Page

Page Contents: Getting Mage & Prekin; Getting kinemages; Teaching with kinemages; Non-molecular uses of kinemages; Tutorials on making kinemages; Mage PlayPen -- experimental Mages

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared in order to better communicate ideas that depend on 3-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program called Mage. A utility called Prekin makes a starting kinemage from a PDB-format coordinate file which can then be modified on-screen in Mage or off-line in any text editor.

Getting Mage, Prekin

The current distributed versions of Mage and Prekin are available free from our software page. Older versions of Mage and Prekin and our open source code are available free from our FTP site. An older version may be needed, if for instance, you will use the programs on an older operating system such as Windows 3.1 or if you use a 68K Macintosh. Mage and Prekin continue to evolve with increased capabilities but, by policy, all earlier kinemages we know of are viewable in the latest Mage.

Places to get Kinemages

You may find this index listing a subset of our kinemages useful. Download links for packages of the various types of kinemages are provided.

Our own full ftp site which includes demos, tutorials, documentation, a format description in the docsdemos subdirectory, and kinemages of general interest in the kinfiles directory.

The BT2kins ftp directory (in the kinfiles directory) contains all the kinemages for the 2nd edition of the Branden & Tooze Introduction to Protein Structure textbook.

The Protein Science site has numerous examples of premade kinemages, primarily those published in Protein Science. Their kinemage index will provide a list of available kinemages. However, we strongly suggest our own site to be used to get the most up-to-date versions of Mage and Prekin.

Teaching with kinemages

Kinemages have been used extensively for teaching purposes. Besides the teaching kinemages on our own ftp site, a number of textbooks have kinemage supplements, including Branden & Tooze Introduction to Protein Structure, Voet, Voet & Pratt Fundamentals of Biochemistry, and Horton et al. Principles of Biochemistry (the supplement to which can be ordered by calling Prentice Hall at 1-800-947-7700).

Some sample sites which use kinemages in teaching protein structures are the Kinemage Authorship Project at University of Southern Mississippi, the "Principles of Protein Structure" courses at Birkbeck and Calvin Colleges, the GroEL/ES lesson at Tulane, and the Bioinformatics Unit at the Weizmann Institute. A resource integrating kinemages in with other protein analysis and modeling tools is the BIMCORE facility at Emory.

The sequential display of a sequence of model states can help in understanding a complex process. As an example, consider the allosteric transitions of the biochemist's favorite "enzyme", Hemoglobin. The kinfile, HbAllo.kin, is used in the graphical and interactive environment of Mage, in combination with the program's animate function, to help us teach these key concepts in our biochemistry coursework. The kinemage file and an associated text file are available:

File	Computer System	Click to download
HbAllo.zip	Windows PC
HbAllo.sit	Macintosh
HbAllo.tar.Z	Unix, Linux

Non-molecular uses of kinemages

Download the kinemages mentioned in this section
kinemage:	platform:
kinemage:	Windows	Macintosh	unix
NonMolDemo.kin
Dancing Bears
Demo5_4b
Sociology

food web Mage is a versatile program and can be used for 3-D rendering of many types of information as illustrated by Joseph Kunkel's biological applications, by the RNA Simplex site, and by several of our kinemages, available on the FTP site, such as the NonMolDemo.kin. Crystallographic symmetry is illustrated by the Dancing Bears kinemage. 3D and 2D plots of data are easily shown in Mage, with the ability to identify any data point by clicking on it; examples can be seen in the Ramachandran section, or in kinemage 6 of Demo5_4b kinemage.

Kinemages are also used by social scientists to visualize social networks in 3D; a simple example is shown in a sociology kinemage. Linton Freeman's web siteincludes several papers discussing this use of Mage. The image at right is taken from a kinemage of the food web in an estuary, from Jeff Johnson at E. Carolina University. Jonathon N. Cummings at Carnegie Mellon has a web server at which one can input or create social network data and use JavaMage to visualize the relationships.

Which brings us to ... with the development of Java Mage, kinemages can be presented in a Java-capable Web browser. Please visit our Java Mage section for examples and more information.

Tutorials on making kinemages

Our tutorial, using the ricin structure, can be downloaded in either plain text format or as a PDF file. Or, it can be viewed as an HTML page on the web.

A tutorial written for the Kinemage Authorship Project (an NSF funded project; Robert Bateman at University of Southern Mississippi is the PI.)

Also available for download, or display in your browser if you have the appropriate plug-in, is a tutorial in PDF format which was developed by Gary Manfredy.

Designer Mage (experimental, special function)

Occasionally, special functionality is added to Mage either in the course of our lab's research or in collaboration with others. These "experimental" versions may not be stable and other functions of Mage may not work or work differently. So, we obviously don't recommend use of these programs for anything other than the limited scope of the added functionality.

File name (Click to download)	Release date	size (kB)	Description	README file (click to read)
mage.6.11.020718.gz	18-Jul-02	1741	Mage as viewer of simulation output. Mage can do a "tail" from a file into which a simulation program is writing frames. The version of Mage that can do this is posted here.
mage.6.11.020718.tgz	18-Jul-02	2301	The source for the version of Mage that can do this is posted here.
explode.x.x.020725.gz	25-Jul-02	8	Mage can do a "tail" from a file into which a simulation program is writing frames. An example simulation program called explode is included here as something to test Mage and demo this trick.
simulate.x.x.020725.tgz	25-Jul-02	30	This directory has the source and supporting files for an example simulation program called explode as something to test Mage and to provide example code that is needed in your simulation program to produce kinemage output for Mage.

If you are a kinemage user, please complete our KINEMAGE SURVEY.

As examples of kinemages, the top illustration on this page is a ribbon portrayal of carbonic anhydrase with sidechains at the active site. Below left is a kinemage of ribbons for the two dimers of Cu, Zn superoxide dismutase in the asymmetric unit of the crystal. Below right is a non-convex geometrical figure with 18 equal edges, along with a baseball which shares the same symmetry.