The Kinemage Concept
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 (or more) 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 either the Mage or KiNG graphics program. A kinemage file can be generated either by a program or hand-cobbled. An utility called Prekin makes a starting kinemage from a PDB-format coordinate file. Other kinemage file generators for both molecular and non-molecular applications are discussed below. Additionally, both Mage and KiNG have the ability to edit the kinemages being viewed.
Examples of Kinemages
Before seeing some examples of kinemage use and capabilities look at one or both of the viewers used to display kinemages (click image to enlarge it):
Please note two things seen in either kinemage viewer: the display portion and the right-side selection panel. Both KiNG and Mage are general vector display programs with rich sets of available display objects. Both succeed well in depth cueing and object manipulation (rotation, translation, zooming, etc.) The selection boxes of the right panel are mostly groups and sub-groups as defined in the kinemage and are used to toggle display of defined portions of the display. This allows abstraction and simplification of complex objects, combination and comparison of data groupings, and so forth allowing the kinemage to aid investigation (research) and explanation (teaching).
Further examples of kinemages by functionality:
Kinemages are used in both lectures and homework/project assignments. Example worksheets and .kin files are available - feel free to use as is or modify to suit your needs - by browsing the teaching sections of this website or from this listing of kinemage files.
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.
Some internet sites which use kinemages in teaching protein structures:
In the past few years, as our Laboratory's research has developed the all-atom contact methodology as an aid in macromolecular model validation and construction, we have hammered Mage into a very useful tool for crystallography. KiNG, being based on Mage but also adding some other tools, is also a lab workhorse for those working with rebuilding, evaluating macromolecular models. Some of the functionality that may be of interest are:
- Interactive contact-dot updating as the model is changed
- Display of electron-density maps
- Our "Penultimate" rotamer database is built in, allowing easy evaluation of rotamers.
- Local backbone adjustment in KiNG
- NOE display superimposed on model (under development, please inquire if interested).
See our all-atom contact methods section for more detail.
A resource integrating kinemages in with other protein analysis and modeling tools is the BIMCORE facility at Emory.
As mentioned before, Mage & KiNG are general vector display programs; they are not limited to macromolecule display. They can be used for display and interaction with many types of information as illustrated by:
Kinemages are also used by social scientists to visualize social networks in 3D:
- Linton Freeman's publications page includes 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 MIT has a web server, NetVis, at which one can input or create social network data and use JavaMage to visualize the relationships.
Mage and KiNG are also used to produce hard-copy figures; while, Java-based subsets of Mage or KiNG are used as 3D viewers run from internet graphical-browsers (IE, Netscape, etc.) allowing your data to be presented on the internet or during a lecture/speech/talk.
Mage and KiNG can write out these formats: PNG, JPEG, EPS, PDF, raster3D input. We've found that a useful workpath is to capture the Mage/KiNG display as an EPS and do touchup editing in a vector drawing program such as Adobe Illustrator. Then various renderings of the figure can be generated from that source.
Kinemage files can be displayed as applets in graphical browsers with use of the "java jars" available from our javamage section.
Getting kinemages and the programs to make or display them
The kinemages supplied from this website are "zip-" compressed text files with unix linefeeds. This compression format is public-domain and "unzip-" programs are available for all the major platforms. Reading the kinemage file from within the display program ignores the linefeed type and saving the kinemage from King or Mage will use OS-native linefeeds in the new file.
You can browse two listings of kinemage files:
- a select subset of popular kinemages, or
- a directory listing which includes demos, tutorials, documentation and format descriptions, and kinemages of general interest. The BT2kins subdirectory 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 which were published in Protein Science. Their site has been recently reworked and the best route to finding a kinemage of interest is through their search page.
The current distributed versions of Mage, KiNG, and Prekin are available free from our software page. Older versions of our software and open source code are available from our archive. An older version may be needed, if for instance, you will use the programs on an older operating system. Mage and Prekin continue to evolve with increased capabilities but, by policy, all earlier kinemages we know of are viewable in the latest Mage.
Resources for learning about kinemages
Our tutorial, using the ricin structure, is available on-line in HTML format or it can be downloaded in PDF format makeKinTut_inKiNG.pdf (80KB).
The manual for KiNG, our Java-based kinemage viewer, is available as a pdf: king-manual.pdf (240KB). This is the same document that is used for KiNG's internal help documentation.
An on-line tutorial written for the Kinemage Authorship Project is available (an NSF funded project; Robert Bateman at University of Southern Mississippi is the PI.) This site has other resources, including a kinemage authorship manual in pdf format.
Program extension: Designer Mage & KiNG Plug-Ins
Mage, Prekin & KiNG are all under active development, with new functionality being integrated into the distributed versions.
KiNG's functionality can be expanded via plug-ins. Documentation and a tutorial on how to write a plug-in is available from the KiNG download page.
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. The versions made available to the public are available from our playpen page.