A kinemage (short for kinetic image) is an interactive graphic scientific illustration. It often is used to visualize

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...

s, especially

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

s although it can also represent other types of 3-dimensional data (such as geometric figures, social networks, or tetrahedra o
RNA base composition
. The kinemage system is designed to optimize ease of use, interactive performance, and the perception and communication of detailed 3D information. The kinemage information is stored in a text file, human- and machine-readable, that describes the hierarchy of display objects and their properties, and includes optional explanatory text. The kinemage format is a defined chemical MIME type of 'chemical/x-kinemage' with the

file extension A filename extension, file name extension or file extension is a suffix to the name of a computer file (e.g., .txt, .docx, .md). The extension indicates a characteristic of the file contents or its intended use. A filename extension is typically d ...

'.kin'.

Early history

Kinemages were first developed by David Richardson at Duke University School of Medicine, for the Protein Society's journal

Protein Science ''Protein Science'' is a peer-reviewed scientific journal covering research on the structure, function, and biochemical significance of proteins, their role in molecular and cell biology, genetics, and evolution, and their regulation and mechan ...

that premiered in January 1992. For its first 5 years (1992–1996), each issue of Protein Science included a supplement on floppy disk of interactive, kinemage

3D computer graphics 3D computer graphics, or “3D graphics,” sometimes called CGI, 3D-CGI or three-dimensional computer graphics are graphics that use a three-dimensional representation of geometric data (often Cartesian) that is stored in the computer for t ...

to illustrate many of the articles, plus the Mage software (

cross-platform In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software ...

, free, open-source) to display them; kinemage supplementary material is still available on the journal web site. Mage and RasMol were the first widely used macro

molecular graphics Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekul� ...

programs to support interactive display on

personal computer A personal computer (PC) is a multi-purpose microcomputer whose size, capabilities, and price make it feasible for individual use. Personal computers are intended to be operated directly by an end user, rather than by a computer expert or tec ...

s. Kinemages are used for teaching, and for textbook supplements, individual exploration, and analysis of macromolecular structures. RibonucleaseA Uvan inhibitor contacts 1ruv

RibonucleaseA Uvan inhibitor contacts 1ruv

Research uses

More recently, with the availability of a much wider variety of other

tools, presentation use of kinemages has been overtaken by a wide variety of research uses, concomitant with new display features and with the development of software that produces kinemage-format output from other types of molecular calculations. All-atom contact analysis adds and optimizes explicit hydrogen atoms, and then uses patches of dot surface to display the hydrogen bond, van der Waals, and steric ''clash'' interactions between atoms. The results can be used visually (in kinemages) and quantitatively to analyze the detailed interactions between molecular surfaces, most extensively for the purpose of validating and improving the molecular models from experimental

x-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...

data. Both Mage and KiNG (see below) have been enhanced for kinemage display of data in higher than 3 dimensions (moving between views in various 3-D projections, coloring and selecting candidate clusters of datapoints, and switching to a

parallel coordinates Parallel coordinates are a common way of visualizing and analyzing high-dimensional datasets. To show a set of points in an ''n''-dimensional space, a backdrop is drawn consisting of ''n'' parallel lines, typically vertical and equally spaced. ...

representation), used for instance for defining clusters of favorable RNA backbone conformations in the 7-dimensional space of backbone dihedral angles between one ribose and the next.

Online web use

KiNG is an open-source kinemage viewer, written in the programming language

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...

by Ian Davis and Vincent Chen, that can work interactively either standalone on a user machine with no network connection, or as a web service in a web page. The interactive nature of kinemages is their primary purpose and attribute. To appreciate their nature, the demonstration KiNG in browser has two examples that can be moved around in 3D, plus instructions for how to embed a kinemage on a web page. The figure below shows KiNG being used to remodel a lysine sidechain in a high-resolution crystal structure. KiNG is one of the viewers provided on each structure page at the Protein Data Bank site, and displays validation results in 3D on the MolProbity site. Kinemages can also be shown in immersive

virtual reality Virtual reality (VR) is a simulated experience that employs pose tracking and 3D near-eye displays to give the user an immersive feel of a virtual world. Applications of virtual reality include entertainment (particularly video games), e ...

systems, with the open-source KinImmerse software. All of the kinemage display and all-atom contact software is available free and open-source on th
kinemage web site
KiNG backrubFit modeling in density

References

External links

* {{Official website, kinemage.biochem.duke.edu, Duke University original, with examples and software
kinemage example in a browser

RCSB Protein Data Bank

MolProbity: structure validation, with KiNG on-line kinemages
Chemistry software

Early history

Research uses

Online web use

See also

References

External links