Kinemage
Encyclopedia
A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecule
s, especially protein
s and nucleic acid
s, although it can also represent other types of 3-dimensional data (such as geometric figures, social networks, or tetrahedra of 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 human- as well as machine-readable text file that describes the hierarchy of display objects and their properties, and that also includes optional explanatory text; the kinemage format is a defined chemical MIME type
of 'chemical/x-kinemage' with the file extension '.kin'.
, for the Protein Society's journal Protein Science
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, 3D kinemage graphics to illustrate many of the articles, plus the Mage software (free, open source
, multi-platform) to display them; kinemage supplementary material is still available on the journal web site. Mage and RasMol were the first widely used macromolecular graphics
programs to support interactive display on personal computers. Kinemages are used for teaching and for textbook supplements, as well as individual exploration and analysis of macromolecular structures.
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) as well as quantitatively for analyzing the detailed interactions between molecular surfaces, most extensively for the purpose of validating and improving the molecular models from experimental x-ray crystallography
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
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.
systems, with the open-source KinImmerse software. All of the kinemage display and all-atom contact software is available free and open-source on the kinemage web site.
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
s, especially protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s and nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
s, although it can also represent other types of 3-dimensional data (such as geometric figures, social networks, or tetrahedra of 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 human- as well as machine-readable text file that describes the hierarchy of display objects and their properties, and that also includes optional explanatory text; the kinemage format is a defined chemical MIME type
Chemical file format
This article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...
of 'chemical/x-kinemage' with the file extension '.kin'.
Early history
Kinemages were first developed by David Richardson at Duke University School of MedicineDuke University School of Medicine
The Duke University School of Medicine is Duke University's medical school operating under the auspices of the Duke University Medical Center. Established in 1925 by James B...
, for the Protein Society's journal Protein Science
Protein Science
Protein Science is a peer-reviewed scientific journal publishing research on the structure, function, and biochemical significance of proteins, their role in molecular and cell biology, genetics, and evolution, and their regulation and mechanisms of action...
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, 3D kinemage graphics to illustrate many of the articles, plus the Mage software (free, open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
, multi-platform) to display them; kinemage supplementary material is still available on the journal web site. Mage and RasMol were the first widely used macromolecular graphics
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"...
programs to support interactive display on personal computers. Kinemages are used for teaching and for textbook supplements, as well as individual exploration and analysis of macromolecular structures.
Research Applications
More recently, with the availability of a much wider variety of other molecular graphicsMolecular 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"...
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
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
, van der Waals
Van der Waals force
In physical chemistry, the van der Waals force , named after Dutch scientist Johannes Diderik van der Waals, is the sum of the attractive or repulsive forces between molecules other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral...
, and steric "clash" interactions between atoms. The results can be used visually (in kinemages) as well as quantitatively for analyzing 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
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
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
Parallel coordinates is a common way of visualizing high-dimensional geometry and analyzing multivariate data.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.
On-line Web Use
KiNG is an open-source Java kinemage viewer (written by Ian Davis and Vincent Chen) that can work either stand-alone or interactively in web pages. The interactive nature of kinemages is their primary purpose and attribute; therefore to appreciate their nature, please click here KiNG in browser for two examples that you can move around in 3D, plus instructions for how to embed a kinemage on your own 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 realityVirtual reality
Virtual reality , also known as virtuality, is a term that applies to computer-simulated environments that can simulate physical presence in places in the real world, as well as in imaginary worlds...
systems, with the open-source KinImmerse software. All of the kinemage display and all-atom contact software is available free and open-source on the kinemage web site.