KiNG (Kinemage, Next Generation):
A versatile interactive molecular and
scientific visualization program
Vincent B. Chen, Ian W. Davis, and David C. Richardson*
Biochemistry Department, Duke University Medical Center, Durham, NC 27710
Received 7 July 2009; Revised 9 September 2009; Accepted 10 September 2009
DOI: 10.1002/pro.250
Published online 18 September 2009 proteinscience.org
Abstract: Proper visualization of scientific data is important for understanding spatial relationships.
Particularly in the field of structural biology, where researchers seek to gain an understanding of
the structure and function of biological macromolecules, it is important to have access to
visualization programs which are fast, flexible, and customizable. We present KiNG, a Java
program for visualizing scientific data, with a focus on macromolecular visualization. KiNG uses
the kinemage graphics format, which is tuned for macromolecular structures, but is also ideal for
many other kinds of spatially embedded information. KiNG is written in cross-platform, opensource
Java code, and can be extended by end users through simple or elaborate ‘‘plug-in’’
modules. Here, we present three such applications of KiNG to problems in structural biology
(protein backbone rebuilding), bioinformatics of high-dimensional data (e.g., protein sidechain chi
angles), and classroom education (molecular illustration). KiNG is a mature platform for rapidly
creating and capitalizing on scientific visualizations. As a research tool, it is invaluable as a test
bed for new methods of visualizing scientific data and information. It is also a powerful
presentation tool, whether for structure browsing, teaching, direct 3D display on the web, or as a
method for creating pictures and videos for publications. KiNG is freely available for download at
http://kinemage.biochem.duke.edu.
Keywords: interactive molecular graphics; kinemage graphics; backrub motion; all-atom contact
dots; Molikin; Mage; Java
Introduction
In the field of structural biology, where researchers
seek to gain an understanding of the structure and
function of biological macromolecules, it is important
to have access to visualization programs, which are
fast, flexible, and customizable. Good visualizations
give researchers a more intuitive feel for how molecules
behave. However, it is also important for such
programs to be able to show other types of information
simultaneously with the structural representation,
such as 3D annotations of errors in the models or important
interaction sites.
KiNG (Kinemage, Next Generation) is a Javabased,
modular, easily extensible scientific visualization
tool used primarily for macromolecular visualization.
Like other general purpose molecular viewers
such as PyMOL, SwissPdbViewer, Chimera, RasMol,
and JMol,1–5
KiNG allows for real-time, interactive 3D
rotation, translation, cropping, and zooming, which
are critical for proper sensation of depth and for perceiving
spatial relationships accurately. However,
KiNG separates itself from these other programs in a
number of significant ways, specifically in its
Additional Supporting Information may be found in the online
version of this article.
Vincent B. Chen and Ian W. Davis contributed equally to this
work.
Ian W. Davis’s current address is GrassRoots Biotechnology,
Morrisville, NC 27560.
Grant sponsor: NIH; Grant numbers: GM-073919, GM-073930
(funding for KiNG); Grant sponsor: Howard Hughes Predoctoral
Fellowship (to IWD).
*Correspondence to: David C. Richardson, 211 Nanaline Duke
Bldg, Box 3711 DUMC, Durham, NC 27710. E-mail: dcr@
kinemage.biochem.duke.edu
Published by Wiley-Blackwell. VC 2009 The Protein Society PROTEIN SCIENCE 2009 VOL 18:2403—2409 2403
molecule-agnostic kinemage graphics format, the quality
of its color palette and depth cueing, and in the
tools and features it offers.
KiNG builds on the three decades of successful molecular
graphics experience embodied in the original
protein ribbon drawings6
and in the first kinemage
graphics program, Mage.7
Mage was designed as a tool
for molecular illustration (with the selectivity and artistry
that connotes) for journal articles and classroom
settings. However, we found that Mage quickly became
an integral part of the lab’s research program due to its
tremendous flexibility. Reimplementing the core kinemage
functionality from the ground up in KiNG has
enabled a similar-looking but modern user interface, a
cleaner internal data structure, and greater maintainability
and extensibility. Not surprisingly, KiNG has also
become a central component of the lab’s work.
However, instead of superseding Mage, KiNG and
Mage currently coexist as separate development paths.
In fact, having two different kinemage viewers in active
development has encouraged improvements in both programs.
For example, the high-dimensional visualization
capabilities (see ‘‘Results and Discussion’’) were actually,
at first, independently added to both KiNG and Mage for
different purposes. Then, by collaborating and combining
the strengths of each separate implementation, we
were able to develop functionality that was ultimately
more general-purpose and more powerful.
KiNG and Mage’s flexibility comes from separating
the molecular details (e.g., PDB file) from the
graphical representation (kinemage).7
This strategy
allows traditional macromolecular structural data
(models, ribbons, electron density, NMR data) to coexist
naturally with secondary ‘‘annotations’’ of that data
(e.g., helix axes, local validation outliers, interface contact
dots); it also permits wholly nonmolecular visualizations
using the same tool.
The kinemage format is extensively documented
and numerous examples are available at http://kinemage.biochem.duke.edu
(see also ‘‘Materials and
Methods’’). Kinemage format is plain text, designed to
be both easy to edit by hand and also easily generated
by programs.
When kinemage format alone is not flexible enough,
KiNG itself can be modified. Although the graphics
engine could be reused in a totally new program, more
often new capabilities are added with plug-in modules
that are written in Java and dynamically loaded at run
time. The protein rebuilding and molecular illustration
capabilities in this article were developed as plug-ins,
while the facilities for high-dimensional analysis required
modification of the core program. New modules can be
written quickly and easily to extend functionality, giving
KiNG very open-ended potential.
Results and Discussion
KiNG is freely available to all users, multiplatform,
and open source. In addition to having an extensive
outside user base, KiNG has gradually become one of
the most important research tools within our laboratory.
Because of its modular nature, it has become a
test bed for a variety of new tools and visualization
techniques, enabling the discovery of many new
research results. Several of these tools, techniques, and
results are described here.
Conventional use
A key goal in the development of KiNG (and originally,
in Mage) was to make basic navigation and user interaction
as simple and intuitive as possible. To that end,
in KiNG, most of the basic navigation tasks can be
controlled by the mouse. Rotations, zooming, and clipping
are all controlled with click and drag mouse
actions. Clicking on a point displays associated information
about the point in the graphics window. Clicking
on two successive points displays the distance
between them, an essential tool in structural biology
visualization for determining interatomic distances
and possible interactions. Different aspects of the kinemage
display hierarchy can be turned on or off on the
fly using the check boxes located along the side of the
main graphics window. The main menus enable access
to more advanced features of KiNG. For instance, important
views can be saved and returned to instantly.
More advanced measuring tools can be activated for
measuring angles and dihedrals. There is a whole suite
of tools for editing kinemages directly in KiNG, such
as for changing colors of points or lines, deleting
objects, editing coordinates, or adding additional
graphical elements. Some of the more noteworthy
tools and features of KiNG are described in more
detail below.
Applet mode
KiNG includes an applet mode, which allows it to be
run through web browsers, without users having to
download KiNG separately. This functionality has been
critical in our structural validation website, MolPro-
bity,8
for display of errors within macromolecular
structures. Feedback from MolProbity users has helped
greatly to ensure that KiNG keeps functioning
smoothly for multiple subjects and viewing styles.
Also, the applet feature has allowed KiNG to be used
directly on the website of the Protein Data Bank
(PDB)9
repository of structures. Previously, separate
kinemages had to be generated for use with KiNG on
the PDB website. This led to significant maintenance
difficulties, since whenever PDB files were updated,
the kinemage files would also have to be updated. This
issue has been resolved with the latest version of
KiNG on the PDB website, as it can now use our macromolecular
kinemage generation software Molikin
(see below) directly to generate kinemages on the fly
when a user wants to display a structure. We tested
KiNG against the entire PDB (as of March 2009) and
it successfully generated a valid kinemage for every
2404 PROTEINSCIENCE.ORG KiNG: A Versatile Scientific Visualization Program
file. Also, KiNG truncates input files if it determines it
does not have enough memory allocated, which allows
the typically memory-limited KiNG applet to still successfully
generate some kind of visualization, even for
the largest structures. A king in browser tutorial package
on using KiNG as an applet is available for download
at http://kinemage.biochem.duke.edu.
Protein backbone rebuilding
Although kinemages have been used to display everything
from the flight paths of Russian MIGs to the
social networks in an Antarctic research station, we
use them primarily for viewing biological macromolecular
structures. Also, we often want to modify the
starting structure—for instance, rebuilding to make it
fit the experimental data better (e.g., electron density,
which can be displayed from most map file formats).
Although many tools exist for rebuilding protein struc-
tures,10,11
we found KiNG to be an excellent platform
for testing out some new ideas we recently developed
about protein backbone.
Fitting backbone is difficult because the region of
interest is generally constrained at both ends by the
rest of the chain, and any local change may also disrupt
perfectly good regions nearby. However, we have
recently documented the ‘‘backrub’’ motion, a very
local pattern of nondisruptive conformational change
in protein backbone that frequently occurs as alternate
conformations in native protein structures.12
Simulating
backrub motions as a rebuilding tool has proven
very successful for correcting the kinds of backbone
distortion introduced by fitting a sidechain backwards
into the density, which is a common mistake. Currently,
KiNG is the only software package that offers
backrub motions to correct these kinds of mistakes.
The use of KiNG for backrub modeling, and interactive
display of all-atom contacts and sidechain rotamer
quality, was essential to successful improvement in accuracy
for 29 high-throughput crystal structures by the
SouthEast Structural Genomics Consortium.13
Figure 1 shows the backrub fitting tool in action
in the KiNG graphical user interface. Although the
core of KiNG knows nothing about molecules, the
backrub plug-in reads PDB or mmCIF files and correlates
the atom positions with the kinemage graphics. It
updates the graphics as the model is being refit, and
then writes a new model file at the end. Because the
kinemage format acts as a graphics lingua franca for
communicating to the user, KiNG can incorporate
additional feedback from external programs into the
rebuilding process (in nearly real time). For instance,
if hydrogens have been added to a structure, our
Figure 1. KiNG graphical user interface. An image of the KiNG graphical user interface, showing the Backrub tool being used
to reconstruct an alternate conformation of a lysine residue in a protein structure (PDB: 1US0).14
Contact dots from Probe are
shown (as dots and small spikes). The electron density is shown in gray wire-mesh, the original model in white and cyan, and
the active model in orange. Pop-up windows for controlling aspects of the backrub motion, the electron density, and the
contact dots are also visible.
Chen et al. PROTEIN SCIENCE VOL 18:2403—2409 2405
program Probe15,16
can provide extremely helpful live
updates on all-atom steric contacts and collisions in
the proposed model as backrub fitting is being performed.
A tutorial for using the backrub fitting tool,
along with Probe, is available at http://kinemage.
biochem.duke.edu, under teaching/MolProbity on the
navigation bar.
High-dimensional data
For several recent projects, we have found ourselves
needing to plot data points in high-dimensional
spaces. One example is analyzing the conformations of
protein loops, where it takes seven parameters to completely
define the spatial relationship between the
ends. Another is clustering the conformations of RNA,
where (coincidentally) seven dihedral angles define the
backbone conformation between two bases.17
For the
RNA analysis, we originally used different sets of three
angles to make many different 3-D plots. However,
points that cluster in one plot do not necessarily cluster
in the others, and correlating points from one plot
to another is tedious and error-prone.
To facilitate this type of high-dimensional ‘‘info vis’’
use of kinemages, we added two new features both to
KiNG and Mage. The first is support for high-dimensional
points: rather than just XYZ, each point may
have an arbitrary number of coordinates associated
with it. KiNG then provides tools for quickly switching
among different 3-D projections of the data, that is,
three of the coordinates are mapped to XYZ and the rest
are temporarily ignored. By assigning a distinctive color
to an apparent cluster of points in one projection and
then switching to another projection, it becomes relatively
easier to disambiguate the true 7-D clusters. In
the RNA case, it allowed us to resolve several distinct
conformations that we had previously lumped together.
Figure 2. Information visualization capabilities of KiNG. Figures illustrating different types of representations in KiNG of the
same data: all 21 rotamers of Arg with chi1 trans, from an updated version (unpublished) of our protein sidechain rotamer
library.19
Two custom green colors were defined for this figure (see ‘‘Materials and Methods’’). This figure is also available in
interactive kinemage format, in Supporting Information. Panel A shows stick representations of different arginine rotamers
with their backbone atoms superimposed. Backbone is colored in white, with the different sidechain rotamers in different
colors. Balls are used to indicate nitrogen and oxygen backbone atoms. Text labels were added using Adobe Photoshop.
Panel B shows a 3D plot of the chi2 through chi4 dihedral angles of the arginine rotamers shown in A, with identical coloring.
The data points are represented by balls. Contours were drawn using kin3Dcont.20
Axis text labels were added using Adobe
Photoshop. Panels C and D show the parallel coordinate representation of chi1 through chi4 of the arginine rotamers, where
each polyline spanning the four axes represents one data point. Panel D shows the same data as Panel C, but with
transparency increased. The tick marks and degree indicators were added using Adobe Photoshop.
2406 PROTEINSCIENCE.ORG KiNG: A Versatile Scientific Visualization Program
The second new high-dimensional feature in KiNG
and Mage is plotting data points in parallel coordi-
nates.18
Rather than the orthogonal arrangement of
Cartesian coordinate axes, parallel coordinate displays
place all of the coordinate axes side by side and parallel
to one another. As such, data points become polylines
that pass through the appropriate values on each axis.
In theory, this allows for simultaneous viewing of an
unlimited number of dimensions, although even a moderate
number of data points can produce a visual clutter
of criss-crossing lines that is hard to decipher.
Figure 2 shows an example of the power of using
high-dimensional plotting combined with parallel
coordinates, with three different representations of
related rotamer data, all shown in KiNG. Recently,
using a much larger data set, we have been updating
our previous protein sidechain rotamer libraries.19
The
conformation of the sidechain of arginine is defined by
four dihedral (chi) angles. In Figure 2, only the data
points with chi1 close to 180
are shown. In the traditional
three-dimensional view of the data points, clusters
of points are evident, but in the parallel coordinate
view, the clustering of the points (as polylines)
becomes even more obvious. Using KiNG’s button
panel control, each proposed individual cluster can be
examined individually in the parallel coordinate representation,
to ensure that no split in any dimension is
overlooked. When transparency is enabled on the data
[compare Fig. 2(D) with Fig. 2(C)], all of the major
clusters can be seen even in a complex background.
The projections and parallel coordinates have
complementary strengths and are most effective when
used together. The 3-D projections are better for initial
selection, coloring, and clustering of data, but the parallel
coordinates display provides an important check
that putative clusters really stay together in all dimensions.
KiNG switches between the two modes with a
single keystroke, and markers and point colors are
shared between the two, making it easy to move back
and forth while working. These capabilities of KiNG
were central to the collaborative work that produced
the RNA Ontology Consortium’s nomenclature and
conformer library for RNA backbone.21
Molecular illustration
In our teaching, we ask students to choose a protein
or protein family and use kinemages to illustrate its
important structural or functional features.22
Creating
kinemages leads to a deeper understanding than
merely examining a 3-D display, just as writing about
a subject requires more knowledge than reading. Of
course, making kinemage models from macromolecular
coordinates is also a basic requirement for our
research. Thus, any tool for converting PDB or mmCIF
files to kinemages must be both easy to use and very
flexible—properties often at odds with each other.
Our solution, called Molikin (see ‘‘Materials and
Methods’’), solves this problem by offering two modes
of operation: a ‘‘quick kin’’ mode for rapidly generating
commonly used types of visualizations of macromolecular
structures, and an advanced mode that provides
more control of the visualizations which are produced,
down to a residue level of control if desired. Molikin is
included as a plugin with the KiNG download, accessible
under the ‘‘Import’’ option in the File menu. This
allows users to read PDB files directly into KiNG and
view a kinemage display almost instantly.
As mentioned previously, the kinemage format
itself provides a great deal of flexibility. In addition to
all the built-in kinemage editing and drawing tools in
KiNG, the hand-editable nature of the format allows
users to easily write enhancements to kinemages.
These features mean that KiNG and the kinemage format
are particularly well-suited for students creating
educational projects in our classes; they can start their
project with only a few decisions and gradually refine
their ideas over time without starting over. Also,
researchers can use KiNG and kinemages to quickly
prototype new types of visualizations. For example, we
have various modules and programs that produce kinemages
of electron density for crystallography, NOE
(Nuclear Overhauser Effect) or RDC (Residual Dipolar
Coupling) restraints for NMR,23
and all-atom steric
contacts.15
These kinemages are all combined seamlessly
in KiNG, and so there is no need to reimplement
these algorithms in one monolithic molecular graphics
program.
KiNG is able to export high-resolution 2D views
in a number of widely supported picture formats,
including JPEG, PNG, and PDF, as well as by direct
screen capture such as the ribbon diagram in Figure 3.
It can also export files for use with the rendering
Figure 3. An example of ribbon graphics in KiNG. Screencaptured
2D image of a ribbon diagram of staphylococcal
alpha-hemolysin, a heptameric transmembrane pore (PDB:
7AHL),24
viewed down the pore. This figure is also available
in interactive kinemage format, in Supporting Information.
Chen et al. PROTEIN SCIENCE VOL 18:2403—2409 2407
software Raster3d25
or POV-Ray26
for generating
higher quality images. It also has a movie-maker function,
which makes it easy for users to create movies
for use in presentations. Naturally, KiNG itself can be
used during a presentation, for a live demonstration to
enable even better 3D perception by the audience.
Conclusion
KiNG is a powerful and flexible scientific visualization
software package, which has evolved into more than
just a visualizer; it is an important research tool,
which, due to its existing capabilities and ability to be
extended, will continue to shed new light on macromolecular
structures.
Materials and Methods
Kinemage format
A kinemage is a plain-text file containing both metadata
(title, author, data source, and potentially extensive explanatory
text) and a set of hierarchically grouped display
lists of primitives such as lines, dots, balls, triangles,
and labels; this structure is closely mirrored by a
hierarchy of objects within KiNG’s source code. Briefly,
kinemage files contain two types of lines: keyword lines
and point lines. Keyword lines begin with keywords,
which start with the ‘‘@’’ symbol and define all metadata
info (e.g., @text, @dimensions) and the groups, lists,
and other kinemage properties (e.g., @kinemage,
@group, @master). Point lines, in their simplest form,
contain numbers, separated by whitespace. KiNG will
keep track of the number of coordinates it has encountered,
making each set of three coordinates a new point
(or n coordinates when the list property ‘‘dimension ¼
n’’ is used). This feature allows users to enter data into
KiNG and see what it looks like very quickly. Coordinates
can also be preceded by point identifier information
in curly braces ({}), which is displayed in the
graphics window when the point is left-clicked on. All
the keywords as well as the different types of points
have a wide variety of options, which are described in
the ‘‘format-kinemage.pdf’’ document available at
http://kinemage.biochem.duke.edu.
In addition to all the documented kinemage features
supported by KiNG, when KiNG encounters a
keyword it does not recognize, it will enter a note in
the Error log (accessed through the Help menu). This
mainly occurs in some of the older hand-created
teaching kinemages, which contain lesser-known features
that are only recognized in Mage. Conversely,
Mage does not support some of the newer kinemage
features introduced in KiNG.
Internal palette
Like Mage, KiNG’s internal color palette consists of a
set of 25 named colors. The colors are depth-cued
appropriately, depending on whether they are being
viewed on a black or white background. KiNG includes
an ‘‘Internal palatte’’ kinemage (Help menu ! Built-in
kinemages), which allows users to see the standard
colors, along with the depth-cueing. When the named
colors do not provide enough options, KiNG supports
a new kinemage keyword (@hsvcolor), which allows
users to define custom hue/saturation/value colors,
also which are also depth-cued appropriately.
Implementation
KiNG is implemented in Java, using features added in
Java 1.5. The graphical user interface is implemented
using the Java Swing and AWT libraries. The KiNG
engine handles the viewing calculations, but it has the
option of using the Java Bindings for OpenGL (JOGL)
for improved graphics rendering. Using JOGL is not a
requirement for running KiNG, however, meaning
users with the basic Java installation, as well as web
applet users, can still successfully use KiNG.
Molikin
Molikin is also implemented in Java, using features in
Java 1.5. Molikin enjoys a highly modular design: just
5% of the code interfaces with KiNG, and 95% focuses
on making kinemages. This made it easy to create a
version of Molikin that stands alone from the KiNG
plugin version, using a command-line interface. This
allows scriptable control of Molikin, especially powerful
for generating a large number of visualizations.
Molikin has a number of different options for generating
‘‘raw materials’’; these take the form of (ball and)
stick renderings, space-filling models, and ribbon
drawings. Other options include mainchain versus
sidechains; protein versus nucleic acids versus water;
which models, chains, and residues to include, and so
forth, which are accessible in the plugin GUI shown
when Molikin is accessed in KiNG.
Tools description
Almost all the built-in tools in KiNG are accessed under
the Tools menu. Some are directly accessible from the
Tools menu, and others from a number of sub-menus:
Kin editing, Structural biology, and Specialty. Users can
adjust the layout of the Tools menu, even creating new
submenus or removing tools, by using the ‘‘Customize
tools menu. . .’’ option. The Edit/draw/delete tool, as well
as options for showing coordinates and measuring angles
and dihedrals, is in the main menu. Kin editing includes
other useful tools for editing kinemages, including superposition
tools, a molecular-specific coloring tool, a tool
for adjusting distances, angles, and dihedrals of points,
and the aforementioned movie maker tool. Structural
biology contains all the protein rebuilding tools, including
the Backrub tool and sidechain mutation/rotation
tools. Specialty mainly contains tools which are unsuited
for general users, being either highly specific to our own
research, or beta tested.
Developers can create either a Plugin, which adds
new menu items or dialogs, or a Tool, which can also
2408 PROTEINSCIENCE.ORG KiNG: A Versatile Scientific Visualization Program
alter the effects of mouse actions. Multiple Plugins can
run at the same time, but only one Tool can be active
at a time. Creating a new tool or plugin is straightforward;
developers interested in developing new KiNG
functionality only have to subclass either Plugin or
BasicTool, add new functionality with Java methods,
create a configuration file listing the new tool(s) and/
or plugin(s), and package it in a Java JAR file. After
adding the new JAR package to the Java classpath or
the ‘‘plugins’’ directory in KiNG, KiNG will load the
tools and plugins from the JAR file; tools and plugins
are discovered and loaded dynamically when KiNG is
run, and so users do not have to change any code
within KiNG itself to use new tools. A more thorough
explanation of how to create tools or plugins is
included in the ‘‘hacking-king.pdf’’ document in the
KiNG download, and a sample set of simple plugins
(with source code) is available on the KiNG software
webpage.
Acknowledgment
We thank present and former members of the Richardson
lab, specifically Bryan Arendall, Jeremy Block, Jeff
Headd, Daniel Keedy, Gary Kapral, Laura Murray, Jane
Richardson, Lizbeth Videau, Christopher Williams, and
Bob Immormino, who have provided much feedback and
suggestions during the course of KiNG’s development.
We also thank Stuart Endo-Streeter, a long-time user of
KiNG. A particularly useful plugin, NOEdisplay, was
contributed by Brian Coggins.
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