Tables for
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 21.5, pp. 688-693   | 1 | 2 |

Chapter 21.5. KiNG and kinemages

V. B. Chen,a J. S. Richardsona and D. C. Richardsona*

aDepartment of Biochemistry, Duke University, Durham, NC 27710, USA
Correspondence e-mail:

KiNG and the kinemage interactive three-dimensional graphics it displays are a powerful yet easy to use system for viewing and analysing structures of macromolecules. Kinemages can be used in a variety of ways, from interactive molecular illustrations for teaching or the web, to display of high-dimensional data or detailed structural analysis for research. KiNG also provides a set of crystallographic rebuilding tools, including a novel `backrub' tool for making local, non-disruptive adjustments to protein backbone that couple strongly to side-chain changes, supported by display of electron density, rotamer quality and all-atom contact analysis. KiNG includes a suite of tools for conveniently constructing kinemages from a variety of sources, as well as an extensive set of on-screen editing and drawing functions.

21.5.1. Introduction to aims and concepts

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KiNG and the kinemages it displays provide molecular graphics, organized in an unusual way, that are of interest to crystallographers for uses that range from interactive illustrations for teaching and web display, to high-dimensional data display, to a dot-surface representation of all-atom van der Waals contacts, updated in real time by Probe to help guide model-to-map fitting.

A kinemage (`kinetic image') is an authored interactive three-dimensional illustration that allows open-ended exploration but has viewpoint, explanation and emphasis built in. A kinemage is stored as a human-readable flat ASCII text file that embodies the data structure and three-dimensional plotting information chosen by its author or user. The original kinemage viewer, Mage (Richardson & Richardson, 1992[link], 1994[link]), is a pure graphics display program designed to show and edit kinemages, while Prekin constructs molecular kinemages from PDB (Protein Data Bank; Berman et al., 2000[link]) files. A spiritual successor to Mage, KiNG (Kinemage, Next Generation) is a Java-based kinemage reader (Chen et al., 2009[link]) and has evolved into a fully featured alternative to MageKiNG includes a Java program Molikin, based heavily on Prekin, to construct kinemages from PDB files or mmCIF files. The latest versions of KiNG, Mage and Prekin are available free and open source for Macintosh, PC or Linux from the kinemage web site ( ).

KiNG and Mage operate quite equivalently on the different platforms, and their graphical interfaces differ very little except where each has some unique feature for construction, drawing or modelling. All the major features of KiNG described here are also available in Mage, except for the `backrub' tool (Davis et al., 2006[link]) and the web online display. KiNG has more convenient tools for superposition, electron-density display and built-in kinemage construction, while Mage has a number of historical tools for highly specialized purposes, such as a system for defining separate groups with rotatable bonds (such as an RNA suite or a ligand), and the ability to time, score and save exercise or test results. By policy, later versions of Mage can display all older kinemages back to 1992, and KiNG comes very close. This means that the kinemage format has standard forms but also recognizes many alternative forms likely to occur in human-edited files or those produced by other software (such as `gray' versus `grey', and commas, spaces or line breaks as field separators).

By design, KiNG has no internal knowledge of molecular structure (except for a few built-in libraries used for mutations and rebuilding). A collaboration between the author and the authoring program (e.g. Molikin) builds data organization into the kinemage itself. This two-layer approach has great advantages in flexibility, since an author can show things the programmer never imagined, including non-molecular three-dimensional relationships. Overall, just viewing kinemages demands less work and less expertise from the reader than most molecular graphics, but that ease of use depends on the authoring effort involved in making thoughtful choices, aided by the extensive on-screen editing capabilities described below.

Mage and KiNG are both designed to optimize visual com­prehension: the understanding and communication of specific three-dimensional relationships inside complex molecules. Display speed has been given priority, to ensure good depth perception from smooth real-time rotation, even for a whole ribosome. The interface is extremely simple and transparent, and the colour palette has been carefully tuned for visual comparisons, contrasts and depth cueing. Immediate identification and measurement are always active; views, animations or bond rotations can be built in by the kinemage author. A text window explains the intentions of the author, while a simple hypertext capability allows the reader to jump to the specific view and display objects being described; however, most kinemages can also be successfully understood just by exploring what is available within the graphics window.

Kinemages are suitable for structure browsing or producing static two-dimensional presentation graphics, but those aspects have been kept secondary to effectiveness for interactive visualization and flexibility of author specification. Features and representations have deliberately been chosen to be fast and simple but spatially informative, rather than either showy or traditional, as illustrated by the following examples and their rationales. Mouse-controlled rotation in KiNG depends only on the direction of drag, so that the behaviour of the image is independent of absolute cursor position within the window. Labels are available but seldom needed, since the data structure builds in a `pointID' that is displayed whenever the point is picked. Instead of half-bond colouring, which tends to chop up the image, Molikin by default provides separate colours and button controls for main chain versus side chains, and it can prepare a partial `ball & stick' representation with colour-coded balls on non-carbon, non-hydrogen atoms (see Fig.[link]). Hydrogen atoms are crucial for some research uses, but to minimize the clutter from twice as many atoms, Molikin sets up their display under button control. For effective perception of conformational change, while avoiding either the confusion of overlays or the potential misrepresentation of computed interpolation, KiNG features simple animation switching between known conformations. Very importantly, since molecular information resides mostly in chemical bonds and spatial proximity, kinemages emphasize fully three-dimensional representations, such as vectors, dots or balls, rather than surface graphics that obscure internal structure. A space-filling representation (the `spherelist') is available, but it is suggested that it be used very sparingly – for example, to show the size and shape of a small-molecule ligand. If an extensive surface is needed, a dot surface is more informative, since the underlying atoms and bonds can be seen at the same time. However, a well rendered ribbon is unmatched for conveying overall `fold'. Molikin calculates and KiNG displays spline-smoothed ribbon schematics similar to the original hand-drawn style (Richardson, 1981[link]), with black-line edges to aid depth perception (see Fig.[link]a). For interactive use they serve first as introduction to a structure, and then as context for more detailed ball, vector and dot representations.


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Illustration of combining molecular representations in kinemage format, shown in KiNG. (a) shows a ribbon schematic of the uridine vanadate–ribonuclease A complex at 1.3 Å resolution (PDB code: 1RUV ) (Ladner et al., 1997[link]), with the bound inhibitor in ball representation. (b) shows a close up of the binding pocket, with the contacting side chains (cyan) and backbone (white) of the enzyme as vectors, the uridine vanadate as balls, and all-atom contacts at the enzyme–inhibitor interface as drawn by Probe; hydrogen bonds are pillows of pale green dots, favourable van der Waals contacts are outlined by blue, green and yellow dots, and there are no steric clashes.

For kinemages, the representation style is not a global choice that applies to everything shown, but rather is a set of local options (varied across space or sequence) chosen to provide appropriate emphasis and comprehensible detail within context.

21.5.2. Uses of KiNG and kinemages

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Viewing a pre-existing kinemage file requires almost no learning process: the interface is sufficiently `transparent' that interaction is mainly with the molecule rather than with the program (Richardson & Richardson, 2002[link]). Six simple operations cover all basic functionalities: (1) drag with the mouse to rotate the displayed object; (2) click on a point to identify it; (3) turn things on or off, or animate if that option is present, with labelled buttons; (4) choose preset views from the Views pull-down menu; (5) read the author's explanations in the text window; and (6) change to the next kinemage in the file with the Kinemage selection list on the upper right corner of the GUI. At a slightly more complex level, one can recentre, zoom the scale, move the clipping planes and save a view; measure distances, angles and dihedrals or `Find' by point name (from the Edit pull-down menu); change Display menu options such as stereo or perspective; or consult the Help menu. There are keyboard shortcuts for convenience (such as `a' to animate or `c' for cross-eye versus wall-eye stereo), but they are never the only method and they are defined on the menus. Use for teaching and on the web

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Simplicity of interface, free cross-platform availability and attention to presentation issues (such as a keystroke to make labels and measures large and visible for an audience) make KiNG and kinemages especially well suited for teaching and learning about macromolecular structure or about crystallographic concepts such as handedness and symmetry. Teachers can use, adapt or create kinemage materials for class- or homework, on the computer or on paper (e.g., file HbAllo.kin on haemoglobin). Interactively evaluated exercises (such as HBondPractice.kin) or timed tests (such as 3Dlit2atst.kin) can be set up in Mage. Especially valuable is student construction of reports or projects in kinemage format using KiNG, which they find increases their structural understanding and we find lets us evaluate that understanding. Suggestions can be found in Richardson & Richardson (2002[link]) and examples, documentation and links to other kinemage web sites and materials can be found under Kinemages or under Teaching, at the kinemage web site .

KiNG has a number of options for making illustrations, including direct two-dimensional output of the current graphics window (at enhanced resolution) to JPEG, PNG or PDF image formats, or to POV-Ray for rendering. Movies can be made in KiNG of rotation, motion or changes, and either those or the static two-dimensional images can be inserted into PowerPoint-style presentations. Direct use of interactive three-dimensional graphics on the web without need for user installation [as is central to our MolProbity (Davis et al., 2007[link]; also Chapter 21.6[link] of this volume) structure-validation web service] was a major motivation for writing KiNG in Java. That same convenience can enhance web materials for courses or the presentation of structural results on a laboratory web site. Examples and simple templates in html are given on the kinemage web site under Software/KiNG. Use for research

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For general molecular-structure studies, kinemages act as a three-dimensional laboratory notebook where author and reader are the same person. These kinemages keep a visual record of the research process with selections, views, labels, measurements, superpositions etc., plus a descriptive record in the text window. On-screen editing tools allow easy deletion of unwanted parts, constructions such as ring centres or helix axes and measurements on them, drawing shortened or dotted lines, recolouring or dragging points or regions, and many other operations in addition to the molecular rebuilding described below.

Setting up an animation between conformations or between related structures is an easy and very sensitive way of seeing changes, including correlated motions. Completely new display objects and organizations can be added to kinemages, such as three-dimensional plots of related non-molecular data. Kinemages are an easy and platform-independent way of sharing ideas with collaborators, either side-by-side or at a distance with simultaneous discussion, or just by sending a kinemage with its preset views and notes. [This is easy enough that a co-laboratory function through socket connection in Mage has rarely been used, and was therefore not implemented in KiNG.] Later, the working research kinemages can be used to produce either static two-dimensional or interactive illustrations for lectures or publication.

KiNG has been useful for displaying data other than molecular structure, however, since the kinemage format is a generic plotting format, not tied to display of molecules. For instance, the MolProbity structure validation web server (Davis et al., 2007[link]; Chen et al., 2010[link]; Chapter 21.6[link] ) generates two-dimensional Ramachandran data plots and three-dimensional Cβ deviation scatter plots which can be downloaded and viewed in KiNG. In addition, support for higher-dimensional data has been added to Mage and KiNG. For high-dimensional kinemages, the user chooses on the fly which three dimensions to display at a time. Also, a parallel-coordinate view (Inselberg, 1985[link]) is available with a single keystroke, which displays the multiple axes as a series of parallel lines and each multi-dimensional point as a poly-line across those axes. With this combination of features, users can track, colour and measure the behaviour of clusters of points in many dimensions. Seven-dimensional kinemage analysis was particularly instrumental in defining full-detail RNA backbone conformers (Richardson et al., 2008[link]).

Two important tools for assessing the quality of structures are Probe and Reduce. Probe analyses molecular interactions by calculating small-probe contact dots wherever two atoms are within 0.5 Å of van der Waals contact (Word, Lovell, LaBean et al., 1999[link]), for numerical scoring or for display in KiNG (Fig.[link]b), where the three types of contacts (hydrogen bonds, favourable van der Waals contacts and unfavourable `clash' overlaps) are under separate control. All-atom contact analysis requires all hydrogen atoms; they are added by Reduce (Word, Lovell, Richardson & Richardson, 1999[link]; Davis et al., 2007[link]), which optimizes the orientations of OH, SH and NH3 groups, and possible 180° flips of Asn, Gln or His side-chain ends, considering both van der Waals clashes and hydrogen bonds analysed combinatorially in local networks. These contact-surface tools have research uses that fall into two distinct categories: one is study of the patterns and causes of particular structural features in molecules (best done on atomic resolution structures; Fig.[link]b); the other is sensitive testing, validating and adjusting of an individual molecular model, either computational or experimental (exemplified by the MolProbity validation analysis). Cystallographic rebuilding tools

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In crystallography, the most important use of all-atom contact analysis is for quickly finding, and frequently for fixing, problems with molecular geometry during fitting and refinement. All-atom contacts add independent new information to that process, since the hydrogen atoms make almost no contributions either to the electron density or to the energetic component of refinement as presently done, yet they are undeniably present and cannot significantly overlap other atoms (except in hydrogen bonds). The steric constraints implied by all-atom contacts are significantly more stringent than those based only on non-hydrogen atoms, yet they are obeyed almost perfectly by low-B regions of structures at resolutions near 1 Å, even when hydrogen atoms were not used in refinement.

At any stage of a structure determination, contact dots for the entire molecule or molecules can be calculated by Probe and examined in KiNG, or a list of the severe clashes and other outliers can be generated, for printout or as a scripted `to-do' list for rebuilding in Coot (Emsley & Cowtan, 2004[link]; Emsley et al., 2010[link]).

The most common way to do MolProbity analysis on a structure is on the web site ( ) (Davis et al., 2007; Chen et al., 2010[link]; Chapter 21.6[link] ), which guides the entire process through to both chart and kinemage analysis of the local quality of a macromolecular structure. The resulting `multi-criterion' kinemage flags all the individual outliers on the three-dimensional structure (Fig.[link]): serious clashes (≥0.4 Å overlap), poor side-chain rotamers, backbone bond-length or angle outliers, Cβ deviations, Ramachandran outliers and, for RNA, sugar-pucker and backbone conformer outliers (Richardson et al., 2008[link]). That kinemage can be viewed in KiNG online, but for rebuilding to correct the diagnosed problems a user would download the multi-criterion kinemage and the H- and flip-optimized PDB file for off-line work in KiNG. The multi-criterion kinemage shows where work is needed. However, the most powerful use of all-atom contact information is directly and interactively in the process of fitting and rebuilding. Therefore, the rebuilding tools in KiNG can call Probe on-the-fly during refitting, for display of clashes, hydrogen bonds and favourable van der Waals contacts (as well as updated rotamer quality and checks for ϕ, ψ and τ outliers) (Lovell et al., 2000[link], 2003[link]). This gives instant feedback on how user-proposed changes improve or worsen the model locally. These tools, including a side-chain mutation tool, a side-chain rotator tool, a backrub tool and an RNA rotator tool for adjusting RNA suite conformations, read in PDB files (with H atoms) and save all user modifications directly to PDB format files, for ease of use with other refinement or analysis programs. KiNG can also read in and display most common formats of electron density or difference density files, which are essential to the rebuilding process. Side chains are by default added in ideal geometry and in a choice of ideal rotamers, with user adjustment of torsion angles from there. The `backrub' motion (Davis et al., 2006[link]) is a subtle rotation of the dipeptide, shown to occur frequently in protein molecules and especially valuable in side-chain modelling because of its leverage on the Cα–Cβ orientation. Fig.[link] shows an example of the side-chain rotator, backrub and real-time contact tools in action.


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Screenshot of KiNG presenting interactive three-dimensional validation data directly in the browser, in a MolProbity session for PDB code 2C0Q (Ekstrom et al., 2006[link]), a better-than-average 2.5 Å resolution structure. On the Cα backbone (white) all validation outliers are shown: clashes as clusters of hot-pink spikes, Ramachandran outliers in green, rotamer outliers as gold side chains and Cβ deviations as magenta spheres; no bond-length or angle outliers are visible. The user can centre, zoom in and turn on all atoms to study a given problem in detail.


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Screen capture of side-chain rebuilding in KiNG using the side-chain rotator and backrub tools, with display of electron density, all-atom contacts and rotamer quality. In this example from the 1.1 Å resolution crystal structure of the calponin homology domain of β-spectrin (PDB code: 1BKR ) (Banuelos et al., 1998[link]), a threonine was fitted with its side chain flipped over by 180°. The original (in gold since it is a rotamer outlier) has large bond-angle outliers and steric clashes, and its Cβ is entirely out of density. Using the side-chain rotator tool in combination with the backrub tool allows a much better fit to the density (the thicker orange `mobile' side chain), with an excellent rotamer, ideal geometry and two hydrogen bonds (pale green dot pillows) for the Thr OH. H atoms and van der Waals dots are turned off, for clarity in two dimensions.

A number of other commonly used crystallographic tools have been modified to use Probe and Reduce as well. Historically, both O (Jones et al., 1991[link]) and XtalView (McRee, 1999[link]) included some facility for all-atom Probe analysis. Coot (Emsley & Cowtan, 2004[link]; Emsley et al., 2010[link]) can call Reduce and Probe directly, displaying hydrogens and all-atom contact dots during refitting. Also, MolProbity can write a scheme or Python input script for Coot which produces a list of labelled buttons that take the Coot user to each residue with a MolProbity-diagnosed clash, Ramachandran or rotamer outlier. Most notably, all MolProbity evaluations are available in Phenix (Adams et al., 2010[link]), with display in KiNG and interactive links for outlier corrections in Coot.

In KiNG or in these other systems, using all-atom contact display during refitting often makes conformational choices unambiguous, even when the electron density alone does not distinguish them. This criterion can locate a Met methyl, find the correct orientation for the final branch of an Asn or Gln, or a Thr, Val or Leu, improve the backbone conformation of a Gly, disentangle alternate conformations, or show which direction a ligand binds, all at a lower resolution than otherwise possible.

Side-chain rebuilding in KiNG is also very effective for analysing the suitability and probable effect of single-site mutations or redesigns (e.g. Ghaemmaghami et al., 1998[link]; Grell et al., 2000[link]; Wales et al., 2004[link]; Humphris & Kortemme, 2008[link]). That effectiveness depends on the interactive update of rotamer quality and all-atom contacts, and is enhanced by use of the backrub motion, originally in KiNG and now also in Coot and several protein design systems (Georgiev et al., 2008[link]; Smith & Kortemme, 2008[link]).

21.5.3. Making kinemages

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There are numerous methods of creating kinemages. At the most basic level, users can hand-type a set of three-dimensional coordinates into a text file, adding only a small amount of hierarchical organization, and then view the data. Both KiNG and Mage by policy are very tolerant to parsing alternatives, minor mistakes and missing objects within a kinemage; so as long as an input file is reasonably close to being correct, something will still be displayed. Naturally, though, for large amounts of data, hand-creation of kinemages is impractical, so for viewing three-dimensional (or higher-dimensional) statistical data, KiNG includes a `Data plotter' tool which will read in a delimited spreadsheet text file and automatically create a high-dimensional kinemage from those data.

For creating kinemages from PDB or mmCIF files, KiNG has several options. Molikin allows KiNG to read PDB or mmCIF files directly from the command line, with a small number of command-line flags for specifying some of the most common kinemage options, including ribbons or `lots' (which produces vectors for the main chain, side chains, hydrogen atoms and non-water heterogens, small balls for waters, and pointIDs that include B factors). In the KiNG GUI, the `Import' tool in the File menu provides access to Molikin features as well. For quick browsing of structure files, drag-n-drop or the `Import' [\rightarrow] `To quick kin' menu allows users to quickly import and construct kinemages, similar to the command-line options. For more direct control of the options shown in the kinemage, the `Import'[\rightarrow] `Molecules' option brings up the Molikin GUI, which allows users to choose precisely what is shown. Users can specify what models, chains, residues, side-chain types and atoms to show, in a variety of representation types.

The many modes and options make KiNG and kinemages useful for a myriad of purposes, in addition to simple structure browsing. Making a kinemage for research, teaching, publication or distribution is an iterative and deliberate process. While the built-in kinemages provide a good starting point, finding the optimal colours, views and objects to display can be time consuming. KiNG includes a number of built-in on-screen editing tools which make this task easier.

On-screen editing of a kinemage in KiNG usually begins with setting up a few good views: rotate, pick centre, zoom and clip to optimize each one, and save it with `Save current view' on the Views pull-down menu; it then shows up on the same menu with the given label. For editing of object properties in the kinemage, the `Edit/draw/delete' tool in the Tools menu brings up a separate toolbox containing a variety of editing tools. These options, once selected, utilize mouse clicks in the graphics window to determine the objects that are modified, often with additional options that only appear when the particular option is selected. For example, the `Paint points' option brings up a colour selection drop-down list, as well as a selection-type list. By default, the `Paint points' option allows users to paint all the points that appear within a circle, which is drawn in the GUI window to allow users to see precisely what they are painting before they actually paint. A variety of drawing and deletion tools are also included in the `Edit/draw/delete' tool. `Edit text' (Edit menu) brings up the text window, which allows explanations to be included with the kinemage. Several superposition or docking tools, at varying levels of complexity, allow the user to move one molecule or group onto another similar one, for comparison or animation.

KiNG includes a built-in `Internal palette' kinemage (in the Help menu) which shows the kinemage palette of colours with their names and gives some guidelines for choosing effective colours. The palette includes emphasis colours (green, yellow, hot pink), low-emphasis colours (purple, brown), pastels and a large variety of mid-tones (such as gold, peach, lilac), with a depth-cueing formula that ensures smooth change and maintenance of the perceptual colour value at all depths. In KiNG, if the built-in palette does not suffice, the user can create custom HSV (hue, saturation, value) colours. The default black background works best on the computer screen or for lecture-hall projection, but a white-background mode with a modified palette is available when needed for printed images (e.g. Fig.[link]a) or for projection in high-ambient-light conditions.

Context is important for a kinemage (usually at least overall Cα's) but often it is helpful to delete features that are not directly relevant to the current interest (e.g. Fig.[link]); therefore KiNG includes a versatile set of deletion tools (punch, prune, auger, spherical crop). This selection process is like the simplification and emphasis needed for a good two-dimensional illustration, but in this case it applies to the fully interactive three-dimensional form. For a kinemage, however, it is both possible and advantageous to include some additional details for further exploration, controlled by a button which can start out turned off.

At any stage of kinemage editing, a text editor can be used to look at the plain ASCII kinemage file, with its text, its views, and the hierarchy of group, subgroup and list display objects in human-readable and clearly identified forms. Lists (e.g. @vectorlist {name}) can be of vectors, dots, labels, words, balls, spheres, triangles or ribbons. Any part of the file can be edited, using its existing format as a guide or looking at another kinemage file that provides a desired template. The formal rules are described in format-kinemage.pdf, linked from Software/KiNG on the kinemage web site. One of the few operations that currently must be edited outside rather than inside KiNG is moving points between different lists (for instance, setting up a new list of just active-site side chains in a different colour and controlled by their own button). After editing a file outside KiNG, the kinemage should be saved without formatting, as a plain text file.

All in all, making a simple kinemage is trivial, but making really good ones for use by others is much like making a good web page. There are tools that make the individual steps easy, but one needs to exercise restraint to keep it simple enough to be both fast and comprehensible, patience to keep looking at the result and modifying it where needed, and judgment about both content and aesthetics.

21.5.4. Software notes

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Mage and Prekin were written in C by David C. Richardson. KiNG and Molikin were written in Java by Ian W. Davis and Vincent B. Chen with contributions by Daniel A. Keedy, and are compatible with any Java 1.5+ equipped system. Probe (in C) and Reduce (in C++) were written by J. Michael Word and updated by Andrew Leaver-Fay and other collaborators in Jack Snoeyink's group. The latest versions of all the software, compiled for multiple platforms, plus source and documentation files are available free from the Software section of the kinemage web site ( ). The KiNG documentation is included in its software download package, and is also available there separately as file king-manual.pdf.


Kinemage development is supported by NIH grants GM073919 and GM 73930, and historically by the Protein Society and by GM15000.


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