Section 25.2.8.1. Introduction to aims and concepts

MAGE and the kinemages it displays (Richardson & Richardson, 1992, 1994) provide molecular graphics, organized in an unusual way, that are of interest to crystallographers for uses that range from interactive illustrations for teaching to a representation of all-atom van der Waals contacts, calculated by PROBE (Word, Lovell, LaBean et al., 1999), to help guide model-to-map fitting.

A kinemage (`kinetic image') is an authored interactive 3D 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 3D plotting information chosen by its author or user. MAGE is a pure graphics display program designed to show and edit kinemages, while PREKIN constructs molecular kinemages from PDB (Protein Data Bank; Research Collaboratory for Structural Bioinformatics, 2000) files. The latest versions (currently 5.7) of MAGE and PREKIN are available free for Macintosh, PC, Linux, or UNIX from the kinemage web site (Richardson Laboratory, 2000). The programs operate very nearly equivalently on different platforms and, by policy, later versions of MAGE can display all older kinemages. A Java `Magelet' can show small kinemages directly in suitable web browsers, with their first-level interactive capabilities of rotation, identification, measurement, views and animation.

MAGE has no internal knowledge of molecular structure. A collaboration between the author and the authoring program (e.g. PREKIN) 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 3D relationships. Overall, kinemages demand less work and less expertise from the reader or viewer than do traditional graphics programs, but that ease of use depends on the effort involved in thoughtful authoring choices, aided by the extensive on-screen editing capabilities described below.

MAGE has been designed to optimize visual comprehension: the understanding and communication of specific 3D relationships inside complex molecules. Display speed has been given priority, to ensure good depth perception from smooth real-time rotation. The interface is extremely simple and transparent, and the colour palette is tuned for 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. Text and caption windows explain 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 2D 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, simple and informative rather than either showy or traditional, as illustrated by the following examples and their rationales. Mouse-controlled rotation in MAGE 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 using half-bond colouring which tends to chop up the image, PREKIN provides separate colours and button controls for main chain versus side chains, and it can prepare a partial `ball-and-stick' representation with colour-coded balls on non-carbon, non-hydrogen atoms (see Fig. 25.2.8.1). Hydrogen atoms are crucial for some research uses, but to minimize the clutter from twice as many atoms, PREKIN sets up their display under button control; in addition, a `lens' parameter can be specified for the list, allowing display only within a radius of the last picked centre point. For effective perception of conformational change, while avoiding either the confusion of overlays or the potential misrepresentation of computed interpolation, MAGE features simple animation switching between known conformations. Very importantly, since molecular information resides mostly in chemical bonds and spatial proximity, kinemages emphasize fully 3D representations, such as vectors, dots, or `ball and stick's, rather than surface graphics that obscure internal structure. A space-filling representation (the `spherelist') is available, but it is suggested that it is 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. Nothing matches a well rendered ribbon for conveying overall `fold'; PREKIN calculates and MAGE displays simple ribbon schematics (see Fig. 25.2.8.2) which can be rendered by Raster3D (Merritt, 2000) or POV-Ray (POV-Ray Team, 2000) for a static 2D illustration, but for interactive use they serve mainly as introduction and context for more detailed `ball-and-stick', vector and dot representations.

Figure 25.2.8.1| top | pdf | A typical macromolecular kinemage, combining details with context in the interactive display, for a glucocorticoid receptor–DNA complex (PDB file 1GLU). This view looks down the recognition helix, with one of the 4-Cys Zn sites on the right. Two sequence-specific binding interactions are shown with partial `ball-and-stick' representation: the Arg–guanine double hydrogen bond and the hydrophobic packing of Val to thymine methyl. DNA bases are in gold and protein side chains in pink, while atom balls are colour-coded as N blue, O red, C green, S yellow and Zn grey. Context is provided by the Cα backbone for the protein and a virtual backbone for the DNA (using P, C4′ and C1′), with lines symbolizing the rest of the base pairs.

Figure 25.2.8.2| top | pdf | A ribbon-schematic kinemage of ribonuclease A (PDB file 7RSA), with β strands as sea-green arrows, helices as gold spirals and loops as single splines in white (produced from a built-in script in PREKIN and rotatable in MAGE). Ribbons have edges to give them some thickness and are shaded rather than depth-cued; Cα positions for the active-site His side chains were moved slightly to lie in the ribbon plane.

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.