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International
Tables for Crystallography Volume B Reciprocal space Edited by U. Shmueli © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. B. ch. 3.3, pp. 380-381
Section 3.3.3.1. Systems for the display and modification of retrieved data
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One of the earliest systems designed for information retrieval and display was that described by Meyer (1970![[link]](/graphics/greenarr.gif)
, 1971) which used television raster technology and enabled the contents of the Brookhaven Protein Data Bank (Meyer, 1974; Bernstein et al., 1977) to be studied visually by remote users. It also enabled a rigid two-ring molecule to be solved from packing considerations alone (Hass et al., 1975; Willoughby et al., 1974). Frames for display were written digitally on a disk and the display rate was synchronized to the disk rotation. With the reduction in the cost of core storage, contemporary systems use large frame buffer memories thus avoiding synchronization problems and permitting much richer detail than was possible in 1970. A majority of the systems in this section use raster techniques which preclude real-time rotation except for relatively simple drawings, though GRAMPS is an exception (O'Donnell & Olson, 1981; Olson, 1982) (Section 3.3.3.1.4).
This program, the Oak Ridge Thermal Ellipsoid Program, due to Johnson (1970, 1976) was developed originally for the preparation of line drawings on paper though versions have since been developed to suit raster devices with interactive capability.
The program draws molecules in correct perspective with each atom represented by an ellipsoid which is the equi-probability surface for the atomic centre, as determined by anisotropic temperature factor refinement, the principal axes of which are displayed. Bonds are represented by cylindrical rods connecting the atoms which in the drawing are tapered by the perspective.
In line-drawing versions the problem of hidden-line suppression is solved analytically, whereas the later versions for raster devices draw the furthest elements of the picture first and either overwrite these with nearer features of the scene if area painting is being done or use the nearer features as erase templates if line drawings are being made.
R. J. Feldmann and co-workers (Feldmann, 1983) at the National Institutes of Health, Bethesda, Maryland, USA, were among the first to develop a suite of programs to display molecular structure using colour raster-graphics techniques. Their system draws with coloured shaded spheres, usually with one sphere to represent each atom, but alternatively the spheres may represent larger moieties like amino acids or whole proteins if lower-resolution representations are required. These workers have made very effective use of colour. Conventionally, oxygens have been modelled in red, but this system allows charged oxygens to be red and uncharged ones to be pink, with a similar treatment in blue for charged and uncharged nitrogens. By such means they have been able to give immediacy to the hydrophobic and electrostatic properties of molecular surfaces, and have used these characteristics effectively in studies of the binding possibilities of benzamidine derivatives to trypsin (Feldmann et al., 1978).
The algorithm developed by Porter (1978) for shading spheres to be darkened near their peripheries also computes the proper appearance of the line of intersection of two spheres wherever interpenetration occurs, in contrast to some simpler systems which draw a complete disc for whichever sphere is forward of the other. Provided that all opaque spheres are drawn first, the system is also capable of representing transparent spheres by darkening the colour of the existing background inside, and especially near the edge of, discs representing transparent foreground spheres.
Other systems that produce space-filling pictures of a similar general character have been produced by Motherwell (1978), by Sundaram & Radhakrishnan (1979) and by Lesk (next section).
The complexity of macromolecules is a formidable obstacle to perceiving the basic features of their construction and the stylized drawings produced by this software following the artistry of Richardson (1977, 1981, 1985) enables the internal organization of such molecules to be appreciated readily. The software is capable of mixing several styles of representation, among them the Richardson style of cylinders for α-helices, arrows for β-strands and ribbons for less-organized regions, or the creased-ribbon technique for the whole chain, or a ball-and-stick representation of atoms and bonds, or space-filling spheres. All these styles are available simultaneously in a single picture with depth cueing, colour and shading, and hidden-feature suppression as appropriate. It is also able to show a stylized drawing of a complete molecule together with a magnified part of it in a more detailed style. See Lesk & Hardman (1982, 1985).
This system, due to O'Donnell & Olson (O'Donnell & Olson, 1981; Olson, 1982) provides a high-level graphics language and its associated interpretive software. It provides a general means of defining objects, drawable by line drawings, in such a way that these may be logically connected in groups or trees using a simple command language. Such a system may, for example, define a subunit protein of an icosahedral virus and define icosahedral symmetry, in such a way that modification of one subunit is expressed simultaneously in all subunits whilst preserving the symmetry, and simultaneously allowing the entire virus particle to be rotated. Such logical and functional relationships are established by the user through the medium of the GRAMPS language at run time, and a great diversity of such relationships may be created. The system is thus not limited to any particular type of structure, such as linear polymers, and has proved extremely effective as a means of providing animation for the production of cine film depicting viral and other structures. GRAMPS runs on all Silicon Graphics workstations under IRIX 4.0 or above.
Takenaka & Sasada (1980) have described a system for the manipulation and display of molecular structures, including packing environments in the crystal, using a minicomputer loosely coupled to a mainframe. Their system is also capable of model building by the addition of groups of one or more atoms with a facility for monitoring interaction distances while doing so.
This system, due to Langridge and co-workers (Gallo et al., 1983; Ferrin et al., 1984) is primarily concerned with the display of existing structures rather than with the establishment of new ones, but it may modify such structures by bond rotations under manual control. It is of particular value in the study of molecular interactions since two or more molecules may be manipulated simultaneously and independently. Visual docking of molecules is greatly facilitated by the display of van der Waals surfaces, which may be computed in real time so that the turning of a bond in the underlying structure does not tear the surface (Bash et al., 1983).
This system, originally due to Dayringer et al. (1986), has a functionality similar to MIDAS. It has been replaced by Insight II (current version 2.3.5). It appears to be well suited to the study of intermolecular relationships in docking and in structural comparisons, and it is able to make modifications to structures. Objects for display may be molecular or non-molecular, the former having an atomic substructure and the latter consisting of a vector list which may not be subdivided into referrable components. Map fitting with the current version has been reported.
PLUTO was developed by Motherwell (1978) at the Cambridge Crystallographic Data Centre (CCDC) for the display of molecular structures and crystal-packing diagrams, including an option for space-filling model style with shadowing. The emphasis was on a free format command and data structure, and the ability to produce ball-and-spoke drawings with line shadowing suitable for reproduction in journal publication. Many variant versions have been produced, with essentially the 1978 functionality, its popularity deriving from its ease of use and the provision of default options for establishing connectivity using standard bonding radii. It was distributed as part of the CCDC software associated with the Cambridge Structural Database, with an interface for reading entries from the database.
In 1993 Motherwell and others at the CCDC added an interactive menu and introduced colour and PostScript output. New features were introduced to allow interactive examination of intermolecular contacts, particularly hydrogen-bonded networks, and sections through packing diagrams (Cambridge Structural Database, 1994).
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