Computer graphics system

The inactive (Ag ,Cu )- and (Ag, Co )-derivatives of BESOD have also been prepared. The EPR spectra of (Ag, Cu")- and (Cu ,Cu")-BESOD were very similar like the visible absorption spectra of (Ag ,Co )- and (Cu, Co")-BESOD. From model fitting to the electron-density map at 0.3-nra resolution by an interactive computer graphics system is was concluded that the bridging His-61 is slightly out of the plane of Cu and its three other histidine ligands . ... 

In the fifth step of an X-ray structure determination the electron density map is calculated using the intensities and phase information. This map can be thought of as a true three-dimensional image of the molecule revealed by the X-ray microscope. It is usually displayed as a stereoscopic view on a computer graphics system (Fig. 3-22). It is also often prepared in the form of a series of transparencies mounted on plastic sheets. Each sheet represents a layer, perhaps 0.1 ran thick, with contour lines representing different levels of electron density. 

The primary reason for undertaking this whole exercise was to evaluate vector processors for use in molecular mechanics calculations and as an adjunct to chemical computer graphics systems ... 

The challenge of how to represent the receptor that is deduced from these results is greatly helped by the use of computer graphics systems. For example, it was used to show the complementarity of molecular surfaces in the crystal structure of the complex between an antibody and lysozyme. The contact area is about 20x20 A. Side chains from one, such as Gin 121 of lysozyme, fit in a depression on the surface of the other protein. Interactions with small antigens, such as phosphorylcholine, have also demonstrated the specificity of the interactions between antibodies and antigens. 

Figure 1.15 contains a composite of several planes from an electron density map of a protein. By continually increasing the final coordinate by Az, the electron density map is built up from the series of two-dimensional planes. The individual sections are plotted on some transparent material after contour lines have been drawn around areas within certain density limits. The result is a topological map of the electron density presented on sequential planes of the unit cell as a series of contour levels. When the individual planes are stacked in consecutive order, a three-dimensional electron density image is created. This is discussed in more detail in Chapter 10. Currently, however, the presentation of the electron density is considerably more sophisticated. We use automated computer graphics systems to present detailed density images in three-dimensional space as in Figure 1.16. 

Prior to the advent of computer graphics systems, electron density maps were, in actuality, produced as described above. Each section was printed on paper as a field of numbers, each... 

FIGURE 10.7 Computer graphics systems now allow rapid adjustment of molecular models to fit the electron density generated as three-dimensional mesh images. Two segments of polypeptide chain... 

The availability of high-performance computer graphics systems has made it possible for contoured electron-densitv maps to be displayed on a graphics screen (67). The maps so calculated may have peaks that look like chicken wire. A stick model of the-molecular fragment can be fit, again by computer graphics technology, into this electron density. The whole map with the molecule posi-... 

It was realized some time ago that Richards method of optical comparison could be advantageously implemented in an interactive computer graphics system [30, 31]. The computer has access to data representing the electron density map and is capable of constructing a representation of the molecular model from a library describing the amino acid residues. The electron density map and the model are displayed on a cathode ray tube in a suitable form giving the illusion of three dimensions, and the operator instructs the computer to modify the model. The operator s commands tend to improve the perceived fit between map and model one of the functions of the computer is to maintain the model s bonded geometry. 

Blake, J. E., Farmer, N. A., and Haines, R. C., "An Interactive Computer Graphics System for Processing Chemical Structure Diagrams", J. Chem. Inf. Comnut. Sci.. (1977),... 

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