Computer graphics three-dimensional viewing

Crystal structures are best viewed as three-dimensional computer images that can be rotated and viewed from any direction. Crystal structures can be displayed, and downloadable programs for graphical presentation of crystal structures can be found at the EPSRC s Chemical Database Service at Daresbury. This can be accessed at http //cds.dl.ac.uk/ cds. See also ... 

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. 

Figure 5-32 (A) A three-dimensional computer graphics model proposed by Brimacombe et a/.3 11 for the single chain of E. coli 16S ribosomal RNA. The helices are depicted as cylinders, which are all connected. The small dark squares denote the positions of artificially formed RNA-protein crosslinks, marked with the appropriate protein number. For proteins exhibiting more than one crosslink site (e.g., SI7), the sites are denoted A or B, in each case A being the site nearer to the 5 terminus of the 16S RNA. (B) Stereoscopic view of tentative atomic model of 16S RNA in the 30S ribosomal subunit. The viewing direction is different from that in (A). From Mueller and Brimacombe.342 Courtesy of Richard Brimacombe.

Molecular Manipulation and Superimposition. To facilitate molecular comparisons, a variety of computer graphic techniques are available for three-dimensional manipulation and display of the stored structures in the library file (12,13). In our laboratory lateral stereo pair views of either single line or ball and stick models are displayed on a Tektronix 4014 graphics terminal linked to a Univac 1100/42 computer. 

Three-dimensional flow analysis is much more demanding computationally but is necessary to capture the full detailed characteristics of FSW. Added detail in 3-D includes complete tools with shoulder and probe tool tilt probe features such as threads, helical flutes, and taper in diameter and flow below the pin— important for avoiding root defects. The output of 3-D CFD is essentially the same as in 2-D, but flow paths are more difficult to present graphically, requiring 2-D slices or isometric views. Figure... 

The variety of information conveyed by the different views in Figure 5.5 illustrates the need to visualize three-dimensional biopolymer structure data in unique ways that are not common to other three-dimensional graphics applications. This requirement often precludes the effective use of software from the macroscopic world, such as computer-aided design (CAD) or virtual reality modeling language (VRML) packages. 

In such computer graphics, the three-dimensional effect is arranged by making fainter those parts of the image that should be distant from the viewer. Alternatively a pair of images can be commanded, for viewing with stereospectacles. 

Non-pharmaceutical applications tend to be aimed at accurate stmcture prediction together with properties such as electrostatic potential maps and surface hydrophobic-ity. One consequence of this is a desire for easily understood graphical representations of both the molecules and the calculated properties. An example of this can be seen in Figure 1, which shows a geometry-optimized computed structure of the potassium complex of the macrocycle 18-crown-6. A representation of the complex s electrostatic potential on a van der Waals surface is overlaid on top of this. A cutaway view is depicted so that the connectivity and identity of each atom can be seen clearly and correlated with the local electrostatics. In the example, blue represents an electropositive region, red is electronegative, and green is neutral. As the complex can be rotated on a computer screen, the structure can be considered to be pseudo three dimensional. The representation of physical properties adds a further dimension to this. Snapshots of molecules and associated properties, perhaps modeled at precise intervals... 

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