Computer graphic

Computer graphics has changed the way in which chemical structures are presented and perceived. The facile conversion of macromolecular sequences into three-dimensional structures that can be displayed and manipulated on the computer screen have greatly improved the biochemist s understanding of biomolecular structures. Tools for graphical visualization and manipulation of biomolecular structures are described. 

Molecular graphics (Henkel and Clarke, 1985) refers to a technique for the visualization and manipulation of molecules on a graphical display device. The technique provides an exciting opportunity to augment the traditional description of chemical structures by allowing the manipulation and observation in real time and in three dimensions, of both molecular structures and many of their calculated properties. Recent advances in this area allow visualization of even intimate mechanisms of chemical reactions by graphical representation of the distribution and redistribution of electron density in atoms and molecules along the reaction pathway. 

Screen the atoms by distance. This is the most general approach. For every pair of atoms in the structure, the distance between them is calculated. If the distance is less than the sum of the van der Waals radii of the two atoms, a bond between them is assumed. For proteins or nucleic acids, this approach can be specialized by checking only atoms in the same residue/nucleotide, plus the atoms in the peptide/nucleotide bonds between successive residues/ nucleotides. 

Create an explicit list of bonded pairs. For protein containing only standard amino acids and common ligands, this can be done once and for all. For each residue type, one can make a list of pairs of atom names, each pair corresponding to a bond. Then in drawing a picture of a protein for each residue, one can search the coordinates of each pair of atoms in the list of bonds and add the appropriate line segment to the drawing. Similar considerations apply to nucleic acids. In pdb files, explicit connectivity lists are provided. 

A ball-and-stick drawing is a simple skeletal model, in which the representation of the bond is generalized to a cylinder, and a disc is added at the position of each atom. Additional information may thereby be displayed in that different atom types may be distinguished by size and shading, and bonds of different appearance may be drawn. To create the line segments corresponding to a pure skeletal model, one needs only copy the coordinates of each pair of bonded atoms as the line segment end-points. To create ball-and-stick pictures, one must  

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Marching Cubes A High Resolution 3D Surface Construction Algorithm, Computer Graphics 21(4), pp 163-169 (1987)... 

One of the earliest NDT applications for laser-based profilometry systems was for the inspection of marine boiler tubes. Under funding from the U.S. Navy", several systems were developed that were capable of rapidly and accurately mapping the inside surface of 25 mm and 50 mm diameter boiler tubing. Features such as internal pitting and corrosion can be located and quantitatively assessed using computer-graphic analysis. The system employs an... 

The era of the Evans and Sutherland computer systems vanished in the first half of the 1980s, when powerful and more economical workstations were introduced. In spite of advances in computer graphics and in CPU power, these workstations dominate the everyday life of molecular modeling even today. 

C. Levinthal, CD. Barrv et al.. Computer Graphics in Macromolecular Chemistry. Emerging Concepts in Computer Graphics, D. Secrest, J. Kievergelt (Eds.). W.A. Benjamin, Kew York, pp. 213-253. 

D. Keim, Information Visualization and Visual Data Mining, IEEE Trans. Visualization and Computer Graphics, 2002, 8,100-107. 

Computer graphics has had a dramatic impact upon molecular modelling. It should always be remembered, however, that there is much more to molecular modelling than computer graphics. It is the interaction between molecular graphics and the imderlying theoretical methods that has enhanced the accessibility of molecular modelling methods and assisted the analysis and interpretation of such calculations. 

Molecules are most commonly represented on a computer graphics screen using stick or space-filling representations, which are analogous to the Dreiding and Corey-PauUng-Koltun (CPK) mechanical models. Sophisticated variations on these two basic types have... 

This German stamp depicts a molecular model of urea and was issued in 1982 to commemorate the bun dredth anniversary of Woh ler s death The computer graphic that opened this in troductory chapter is also a model of urea... 

Among the current (ca 1997) selection of software systems which together help to exemplify the promise of computer graphics. Advanced Visualization Systems (AVS), stands out as one of the more extensible and practical of them to use. The premise behind development of the system was to provide modelers with a toolkit of modules having sophisticated intrinsics that would enable even casual programmers to link together multiple simple functionahties into a complex constmct with which to accomplish exactly the types of visualization and manipulations that their work required. Researchers... 

Thermodynamic properties such as heats of reaction and heats of formation can be computed mote rehably by ab initio theory than by semiempirical MO methods (55). However, the Hterature of the method appropriate to the study should be carefully checked before a technique is selected. Finally, the role of computer graphics in evaluating quantum mechanical properties should not be overlooked. As seen in Figures 2—6, significant information can be conveyed with stick models or various surfaces with charge properties mapped onto them. Additionally, information about orbitals, such as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), which ate important sites of reactivity in electrophilic and nucleophilic reactions, can be plotted readily. Figure 7 shows representations of the HOMO and LUMO, respectively, for the antiulcer dmg Zantac. 

The graphics capabiUties of the CAD/CAM environment offer a number of opportunities for data manipulation, pattern recognition, and image creation. The direct appHcation of computer graphics to the automation of graphic solution techniques, such as a McCabe-Thiele binary distillation method, or to the preparation of data plots are obvious examples. Graphic simulation has been appHed to the optimisation of chemical process systems as a technique for energy analysis (84). 

The second area, the implementation of a modem process monitoring and control system, is the most dramatic current appHcation of CAD/CAM technology to the chemical process industry. The state of the art is the use of computer graphics to display the process flow diagram for sections of the process, current operating conditions, and controUer-set points. The process operator can interact directly with the control algorithms through the... 

In the early days of protein crystallography the determination of a protein structure was laborious and time consuming. The diffracted beams were obtained from weak x-ray sources and recorded on films that had to be manually scanned and measured. The available computers were far from adequate for the problem, with a computing power roughly equal to present-day pocket calculators. Computer graphics were not available, and models of the protein had to be built manually from pieces of steel rod. To determine the... 

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