Molecular graphic

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. 

1 Line drawings skeletal and ball-and-stick models. Traditionally, drawings of small molecules have represented either (a) each atom by a sphere or (b) each 

Each atom is shown to represent complete chemical detail of molecules in shaded-sphere pictures. This category includes three basic types of pictures  

Line drawings Each atom is represented as a disc. The picture is a limit of the ball-and-stick drawings as the radius of each atomic baU is made in proportional to the van der Waals radius. 

Color raster devices A raster device can map an array stored in memory on to the screen so that the value of each element of the array controls the appearance of the corresponding point on the screen. It is possible to draw each atom as a shaded sphere, or to simulate the appearance of the Corey-Pauling-Koltun (CPK) physical models to maintain most of the famihar color scheme (i.e. C = black, N = blue, O = red, P = Green, and S = yellow). In such representation, atoms are usually opaque, so that only the front layer of atoms is visible. However, clipping with an inner plane or rotation can show the packing in the molecular interior. 

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 underlying 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-Pauhng-Koltun (CPK) mechanical models. Sophisticated variations on these two basic types have 

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New ways to represent structure data became available through molecular modeling by computer-based methods. The birth of interactive computer representation of molecular graphics was in the 196Ds. The first dynamic molecular pictures of small molecules were generated in 1964 by Lcvinthal in the Mathematics and Computation (MAC) project at the Electronic Systems Laboratoiy of the Massachusetts... 

The first pure molecular graphics system followed after a few years. It was built in 1970 by Langridgc at Princeton University 195], The system was based on the Picture System 2 of Evans and Sutherland and could also display bonds and colored atoms. 

Figure 2-123. The most coinmon molecular graphics representations of phenylalanine a) wire frame b) capped sticks c) balls and sticks d) space-filling.

Figure 2-124. The most common molecular graphic representations of biological molecules (lysozyme) a) balls and sticks b) backbone c) cartoon (including the cylinder, ribbon, and tube model) and of inorganic molecules (YBajCujO , d) polyhedral (left) and the same molecule with balls and sticks (right),...

Molecular graphics representation ofihe paths generated by 32 hard spherical particles in the solid (left) and ht) phase. (Reproduced from Alder B J and T E Wainwright 1959. Studies in Molecular Dynamics. I. Method. Journal of Chemical Physics. 31. 459-466.)... 

C and T E Klein 1986. Molecular Graphics and QSAR in the Study of Enzyme-Ligand ractions. On the Definition of Bioreceptors. A ccounts of Chemical Research 19 392-400,... 

Snarey M, N K Terrett, P Willett and D J Wilton 1997. Comparison of Algorithms for Dissimilaritj based Compound Selection. Journal of Molecular Graphics and Modelling 15 372-385. 

The book divides itself quite naturally into two parts The first six ehapters are on general seientifie eomputing applieations and the last seven ehapters are devoted to moleeular orbital ealculations, moleeular meehanies, and molecular graphics. The reader who wishes only a tool box of eornputational methods will find it in the first part. Those skilled in numerieal methods might read only the second. The book is intended, however, as an entity, with many eonneetions between the two parts, showing how ehapters on moleeular orbital theory depend on eornputational teehniques developed earlier. 

B. R. Brooks and co-wotkets. Molecular Graphics and Simulation Laboratory, NIH, Bethesda, Md., private communication, Aug. 1991. 

Lederer, F., et al. Improvement of the 2.5 A resolution model of cytochrome bsea by redetermining the primary stmcture and using molecular graphics. 

The reaction flow-charts of Part Two, and indeed all chemical formulae which appear in this book, were generated by computer. The program used for these drawings was ChemDraw adapted for the Macintosh personal computer by Mr. Stewart Rubenstein of these Laboratories from the molecular graphics computer program developed by our group at Harvard in the 1960 s (E. J. Corey and W. T. Wipke, Science, 1969,166, 178-192) and subsequently refined. 

In Fig. 1 lb are depicted sets of molecular graphics images of flattened toroidal structures which are... 

Fig. 11. The sealed lip of a PCNT heat treated at 2800°C with a toroidal structure (T) and, (b) molecular graphics images of archetypal flattened toroidal model at different orientations and the corresponding simulated TEM images.

Fig. 3. Molecular graphics images of an archetypal flattened toroidal model of a nanotube with n = 5 and m = 4al three different orientations in a plane perpendicular to the paper. Note the points on the rim where...

FIGURE 17.30 (a) A ribbon diagram and (b) a molecular graphic showing two slightly different views of the structure of troponin C. Note the long a-helical domain connecting the N-terminal and C-terminal lobes of the molecule. 

FIGURE 21.24 Molecular graphic images (a) side view and (b) top view of the Fj-ATP synthase showing the individnal component peptides. The 7-snbnnit is the pink strnctnre visible in the center of view (b). 

We have seen here that these simple methods which only rely upon the optimal use of molecular graphics tools can address highly specific receptor-ligand interactions. 

DeLano WL (2002) The PyMOL molecular graphics system, DeLano Scientific, Palo Alto, CA, USA... 

Figure 1. Molecular graphics (ANIMOL) views of the dihydro-xybenzenes. The gray atoms are carbons, the dark atoms are oxygens and the light atoms are hydrogens. a) ortho b) meta c) para.

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