Computer programs Ball Stick

Figure 2. Views of some carcinogenic molecules showing K- and bay- regions. Views are given of BP (I), DMBA (II), 3-methyl-cholanthrene (III), ll-methyl-15,16-dihydrocyclopenta[a]phen-anthracene (VII) and 5-methylchrysene (VIII). These and all subsequent ball-and-stick diagrams were drawn using the computer program VIEW (141).

I wish to thank Andrew B. Carrell, who assisted with many of the calculations and figure preparations necessary for the production of this chapter. I also thank H. L. Carrell, G. D. Markham, A. S. Mildvan, and E. K. Patterson for many helpful discussions. Ball-and-stick drawings were drawn with the computer program VIEW (Carrell, 1976). Use of the Cambridge Structural Database (Allen etal., 1979) and the Protein Data Bank (Bernstein el al., 1977) is acknowledged. This work was supported by National Institutes of Health grants GM 44360, CA 10925, and CA 06927 and by an appropriation from the Commonwealth of Pennsylvania. 

Figure 20-2 Representation of the desulforedoxin dimer (A) Ribbon diagram calculated with computer programs MOLSCRIPT [82] and RASTER-3D [83]. Both iron atoms and coordinating cysteines are represented in stick-and-ball mode. (B) Viewed along the non-crystallographic two-fold axis (view perpendicular to (A)).

Another approach to the introduction of molecular mechanics into the curriculum is described in a paper by Biali. The stereochemical exercise discussed here involves the calculation of relative energies of the six possible isomers/conformers of [3.3]metacyclophanes. Even in this case, however, the input coordinates are calculated laboriously from framework molecular models and the calculations performed on a VAX 11/750 computer. An important development, however, described in this paper, is the transfer of coordinate data files to a visualization program (Ball and Stick) on the Macintosh microcomputer for simple visualization. This is one of the first descriptions of the use of file transfer on simple microcomputer programs to produce visually attractive structural representations. 

Fortunately, the need to amass coordinates of atoms in reported crystal structures has already been appreciated, and efficient computer-based databases are now available. As a result, it is not necessary to type large sets of numbers into a computer, because they can be derived in computer-ready form from a database. In addition to the ready access to atomic coordinate tables, there are many excellent computer-graphics, geometrical, and statistical programs available for comparisons of structures. In practice, however, it is additionally advantageous to build molecular models either of the ball-and-stick variety or the space-filling variety, if chemical or biochemical insight is required from a comparison of molecular structures observed by crystal structure analyses. 

Draw the sawhorse diagram of syn- and anti-2,2,5,5-tetramethylhexane sighting down the C3-C4 bond. If you have access to a computer modehng program, convert this structure to its 3D structure (both a ball and a stick drawing and a space-filling model). Comment on the steric hindrence found in each rotamer. 

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