Computer graphics programs

Dittmar, Paul G. and Joseph Mockus, "An Algorithmic Computer Graphics Program for Generating Chemical Structure Diagrams," submitted to Journal of Chemical Information and Computer Science. 

Describe the color of the reaction mixtures just before loading onto the column. Make observations about the column development process. Analyze the absorbance data by preparing an elution curve. On graph paper or a computer graphics program, plot 520 (j-axis) versus fraction number. How many peaks were obtained What are the components represented by each peak Use this elution curve to explain the action of a gel filtration column. Explain the fact that phenol red is present in both colored fractions. In what fraction is the bovine serum albumin ... 

The proposed functions for the Rhodonines are all plotted to the same reference excitation level. The comers of the ultraviolet spectrum are truncated slightly because of the computer graphics program to implement the... 

J. Erlebacher and H. L. Carrell, ICRVIEW. Computer graphics program , from The Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, 1992. 

The preparation of this article was aided by grants from the Department of Energy, the National Science Foundation, and the Alfred P. Sloan Foundation. Molecular orientations of some of the figures were developed using the computer graphics program of Professor Warren J. Hehre. 

Hummel, W., Hauser, J., and Biirgi, H.-B. PEANUT computer graphics program to represent atomic displacement parameters. J. Molec. Graphics 8, 214-220 (1990). 

K. Brandenburg, DIAMOND, 1998, computer graphics program, Germany. 

Even the most basic computer graphics program provides some standard facilities for the manipulation of models, including the abihty to translate, rotate and zoom the model towards and away from the viewer. More sophisticated packages can provide the scientist with quantitative feedback on the effect of altering the structure. For example, as a bond is rotated then the energy of each structure could be calculated and displayed interactively. 

Enderle, G.j Kansy, K,> Pfaff, G. Computer Graphics Programming. GKS - the Graphic Standard Springer Berlin, 1984... 

Schematic plans are often difficult to fully interpret, and so three-dimensional (3D) sketches are quite useful in judging the success of the plan in meeting the objectives set out in the program. Figure 38.16 shows a 3D sketch drawn with a computer graphics program that very clearly demonstrates the various elements of the plan. Physical models also can be employed to illustrate elements of the schematic plan, but their usefiilness is somewhat limited by the comparative lack of detail available.

If the studied crystals were perfectly ordered, then all the atoms would scatter in phase and the electron density map would have peaks at each of the atomic positions. However, in electron density maps of most protein atoms are not resolved from each another we need a model to be fitted to the electron density. Fitting models to density requires the use of computer graphics programs such as COOT (Emsley and Cowtan 2004) and as a result the electron density map is interpreted in terms of a set of atoms. In most cases the protein backbone is fitted first then, if the resolution permits, the side-chain atoms are positioned. The result is dependent on the resolution and the quality of the phases (O Fig. 30-1). Often regions of high flexibility (e.g., surface lysine side chains) are not visible since the corresponding electron density is smeared. 

Levinthal (1966) and Katz and Levinthal (1972) described protein molecules in a united atom approximation and used a molecular modeling system in conjunction with an interactive computer graphic program. More recently (Honig et al, 1976), the same group developed a procedure based... 

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