Graphical output

The raw output of a molecular structure calculation is a list of the coefficients of the atomic orbitals in each molecular orbital and the energies of these orbitcds. The graphical representation of a molecular orbited uses styKzed shapes to represent the basis set and then scales their size to indicate the Vedue of the coefficient in the LCAO. Different signs of the wavefunctions effe represented by different colors (as we saw in Figs 10.36,10.37, and 10.39). 

Once the coefficients are known, we can build up a representation of the electron density in the molecule by noting which orbitals are occupied and then forming the squares of those orbitals. The total electron density at any point is then the sum of the squares of the wavefunctions evaluated at that point. The outcome is commonly represented by an isodensity surface, a surface of constant total electron density (Fig. 10.47). There are several styles of representing an isodensity surface as a solid form, as a transparent form with a ball-and-stick representation of the molecule within, or as a mesh. A related representation is a solvent-accessible surface, which is generated by plotting the location of the center of a sphere (representing a solvent molecule) that is imagined to roll across the exposed surfaces of the atoms. 

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Kinetic studies have benefited immensely from microcomputers. Whereas dedicated software is often necessary for interfacing to specific instmments, data analysis can be carried out using readily available software materials capable of producing high quaUty graphical output. Most recentiy, it has become common to measure concentrations in some way that produces digital data that is entered automatically into the computer (see Computer technology). 

Models toxic gas releases. Two models available SHELL SPILLS and TRPUF (based on EPA PUFF). Graphical output. Requires 512K memory and 132 column printer. 

The drawings were produced using the computers and substantial array of graphical output devices at the Center for Research in Computing Technology at Harvard University.5... 

Figure 3. Example of Graphical Output from Analysis Mode. Reaction progress for water-jacketted reactor, with Cascade coupled temperature controllers, both in self-tuning mode.

Graphical output obtained by the GRAPH command, for the above example is shown in Chapter 5. 

The graphical outputs in Figs. 5.250 and 5.251 exhibit the iterations necessary to satisfy the boundary conditions, involving integration from the centre at X = 0 to the outside at X = 1. 

Scripts are often fairly simple software components that can be generated very quickly to execute recurring operations or collect multiple operations into a large block for efficient usage. Scripts can be simple shell scripts with no graphical output capability, but the use of extended graphical toolbox scripts provides a simple way of implementing software features with easy user interaction. 

In addition to the programs to select the optimum discussed previously, graphic approaches are also available and graphic output is provided by a plotter from computer tapes. The output includes plots of a given response as a function of a single variable (Fig. 11) or as a function of all five variables (Fig. 12). The abscissa for both types is produced in experimental units, rather than physical units, so that it extends from—1.547 to + 1.547 (see Table 5). Use of the experimental units allows the superpositioning of the single plots (see Fig. 11) to obtain the composite plots (see Fig. 12). 

User friendly data input procedure and graphical output... 

At the present time the only online facility that we provide for analyzing the data is the display function, which provides graphical outputs tailored to the data in the diffraction data files. The user specifies the run number for the data he wishes to plot. The display program then loads the header from the appropriate data file and determines what kind of plot to display. The user can dump the resulting plot to the printer to provide a record of his experiment. The "revise file" function can be used to create auxiliary files for plotting selected features of the data. 

FIGURE 6.13 Example of selected graphical output for ratiometric assay analysis. 

The predicted metabolites are also the starting point for the phase II metabolic prediction, to find where glucuronidation could occur. All the probable metabolites obtained from CYP metabolism reactions are submitted to a possible phase II reaction catalyzed by UGTs, using the UGT structure(s) as a template. The accessibility component is computed in the UGTcavity to prioritize glucuronic acid transfer. The final metabolite structures are then reported in graphical output or saved to a file. 

The programs are written modular. The reader can replace the artificial data, generated by a function, with real data from the lab. There is extensive use of graphical output. While the plots are minimal they efficiently illustrate the results of the analyses. In order to keep the programs concise, no effort was made to build comfortable user-interfaces. 

Another very useful exploration technique is cluster analyis, which quantifies similarities by calculating mathematic distances. The typical graphic output is a dendrogram. A common method of cluster analysis is Hierarchical cluster analysis (HCA). 

The user asks to view two sub-jgraphs. Eventually, graphical output (will be possible. 

The TRAACS 800+ is controlled by a personal computer and the features provided include complete interactive control via keyboard or mouse calculation of results as necessary taking into account baseline or sensitivity drift, graphical output of calibration curves for all calibration types—either Hnear or non-hnear, input facility for sample identification data allowing storage on disc and real-time results together with chart traces on a computer printer. The programs allow easy access to input or data files and connection to other computers, and gives system performance verification to CLP standards and built-in QC charts. 

Cluster analysis is far from an automatic technique each stage of the process requires many decisions and therefore close supervision by the analyst. It is imperative that the procedure be as interactive as possible. Therefore, for this study, a menu-driven interactive statistical package was written for PDP-11 and VAX (VMS and UNIX) series computers, which includes adequate computer graphics capabilities. The graphical output includes a variety of histograms and scatter plots based on the raw data or on the results of principal-components analysis or canonical-variates analysis (14). Hierarchical cluster trees are also available. All of the methods mentioned in this study were included as an integral part of the package. 

Next choose SOLVE from the PROBLEM window. Finally, use the NEW command from the GRAPH menu to create graphical output for the problem or create tabular output for more accurate numerical solutions. 

Fig. 3. Examples of input and output of SAMURAl-GUl system. An example of analysis with queries tnts (a) the CellMontage format as input and (b) graphical output of modules that share common biological function. Four example modules are searched by Benzbromarone, Fenbufen, Clofibrate, and Dichloroacetate. KEGG pathway functions for each module with the first and the second most significant p values are only shown.

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