Graphs Available
Various graphs are available from the results and composition forms in Sednterp. All of these graphs use a standard form with many options for formatting and printing based on John Philos graphing package used in his programs Svedberg and XLGraph. A separate Help file is available that describes the menu options and features of this graphing package. This Help file can be accessed from the Help menu within the graphing window whenever a graph is displayed.
These graphs can be printed on any Windows printer or copied to the Clipboard as high-resolution Windows metafiles and pasted into other documents.
On the Results Form, graphing of the estimated shape of the sample is available. This graph shows both the shape and size of the sample (in nanometers) and the surrounding layer of hydration. The graph shows a side view and a view down the central axis, with the water of hydration shown as a separate layer on the outside.
On the Results Form a graph of a/b vs hydration is also available. This is a useful x-y plot of the dependence of these two interrelated parameters. It is helpful when there is no independent estimate of hydration or asymmetry, and to show how much the axial ratio would change if the hydration estimate was revised.
On the Sample Composition Form, x-y graphs of titration estimates are available. (The button to display this graph is only visible after you press the Show Charge and Absorbance Data button.) This graph shows charge vs pH computed from the AA and conjugate composition. The pKa of each residue is used in the calculation, so the charge estimate is an aggregate summation and does not take into account modifications to the pKas of individual residues by the tertiary structure of the protein.
On the Sample Composition Form, an x-y graph of the absorbance spectrum of a protein is also available. (The button to display this graph is only visible after you press the Show Charge and Absorbance Data button.) This graph likewise is an aggregate sum of the absorbances of the residues in the sample and does not take into account modifications to absorbance due to structure. Also, there is very sparse information in the phyconst.mdb database concerning conjugate absorbance properties. Thus some estimates of absorbance will be considerably in error if a heavily absorbing conjugate is present in the sample.
