Programming Strategy

From Sednterp
Jump to: navigation, search

The overall strategy of the Sednterp program is to allow the user to enter information quickly and easily. The program will default to guessed values for all parameters that admit even any guess. Thus, by entering just a few parameters directly from the experiment, a somewhat reasonable calculation of molecular parameters will be performed by the program. For instance, the program will assume that the buffer density is that of pure water. Not many relevant biological molecules will even dissolve in water, so this guess is almost always wrong! Yet since many dilute buffers have densities close to water, this guess is reasonable for quick calculations.

Yet, Sednterp also allows the user to calculate or enter almost every value used in the calculations. Entering three numbers (sigma, RPM, and s*) will allow the program to calculate reasonable results. Yet over twenty four parameters that affect the calculation may be entered, including the individual buffer components. Even new buffer components can be added to the database so that Sednterp can calculate the density and viscosity of any buffer for which the experimenter has the proper information. Of course, the entering of more information will increase the accuracy of the calculations performed.

Also, the Sednterp program has the strategy to follow flexible paths of computation. The exact order of calculations depends on the users input of information. For example, if the sequence of a protein sample is entered, Sednterp will calculate and use the molecular weight by sequence for further calculations. But the user is allowed to override this calculation by entering sedimentation equilibrium data or directly entering another molecular weight. The molecular weight by sequence is generally more accurate than other computed weights, yet if the protein undergoes post-translational modification, its weight may have to be determined by experiment and not by sequence. Sednterp would allow you to estimate the vbar of the protein by sequence and still use a molecular weight determined by sedimentation equilibrium.

Finally, Sednterp attempts to save all the information entered by the user in separable segments in a unified database. In this way, analysis can be saved and modified easily at a later date.