File Menu

The file menu on the main form contains the following options.

1. New data entry form. This choice re-initializes the main form. Choose this option to start over on a new experiment. It will also reinitialize values to those of the program defaults.

2. Open different database. This choice opens a file dialogue window to allow you to choose a new database for saving experimental, sample, and buffer data. The standard name for this database is Sednterp.mdb. Do not attempt to open the Phyconst.mdb database as an alternate database, since this database does not contain experimental information, but instead contains essential extrapolation data for the Sednterp program. Users can create their own experimental information databases in the saving data in database form which pops up from the file menu when any of the next four menu choices are chosen. (When their are multiple users of the program it may be useful to give each a separate database).

3. Save Sample Info in Database.

4. Save Buffer Info in Database.

5. Save Experiment Info in Database.

6. Save Results Info in Database.

All of these choices open the Saving Data in Databases form. In this form, experimental data is saved as records. Sample data (Name, Vbar, composition), Buffer data (Name, density, viscosity, components, pH, heavy water percentage), Experimental data (Name, temperatures, sedimentation coefficient, sample concentration, RPM, sigma), and Results (R, prolate/oblate, a/b ratios, etc.) are saved as records in different tables in one database. The data is saved in this way in order to make series of experimental data reusable. The Saving Data in Databases form provides a common interface for saving any part of the data. Saving experimental data automatically records which Sample and Buffer records are associated with that experiment; saving Results data automatically saves which Sample, Buffer, and Experiment records are associated with that result.

Experiment records have a Reference Date. This is useful because you may have repeated the same experiment on more than one date, e.g. duplicate sedimentation velocity experiments. Since the Sample and Buffer records would be identical, assigning a different date to the Experiment record allows you to store the different sedimentation coefficients obtained in these experiments as different Experiment records. Normally the date assigned would be the actual date of the experiment, but if this experiment uses a molecular weight obtained by sedimentation equilibrium as well as a sedimentation coefficient measured on a different day, then you will have to decide what date is most appropriate. Experiment records can be retrieved on the basis of this date by using the date combo box on the Sample form.

Loading the saved Experiment, Sample, or Buffer data records is accomplished by choosing the record name from the combo boxes on the main form (loading an Experiment record automatically loads the associated Sample and Buffer Records). Loading Result data is accomplished from the combo box on the Results form, and automatically loads the associated Experiment, Sample, and Buffer Records.

7. Change Program Defaults.

This choice initiates a series of dialogue boxes in which the user can change program defaults (the value of these defaults are found in the sednterp.ini file). The default database name for experimental, sample, buffer, and results may be changed; the original default name is sednterp.mdb. If a user creates a new personally named database, the new database can be set as the default here. The default values that appear automatically in the buffer density, viscosity, and pH can be changed. These values are overridden whenever the user enters data, so the default ought to be changed only when certain values are always used. The original default for the buffer is pure water at pH 7 at 20 degrees C: density = 0.998324 and viscosity = 1.002 centipoise. The default value for vbar likewise appears upon program startup and can be overridden by any data entry by the user. The standard default value is 0.74, a good guess for globular proteins. One value, the coefficient used to calculate the concentration dependence of s* can be changed only by changing this default. Finally, whether the program expects 3 letter or one letter amino acid codes at startup can be set here.

Any change in default values takes effect only when the program is reinitialized by being restarted or by the New Data Entry choice of this menu. There is a separate Save Defaults procedure associated with the graphing package, which can be accessed from the File... menu of the graphing window.

8. Additional Modules List additional javascript modules available for use in sednterp.

9. Import Databases Allows you to import databases for sednterp base calculations off of.

10. Debug Console Outputs any error messages, notifications etc that the program encounters.

11. Exit. This choice terminates the program run.