Index:
The database operations in the Pronto program contain a limited amount of consistency check of the information stored in the database. You can assign two cross peaks to a HN atom, and the chemical shift values referring to that proton could be 7.1 ppm for the first cross peak, and 10.2 ppm for the second, and the program does not complain.
The Report menu in the Tools menu contains three separate checks. Note, that these checks cannot be used to locate errors in the database structure, for instance, if one of the data files is corrupted. All the check facilities only report errors, they do not make any changes in the database.
All the setup windows have a field with the Output File Name. The file will be stored in the $PRONTO_WORK directory, when the Make Check button is pressed. The file can be viewed by pressing the View Result button. The Warning limit fields define the standard deviation allowed when comparing chemical shift values.
Note: The messages produced are not always errors: They just mean that you will have to go in and check out things an extra time.
The setup window for the cross peak checker is shown in Figure 1. By default, all peaks for all spectra are checked. To limit the check to just the peaks located for one spectrum, click in the spectrum name in the Check Peaks from all Spectra field. Three kinds of checks can be made:
1. Check Peak Unassigned. A list of unassigned peaks is produced. Each dimension of the peak is treated separately, i.e. if the atom at w1 is assigned, but the one at w2 is not, an error is produced.
2. Check Peak Multiply Assigned. A list of peaks where more than one atom is attached to a dimension is listed.
3. Check Outline Peaks. List peaks where the chemical shift value in one axis differs from the average of the chemical shift values for other peaks attached to the same atom.
The setup window for the atom checker is shown in Figure 2. All atoms are checked.
Three kinds of checks can be made:
1. Check Assigned Peaks. Check that at least one cross peak is attached to each atom.
2. Check Spin System Assignment. Check that each atom is attached to just one spin system.
3. Check Atom Derivation. Check the distribution of the chemical shift values of the peaks attached to this atom.
The setup window for the spin system checker is shown in Figure 3. All spin systems are checked.
Three kinds of checks can be made:
1. Check Sequential Assignment. Check that each spin system is contained in just one sequential assignment, and that this sequential assignment is attached just in one position in the sequence.
2. Check Amino Acid Assignment. Check that just one amino acid name is attached to this spin system.
3. Check Atoms. Check that the spin systems contain at least one atom.