The first catalog to insert information in is the spectrum catalog. This catalog must contain one entry for each of the spectra to work with. The spectrum files themselves need not be present on the disk when the information is entered into the catalog.
The program currently can work with the following spectrum formats:
1. UXNMR or UXNMR/P (From Bruker). The files must be stored under the following name for 2D data:
/Disk/data/User/nmr/Name/Expno/pdata/Procno/2rr
or for 3D:
/Disk/data/User/nmr/Name/Expno/pdata/Procno/3rrr
The parameter files must be stored there as well.
2. MNMR data (from a program package available separately from Carlsberg A/S) are stored under the following name:
/Disk/nmr/User/data/Name
3. Felix data are stored under the following name:
/Disk/felix/User/data/Name
4. Varian data a searched using the following pattern:
/Disk/User/expExpno/datdir/phasefile
Note: This does not work very well.
Note that the Disk, User, and Name fields can contain slashes and thus refer to another subdirectory structure than one would think of from the names above, for example, the Disk field could contain the string: "usr/people". If the directory structure does not match the structure you use for the spectrum files, many things are possible if you set up a directory containing logical links to the directories with your spectra.
An example of a spectrum window is shown in Figure 1. Select one of the entries (or create a new one by pressing the New button). Open the Zoom window by pressing the Zoom button. Highlighting an entry and pressing the Copy button will copy the selected entry, including all the cross peaks and assignments.
An example of a Spectrum Zoom Window is shown in Figure 2. The record shown contains information about a 2D TOCSY spectrum. The first five editable fields contain the information necessary to locate the spectrum file on the disk. The Type field can be filled in with the type of spectrum recorded, however, the information is only used to select a color code for the information relating to this spectrum. Currently, only the names of the classical 2D experiments exist. The Scale Factor field will initially be set to one. Pressing the Norm. button initiates a scan of the whole spectrum to estimate the noise level, using the parameter in the field to the right of the Scale Factor button. If you use 70 as a parameter for NOESY-type experiments and 85 for COSY-type experiments, the spectrum will be normalized so that the noise is around 1.0. You don't need to use the normalize facility if the spectrum inserted already has been normalized when using the NORMALIZE command to the MFFT program in the MNMR package. The Dimension parameter can be 2, 3, or 4, indicating the number of dimensions in the spectrum. The Axis Order parameter is a permutation of the digits from one to the value of Dimension. This is used to correlate the chemical shift values in the cross peak list with the actual dimensions in the spectrum, thus if 132 is entered for a 3D spectrum, the first value in the cross peak list corresponds to dimension 0, the second value to dimension 2, and the last value to dimension 1. The Axis Name lines each contain two fields: The first field is used to select the nucleus recorded in that dimension. This is selected using a popup-menu. The second field is a user-defined text string. This will be used as a title when referring to this axis in the other windows. The Name field is a short user-defined name. This will normally be used when referencing to this spectrum.
Before you have started working with Pronto, you should have recorded a series of spectra to be analyzed. This could typically be: COSY, NOESY, and TOCSY spectra recorded in H2O, and a similar set recorded in D2O. If you have a labelled protein, you should also consider recording a 15N-HMQC-TOCSY and a 15N-HMQC-NOESY spectrum. It is a good thing to enter all relevant spectra in the database from the beginning. If you later find out that a certain spectrum is useless, simply deleting the spectrum from the catalog will remove all cross peaks and all references to the spectrum deleted.
Note: Spectra can be present in the Pronto database, but not necessarily be located online on the system.
Only the disk space limits the number of spectra you can work with using Pronto.