Introduction

ProSpectND is a processing package for 1/2/3/4/5D NMR data. The program has been used to process 1/2/3D NMR Bruker and Varian files. For larger dimensions, it has only been tested with computer generated 4/5D files. The program includes special features like, linear prediction, watwa water suppression, and Hilbert transform. Also, a simulation module, based on the LOACOON simulation program for isotropic nmr spectra of spin-1/2 systems, has been included. Most functions can be accessed from menu's as well as from the command line. The nD-processing part is handled by scripts for maximum flexibility. These scripts can be generated automatically by the program for standard nD processing. If needed, the scripts can be modified before execution.

Example of the processing of a 2D NMR spectrum.

Conversion of Bruker and Varian NMR files

NMR data sets that have been recorded by Bruker or Varian Spectrometers must be converted to the program's own file format, before they can be processed. This conversion is handled by scripts what ensures maximum flexibility. These scripts can be found in the default script directory (if the environment variable PSNDSCRIPTDIR has been set). To prepare a file with scripts, a simple setup utility ha been created that can handle the most common cases. Select under the 'File' menu the option ' Prepare Bruker/Varian file'.


 
 

Data dir

The directory where the ser or fid file resides. It also should contain parameters (acqus, acqu2s or procpar). It is ok to append 'ser'
or 'fid' to this parameter.

Output file Name

The output file name. If a full directory is specified, the program makes this the current working directory.

Prepa script

prepa_bruker.au or prepa_varian.au

Bruker modes

States, TPPI, Echo-antiecho, States-TPPI

Bruker 2D acq. order

For 3D files: acquisition order is 321 or 312

Dimension NMR data

There are currently only prepa scripts for 1/2/3D data.

When OK is pressed, the script editor is displayed with the above values added to the 'Script arguments'.  When OK is pressed here, a file conversion takes place and the first record of the new file is loaded and displayed.

Alternatively, press  This will display the Script Editor. Load the correct prepa script and add the arguments by hand.



Use Read Script to select an appropriate processing script. Edit the names of the input and output files and press OK.

The prepa Bruker script is called prepa_bruker.au, and can be initiated with some arguments. To view those arguments, use

prospectnd -b prepa_bruker.au -h

This means, run the prospectnd program in the background mode (-b flag) with the script name prepa_bruker.au (this is a script available from the standard script directory) and with the argument help (-h).  The output will be something like:

-i file_or_directory_name   - Define input file or directory
-o output_file              - Define output file
-d ndim                     - Define the dimensionality of the file
-m n mode                   - Define datatype in direction n (n=1,2,3,4)
 -m n 0                     - Set mode for tn from file (default) (n=1,2)
 -m n c or -m n s or -m n 1 - Set mode for tn to States (i.e. complex)  (n=1,2)
 -m n r or -m n t or -m n 2 - Set mode for tn to TPPI (i.e. real)       (n=1,2)
 -m n e or -m n 3           - Set mode for tn to echo-antiecho          (n=1,2)
 -m n z or -m n 4           - Set mode for tn to States-TPPI            (n=1,2)
-s n size                   - Define size in direction n (n=1,2,3,4)
-h                          - This help overview

The actual output will depend on the current version of the script. Now one can prepare a file in batch mode with the following command:

prospectnd -b prepa_bruker.au -i data/2/ -o 2dfile.p -m 1 e -m 2 c

This means, convert the file that can be found in the directory data/2 (ser + acqus files) into the output file 2dfile.p. The optional arguments with the -m flags specify that the spectrum was echo-antiecho in direction 1 and complex in direction 2. Of course, the same can be done by loading the script in the script editor, an put the arguments in the Script arguments text area.

Conversions used by the prepa script. Examples are for the first 4 data points.

States - odd data points are written to the real data array and even data points to the imaginary data array.
source 1 2 3 4 = real 1 3 + imaginary 2 4

TPPI - data are copied to the real data array.
source 1 2 3 4 = real 1 2 3 4

Echo-antiecho - 4 data points are mixed and written to the real and imaginary data arrays.
source 1 2 3 4 = real 1+3 4-2 + imaginary 2+4 1-3

States-TPPI - Same as States, but every second real and imaginary data point is multiplied by -1.
source 1 2 3 4 = real 1 -3 + imaginary 2 -4

Read the NMR file

When a new file has been created with a 'prepa' script, the first record of this file is loaded automatically. Otherwise,  see Open and Read Files on how to accomplish this. At this stage, all processing parameters are disabled. The strategy is now to process the first record of the file. That is the one that is currently displayed. By doing so, the relevant parameters will be defined. From these parameters a script can be generated by the program that will process all records of the NMR data set in the current direction. The same principle can be applied for each dimension until all have been processed. Each processing step produces a new file.

Use a Window Filter

For all the options, see Window . Use the Wn button to select the window-type + parameters. When the Window popup menu appears for the first time, the 'Window' option says 'No window'. After a window filter has been applied this changes to 'Do window', what means that the current settings have been stored and will be used for the creation of a processing script. You don't have to set this by hand. To remove the window filter from the chain of events, go to the 'Parameters' menu, select 'Window', set the option back to "no window', and press OK.

Do a Fourier Transform

See Fourier Transform

Apply Phase Correction

See Phase correction

Create 2D processing script

Use again  the get the script editor. Use "Create script from Parameters" to produce something like the following script:

        # Script generated by prospectnd
        file1 = "/home/kuik/nmrdata/2dvar.p"
        file2 = "/home/kuik/nmrdata/2dvar.f2"
        # Open input file
        ropen file1
        # Set processing direction
        dr 2
        # Set store mode to complex
        sm 2
        # Open output file
        wopen file2
        # For all records do ...
        for $i in sorted [..] do
            print "\rProcessing record " + i
        # Read record
            rn $i
        # Window
            sq 2.20, [1..2048]
        # Fourier transformation
            ft 1
        # Phase correction
            pk 137.9, 6.2, 1
        # Write result
            rw
        done
        println "\nDone"
        # Close output file
        wclose
        # Reopen the output file for reading
        ropen file2
        # Set direction
        dr 2
        # Read first record
        rn 1

Press OK to run this script.

Process direction 1

All records in direction 2 now have been processed and the first record (in direction 2) of the new file has been loaded. One way to proceed is to select a number of records in direction 1 to define new parameters. Get the Row/Column select mode with  .



One can use the bookmark option . Press 'Add Bookmark' to add the current record to the list.



Now apply a window function, a Fourier transformation and a phase correction, in the same way as for direction 2.
 



Now go back to direction 2, by pressing the   (= Undo record selection) button.



Select some other records from direction 1, so that we do not only have peaks at the right side of the spectrum. IMPORTANT: use AU to repeat all processing steps for the newly selected record. Next do some additional phase correction. Test all these processing steps on yet another record.



There is also another way of doing a 2D phase correction  Finally one can end with a baseline correction. Again use "Create script from Parameters" to create a script and process the file.

Use 2D options to analyse the 2D spectrum

See 2D options