Spectral processing

Spectral processing

1. Now we need to spectral process the spectra.
2. Process one of the files normally and the next script will copy the processing script to the other folder.
3. [m]->Right-Click Process 2D->Basic 2D
4. Save->Execute->Done; then; RClick File->Select File->test.ft2->Read/draw->Done
5. If your spectra look reversed (i.e. if your peaks do not seem to match your reference spectrum) it might be solved by changing to
6. [m] '| nmrPipe -fn FT -neg \' to the script to the third lowest line.
7. Save->Execute->Done. Then push [r] to refresh.
8. Press [h], and find P0 and P1, and push [m], change parameters and update script
9. The changes to '| nmrPipe -fn PS xxx \' should be the FIRST line (The proton dimension) with PS
10. save/execute, push [r] (read) and the [e] (erase settings) to see result in NMRdraw
11. And then run the next CPMG script

As suggested in the relax manaul, section 5.2.2 Spectral processing, the spectral processing script could look like:

NOTE only put EXT in, AFTER you are done with phasing, or you will get problems phasing.

NOTE for GM you would have to play with the constants -g1 5 -g2 10. The NMRPipe manual on GM suggest to try as a start: -g1 20 -g2 35. -g2 specifies the Gaussian to apply in terms of a line broadening in Hz. It is usually adjusted to be larger (x 1.25 - 4.0) than the line sharpening specified by the -g1 option.

File: nmrproc.com

#!/bin/csh

nmrPipe -in test.fid \
| nmrPipe  -fn SOL                                    \
| nmrPipe  -fn GM  -g1 5 -g2 10 -c 1.0                \
| nmrPipe  -fn ZF -auto -size 8000                    \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 214.00 -p1 -21.00 -di -verb     \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto -size 8000                    \
| nmrPipe  -fn FT -neg                                \
| nmrPipe  -fn PS -p0 0.00 -p1 0.00 -di -verb         \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn POLY -auto                             \
| nmrPipe  -fn EXT -left -sw                          \
   -ov -out test.ft2

Understand spectral processing

To understand the NMRPipe functions, you can look them up in the manual page: http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/

See also the relax online manual for spectral processing.

A good book to loop up in, is Keeler, Understanding NMR Spectroscopy, Second edition.

nmrPipe	Desc.	Comments
nmrPipe -fn SOL	Solvent Filter
nmrPipe -fn GM -g1 5 -g2 10 -c 1.0	Lorentz-to-Gauss Window, here for the measured direct dimension.	-c 1.0' The constant c is set to 1.0, since the phase P1 correction is different from 0.0, here -p1 -21.00, if -p1 0.0 then c 0.5.
nmrPipe -fn ZF -auto -size 8000	Zero Fill, here for the measured direct dimension.	The -auto will auto round to final size to power of 2. So here it is equivalent to: nmrPipe -fn -size 8192
nmrPipe -fn FT -auto	Complex Fourier Transform, here for the measured direct dimension.	Do Fourier Transform.
nmrPipe -fn PS -p0 214.00 -p1 -21.00 -di -verb	Phase Correction, here for the measured direct dimension.
nmrPipe -fn TP	2D Transpose XY->YX (YTP)	Transpose matrix to work in in-direct dimension.
nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5	Adjustable Sine Bell Window. The -pow 2 means is sinus^2 function. See Keeler p. 93 and p. 98 for the sine window desc	The -end 0.98 means that you cut 2% data. -c 0.5 is set 0.5 since the p1 phasing is 0.0 in the in-direct dimension.
nmrPipe -fn ZF -auto -size 8000	Zero Fill, here for the in-direct dimension.	The -auto will auto round to final size to power of 2. So here it is equivalent to: nmrPipe -fn -size 8192
nmrPipe -fn FT -neg	Complex Fourier Transform, here for the measured direct dimension.	Do Fourier Transform, but here negative, since the CPMG element in the Puls Sequence makes the magnetization end up negative.
nmrPipe -fn PS -p0 0.00 -p1 0.00 -di -verb	Phase Correction, here for the in-direct dimension.	No-phase correction needed.
nmrPipe -fn TP	2D Transpose XY->YX (YTP)	Transpose matrix back to work in direct dimension.
nmrPipe -fn POLY -auto	Polynomial Subtract for Time-Domain Solvent Correction and Frequency-Domain Baseline Correction.
nmrPipe -fn EXT -left -sw	Extract Region. NOTE only put this in, AFTER you are done with phasing, or you will get problems phasing.	-left extract left half on the sweep-width which have been centered on water.