Spectral processing
From relax wiki
Spectral processing
- Now we need to spectral process the spectra.
- Process one of the files normally and the next script will copy the processing script to the other folder.
- [m]->Right-Click Process 2D->Basic 2D
- Save->Execute->Done; then; RClick File->Select File->test.ft2->Read/draw->Done
- 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
- [m] '| nmrPipe -fn FT -neg \' to the script to the third lowest line.
- Save->Execute->Done. Then push [r] to refresh.
- Press [h], and find P0 and P1, and push [m], change parameters and update script
- The changes to '| nmrPipe -fn PS xxx \' should be the FIRST line (The proton dimension) with PS
- save/execute, push [r] (read) and the [e] (erase settings) to see result in NMRdraw
- 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:
Caution 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. |