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# 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 See [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 [[Manual | relax manaul]], section '''5.2.2 Spectral processing''', the spectral processing script could look like:<br> '''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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/gm.html NMRPipe manual on GM] suggestto 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'''<source lang="bash">#!/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</source> === 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/ <br> See also the [http://www.nmr-relax.com/manual/Spectral_processing.html relax online manual for spectral processing]. A good book to loop up in, is '''Keeler, Understanding NMR Spectroscopy, Second edition'''. {| class="wikitable sortable" border="1"|-!nmrPipe!Desc.!Comments|-|nmrPipe -fn [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/sol.html SOL]|Solvent Filter||-|nmrPipe -fn [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/gm.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/zf.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/ft.html FT] -auto|Complex Fourier Transform, here for the measured direct dimension.|Do Fourier Transform.|-|nmrPipe -fn [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/ps.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/sp.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/zf.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/ft.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/ps.html 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 [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/poly.html POLY] -auto|Polynomial Subtract for Time-Domain Solvent Correction and Frequency-Domain Baseline Correction. ||-|nmrPipe -fn [http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/ext.html 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.|}
== Spectral processing ==
== Fourier transform all spectra ==
