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== 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 [[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] 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'''
<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.
|}
# 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 [[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] 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'''
<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.
|}