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This tutorial presently cover the [http://svn.gna.org/svn/relax/branches/ relax_disp branch].<br>
This branch is under development, for testing it out, you need to use the source code. See [[Installation_linux#Checking_out_a_relax_branch]].
# 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 This step can 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 following wiki 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.|}
== making a spin file from SPARKY list ==
relax does not yet has the possibility to read spins from a sparky file. [https://gna.org/support/?3044 See support request].
So we create one.
<source lang="bash">
set ATOMS=`tail -n+4 peaks_list.tab | awk '{print $7}'`
set SCRIPT=relax_2_spins.py
foreach I (`seq 1 ${#ATOMS}`)
set ATOM=${ATOMS[$I]}; set SPIN=`echo $ATOM | sed -e "s/N-HN//g"`; set RESN=`echo $SPIN | sed -e "s/[0-9]*//g"`; set RESI=`echo $SPIN | sed -e "s/[A-Za-z]//g"`
echo $ATOM $SPIN $RESN $RESI
echo "spin.create(spin_name='N', spin_num=$I, res_name='$RESN', res_num=$RESI, mol_name=None)" >> $SCRIPT
end
cat $SCRIPT
</source>
cp relax_2_spins.py ../relax
scriptspectrum.read_spins(file='relax_2_spins"peaks_list_max_standard.py'ser", dir=None)
→Intro: Deleted the out of date svn branch information.
__TOC__
= Intro =
This tutorial is based on the analysis of NMR data from the paper:
<blockquote>
== Spectral processing ==
== Fourier transform all spectra ==
As stated in the [[manual | relax manual]] section '''5.2.1 Temperature control and calibration''', the pulse sequence can put a lot of power into the sample. <br>
You could read these sections in the relax manual:<br>
[http://www.nmr-relax.com/manual/Temperature_control_calibration.html Importance of Temperature control and calibration]<br>
[http://www.nmr-relax.com/manual/relax_data_temp_control.html Temperature control]<br>
= Analyse in relax =
== Extract the spectra settings from Varian procpar file ==
== Measure the backgorund noise "RMSD" in each of the .ft2 files ==
=== RMSD via sparky ===
There exist two ways to get the background RMSD noise
0 0.06 0 599.8908622 2.39e+03
24 0.06 400.00000000000000000000 599.8908622 2.45e+03
</source>
=== RMSD via nmrpipe showApod ===
We can also use the showApod rmsd.
<source lang="bash">
set FIDS=`cat ft2_files.ls`
set OUT=${PWD}/apod_rmsd.txt
set CWD=$PWD
rm $OUT
foreach I (`seq 1 ${#FIDS}`)
set FID=${FIDS[$I]}; set DIRN=`dirname $FID`
cd $DIRN
set apodrmsd=`showApod *.ft2 | grep "REMARK Automated Noise Std Dev in Processed Data:" | awk '{print $9}'`
echo $apodrmsd $DIRN >> $OUT
cd $CWD
end
cat $OUT
mv ncyc.txt ncyc_or.txt
paste ncyc_or.txt $OUT > ncyc.txt
</source>
cp ncyc.txt ../relax
cp peaks_list* ../relax
cd ../relax
</source>
# Set the current experiment type.
relax_disp.exp_type(spectrum_id=current_id, exp_type='cpmg fixedSQ CPMG')
# Set the peak intensity errors, as defined as the baseplane RMSD.
# Set the relaxation dispersion CPMG frequencies.
relax_disp.cpmg_frqcpmg_setup(spectrum_id=current_id, cpmg_frq=vcpmg)
i += 1
# Shift+Ctrl+s OR File-> Save as... '''ini_run.bz2''' in the '''model_sel_analyt''' directory.
# Now push "Execute"
The analysis will probably take between 4-10 hours.<br>
=== Analyse via script ===
# Create the spins
# Name the isotope for field strength scaling.
relax_disp relax_4_model_sel.py -t log_relax_4_model_sel.log
</source>
The analysis will probably take between 4-10 hours.<br>
== Rerun from a "ini_setup.bz2" file ==
If you made a logfile, then you can do convert it to the full relax script.<br>
See [[Grep_log_file]] for this.
== Compare values ==
For the '''TSMFK01''' and for example the '''CR72''', the '''k_AB''' value can be compare
<source lang="bash">
cd model_sel_analyt
paste "TSMFK01/k_AB.out" "CR72/k_AB.out" | awk '{print $2, $3, $6, $13}'
</source>
== Inspect model selection for residues ==
</source>
=== In relax prompt get spin.model ===
See [[:Category:List_objects]] to get inspiration how to loop through the data class containers.
= See also =
[[Category:Relaxation dispersion analysis]]
[[Category:Tutorials]]
