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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]].
== 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 $SCRIPT
</source>
cp relax_2_spins.py ../relax
scriptspectrum.read_spins(file='relax_2_spins"peaks_list_max_standard.py'ser", dir=None)
→Intro: Deleted the out of date svn branch information.
__TOC__
= Intro =
This tutorial is based on the analysis of NMR data from the paper:
<blockquote>
= Analyse in relax =
== Extract the spectra settings from Varian procpar file ==
== Measure the backgorund noise "RMSD" in each of the .ft2 files ==
=== RMSD via sparky ===
There exist two ways to get the background RMSD noise
0 0.06 0 599.8908622 2.39e+03
24 0.06 400.00000000000000000000 599.8908622 2.45e+03
</source>
=== RMSD via nmrpipe showApod ===
We can also use the showApod rmsd.
<source lang="bash">
set FIDS=`cat ft2_files.ls`
set OUT=${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='SQ 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
# Create the spins
# Name the isotope for field strength scaling.
= See also =
[[Category:Relaxation dispersion analysis]]
[[Category:Tutorials]]
