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== Intro ==
Made from [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved | Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved]]
== Get the process helper scripts ==
# [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#stPeakList.pl | stPeakList.pl]]
== Check the peak list matches ==
[[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Check_the_peak_list_matches | Check the peak list_matches list matches ]] sparky 0/test.ucsf == Prepare files == === Make standard peak list === stPeakList.pl 0/test.ft2 peak_list_SPARKY.list > peak_list_SPARKY.tab cat peak_list_SPARKY.tab === Find *.ft2 files === ls -v -d -1 */*.ft2 > ft2_files.ls cat ft2_files.ls === Measure heights === seriesTab -in peak_list_SPARKY.tab -out peaks_list_max_standard.ser -list ft2_files.ls -max cat peaks_list_max_standard.ser === Extract the spectra settings from Varian procpar file ===<source lang="bash">set RELAXT=`awk '/^relaxT /{f=1;next}f{print $0;exit}' procpar`; echo $NCYCLISTset SFRQ=`awk '/^sfrq /{f=1;next}f{print $2;exit}' procpar`; echo $SFRQ foreach I (`seq 2 ${#RELAXT}`) set T=${RELAXT[$I]}; echo $T $SFRQ >> relaxt.txtend cat relaxt.txt</source> === Measure RMSD in spectra ===[[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Measure_the_backgorund_noise_.22RMSD.22_in_each_of_the_.ft2_files | Measure the backgorund noise .22RMSD.22 in each of the .ft2 files ]] ==== Very fast way - RMSD via nmrpipe showApod ====We can also use the showApod rmsd.<source lang="bash">set FIDS=`cat ft2_files.ls`set OUT=${PWD}/apod_rmsd.txtset CWD=$PWDrm $OUT foreach I (`seq 1 ${#FIDS}`)set FID=${FIDS[$I]}; set DIRN=`dirname $FID`cd $DIRNset apodrmsd=`showApod *.ft2 | grep "REMARK Automated Noise Std Dev in Processed Data:" | awk '{print $9}'`echo $apodrmsd $DIRN >> $OUTcd $CWDendcat $OUT paste relaxt.txt $OUT > settings.txt</source>
