Tutorial for R1/R2 Relaxation curve-fitting analysis on varian recorded as fid interleaved

Intro

Made from Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved

Get the process helper scripts

1. stPeakList.pl

Check the peak list matches

Check the peak 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

set RELAXT=`awk '/^relaxT /{f=1;next}f{print $0;exit}' procpar`; echo $NCYCLIST
set 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.txt
end

cat relaxt.txt

Measure RMSD in spectra

Measure the backgorund noise RMSD in each of the .ft2 files

Very fast way - RMSD via nmrpipe showApod

We can also use the showApod rmsd.

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

paste relaxt.txt $OUT > settings.txt