Difference between revisions of "Tutorial for R1/R2 Relaxation curve-fitting analysis on varian recorded as fid interleaved"

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

Revision as of 11:27, 3 February 2014

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 .22RMSD.22 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
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