Tutorial for Relaxation dispersion analysis r1rho fixed time recorded on varian as sequential spectra

Intro

This tutorial presently cover the relax_disp branch.
This branch is under development, for testing it out, you need to use the source code. See Installation_linux#Checking_out_a_relax_branch.

This tutorial is based on the analysis of R1rho data, analysed in a master thesis.

The spectra is not recorded interleaved, but as a series of spectra with experimental changes.

Preparation

You want to make a working dir, with different folders

peak_lists
spectrometer_data
scripts

You can create the folders by

mkdir peak_lists spectrometer_data scripts

In the folder peak_lists should contain SPARKY list in SPARKY list format.
In the folder scripts we put scripts which help us processing the files.
In the folder spectrometer_data should be a directory containing directories with all experiments where each directory contain files: fid and procpar as the output from recording on Varian.

Establish file-overview

Make file with paths to fid files

We make a file list of filepaths to fid files.

ls -v -d -1 */fid > fid_files.ls
cat fid_files.ls

Do something in each directory

With the fid_files.ls, we can do something in each directory.
For example do a list files in each direcory.

set FIDS=`cat fid_files.ls`

foreach I (`seq 1 ${#FIDS}`)
set FID=${FIDS[$I]}; set DIRN=`dirname $FID`
cd $DIRN
ls 
cd ..
end

Extract the spectra settings from Varian procpar file

Now we want to make a settings file we can read in relax.

set FIDS=`cat fid_files.ls`
set OUT=$PWD/exp_parameters.txt

echo "# DIRN I deltadof2 dpwr2slock ncyc ss sfrq" > $OUT
foreach I (`seq 1 ${#FIDS}`)
set FID=${FIDS[$I]}; set DIRN=`dirname $FID`
cd $DIRN
set deltadof2=`awk '/^deltadof2 /{f=1;next}f{print $2;exit}' procpar`
set dpwr2slock=`awk '/^dpwr2slock /{f=1;next}f{print $2;exit}' procpar`
set ncyc=`awk '/^ncyc /{f=1;next}f{print $2;exit}' procpar`
set ss=`awk '/^ss /{f=1;next}f{print $2;exit}' procpar`
set sfrq=`awk '/^sfrq /{f=1;next}f{print $2;exit}' procpar`
echo "$DIRN $I $deltadof2 $dpwr2slock $ncyc $ss $sfrq" >> $OUT
cd ..
end

cat $OUT

You can check, if you have repetitions of experiments, by sorting the parameters, and see if they are dublicated.
We do this, by numerical sort columns 3,4 and 5 with the values for "deltadof2, dpwr2slock, ncyc".

sort -b -k 3,3n -k 4,4n -k 5,5n exp_parameters.txt | awk '{print $3, $4, $5}'

Get the process helper scripts

Go into the scripts directory and download these scripts to there.

1. convert_all.com
2. fft_all.com
3. CPMG_2_convert_and_process.sh
4. CPMG_3_fft_all.sh
5. NMRPipe_to_Sparky.sh
6. sparky_add.sh
7. stPeakList.pl

Then make them executable, and add to PATH.

cd scripts
# Change shell
tcsh

# Make them executable
chmod +x *.sh *.com *.pl

# Add scripts to PATH
setenv PATH ${PWD}:${PATH}

# Go back to previous directory
cd ..

Spectral process files

Copy data

We first copy the data

# Copy data
cp -r spectrometer_data spectrometer_data_processed
cd spectrometer_data_processed

Change format to NMRPipe

set FIDS=`cat fid_files.ls`
set DIRN=`dirname ${FIDS[1]}`
cd $DIRN
varian

Now we make a file to convert from binary format of Varian to NMRPipe.

1. Now click, 'read parameters', check 'Rance-Kay'
2. Remember to set Y-'Observe Freq MHz' to N15
3. Click 'Save script' to make 'fid.com' file, and 'Quit', and run the script.

Now it is time to convert all the fid from varian format to NMRPipe with the script CPMG_2_convert_and_process.sh .

CPMG_2_convert_and_process.sh