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, $5}'
Spectral process files
Copy data
We first copy the data
# Copy data
cp -r spectrometer_data spectrometer_data_processed
cd spectrometer_data_processed
Change format to NMRPipe
set CWD=$PWD
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.
- Now click, 'read parameters', check 'Rance-Kay'
- Remember to set Y-'Observe Freq MHz' to N15
- Click 'Save script' to make 'fid.com' file, and 'Quit', and run the script.