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

Revision as of 14:18, 16 September 2013 by Tlinnet (talk | contribs) (→‎Check the peak list matches)

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 DIRS=`cat fid_files.ls | sed 's/\/fid//g'`
cd ${DIRS[1]}
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. Remove sleep 5 from the script.
  4. Click 'Save script' to make fid.com file, and 'Quit', and run the script.

Spectral processing

This step can be done by following wiki page Spectral_processing.
Start nmrDraw by command 

nmrDraw

Convert and spectral processing all

Now we want to convert all spectra.
You should have a fid.com and nmrproc.com in the first FID folder.
We now copy these script into all of the experimental folders, and execute them. 

cd $CWD

set FIDS=`cat fid_files.ls`
set DIRN1=`dirname $PWD/${FIDS[1]}`
 
foreach I (`seq 2 ${#FIDS}`)
set FID=${FIDS[$I]}; set DIRN=`dirname $FID`
cd $DIRN
echo $DIRN
cp -f $DIRN1/fid.com .
cp -f $DIRN1/nmrproc.com .
./fid.com
./nmrproc.com
cd ..
end

Convert NMRPipe to Sparky

Next we also want to convert them to SPARKY format. 

set FTS=`ls -v -d -1 */*.ft2`

foreach FT ($FTS)
    set DNAME=`dirname $FT`
    set BNAME=`basename $FT`
    set FNAME=`echo $BNAME | cut -d'.' -f1`
    echo $FT $DNAME $BNAME $FNAME
    pipe2ucsf $FT ${DNAME}/${FNAME}.ucsf
end

Working with peaks

Check the peak list matches

Check that your peak list matches your spectrum.
Read the section in Check the peak list matches. 

set DIRS=`cat fid_files.ls | sed 's/\/fid//g'`
sparky ${DIRS[1]}/test.ucsf

Check for peak movement

Your should check, that the peaks do not move at the different experiments. Try opening some random spectra, and overlay them in SPARKY.
Read the section in Check for peak movement. 

sparky ${FIDS[1]}/test.ucsf ${FIDS[10]}/test.ucsf ${FIDS[25]}/test.ucsf ${FIDS[50]}/test.ucsf

Measuring peak heights

We will use the program NMRPipe seriesTab to measure the intensities.

seriesTab needs a input file, where the ppm values from a SPARKY list has been converted to spectral points.
The spectral points value depends on the spectral processing parameters.

Generate spectral point file

Create a file with spectral point information with script stPeakList.pl . 

stPeakList.pl 0.fid/test.ft2 ../peak_lists/peaks_corr_final.list > peaks_list.tab
cat peaks_list.tab

Make file with paths to .ft2 files

Then we make a file list of filepaths to .ft2 files. 

ls -v -d -1 */*.ft2 > ft2_files.ls
cat ft2_files.ls

Measure the height or sum in a spectral point box

seriesTab -in peaks_list.tab -out peaks_list_max_standard.ser -list ft2_files.ls -max
seriesTab -in peaks_list.tab -out peaks_list_max_dx1_dy1.ser -list ft2_files.ls -max -dx 1 -dy 1

OR make the sum in a box: 

seriesTab -in peaks_list.tab -out peaks_list_sum_dx1_dy1.ser -list ft2_files.ls -sum -dx 1 -dy 1
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