Difference between revisions of "Tutorial for Relaxation dispersion analysis r1rho fixed time recorded on varian as sequential spectra"
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Check that your peak list matches your spectrum.<br> | Check that your peak list matches your spectrum.<br> | ||
Read the section in [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Check_the_peak_list_matches | Check the peak list matches]]. | Read the section in [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Check_the_peak_list_matches | Check the peak list matches]]. | ||
+ | |||
+ | <source lang="bash"> | ||
+ | sparky ${FIDS[1]}/test.ucsf | ||
+ | </source> | ||
== Check for peak movement == | == Check for peak movement == |
Revision as of 14:08, 16 September 2013
Contents
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
- Remove sleep 5 from the script.
- 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.
sparky ${FIDS[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.
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