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

= Intro =
This tutorial presently cover the [http://svn.gna.org/svn/relax/branches/ relax_disp branch].<br>
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

<source lang="text">
peak_lists
spectrometer_data
scripts
</source>

You can create the folders by
<source lang="text">
mkdir peak_lists spectrometer_data scripts
</source>

In the folder '''peak_lists''' should contain SPARKY list in [[SPARKY_list | SPARKY list format]]. <br>
In the folder '''scripts''' we put scripts which help us processing the files. <br>
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.<br>

= Establish file-overview =

== Make file with paths to fid files ==
We make a file list of filepaths to '''fid''' files.
<source lang="bash">
ls -v -d -1 */fid > fid_files.ls
cat fid_files.ls
</source>

== Do something in each directory ==
With the '''fid_files.ls''', we can do ''something'' in each directory. <br>
For example do a list files in each direcory.

<source lang="bash">
set FIDS=`cat fid_files.ls`

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

== Extract the spectra settings from Varian procpar file ==
Now we want to make a settings file we can read in relax.

<source lang="bash">
set FIDS=`cat fid_files.ls`
set OUT=$PWD/exp_parameters.txt

echo "# DIRN I deltadof2 dpwr2slock ncyc trim 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 trim=`awk '/^trim /{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 $trim $ss $sfrq" >> $OUT
cd ..
end

cat $OUT
</source>

You can check, if you have repetitions of experiments, by sorting the parameters, and see if they are dublicated.<br>
We do this, by numerical sort columns 3,4 and 5 with the values for "deltadof2, dpwr2slock, ncyc".
<source lang="bash">
sort -b -k 3,3n -k 4,4n -k 5,5n exp_parameters.txt | awk '{print $3, $4, $5}'
sort -b -k 3,3n -k 4,4n -k 5,5n exp_parameters.txt > exp_parameters_sort.txt
</source>

= Spectral process files =
== Copy data ==
We first copy the data
<source lang="bash">
# Copy data
cp -r spectrometer_data spectrometer_data_processed
cd spectrometer_data_processed
</source>

== Change format to NMRPipe ==
<source lang="bash">
set CWD=$PWD
set DIRS=`cat fid_files.ls | sed 's/\/fid//g'`
cd ${DIRS[1]}
varian
</source>

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]].<br>
Start '''nmrDraw''' by command
 nmrDraw

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

<source lang="bash">
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
</source>

== Convert NMRPipe to Sparky ==
Next we also want to convert them to SPARKY format.
<source lang="bash">
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
</source>

= Working with peaks =

== Check the peak list matches ==
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]].

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

The final peak list is expected to be in:
<source lang="bash">
/peak_lists/peaks_corr_final.list
</source>
And have been saved by SPARKY, so it is in this format [[SPARKY_list]].

== 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.<br>
Read the section in [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved#Check_for_peak_movement | Check for peak movement]].

<source lang="bash">
sparky ${DIRS[1]}/test.ucsf ${DIRS[10]}/test.ucsf ${DIRS[25]}/test.ucsf ${DIRS[50]}/test.ucsf
</source>

== Measuring peak heights ==
We will use the program [[NMRPipe_seriesTab | NMRPipe seriesTab]] to measure the intensities.

'''seriesTab''' needs a input file, where the ppm values from a [[SPARKY_list | SPARKY list]] has been converted to spectral points.<br>
The spectral points value depends on the spectral processing parameters.

=== Generate spectral point file ===
Create a file with spectral point information with script 
[[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#stPeakList.pl | stPeakList.pl]] .

<source lang="bash">
stPeakList.pl ${DIRS[1]}/test.ft2 ../peak_lists/peaks_corr_final.list > peaks_list.tab
cat peaks_list.tab
</source>

=== Make a file name of .ft2 fil ===
<source lang="bash">
echo "test.ft2" > ft2_file.ls
</source>

=== Measure the height or sum in a spectral point box ===
<source lang="bash">
mkdir peak_lists
 
foreach line ("`tail -n+2 exp_parameters.txt`")
  set argv=( $line )
  set DIRN=$1
  set I=$2
  set deltadof2=$3
  set dpwr2slock=$4
  set ncyc=$5
  set trim=$6
  set ss=$7
  set sfrq=$8
  echo $I
  set FNAME=${I}_${deltadof2}_${dpwr2slock}_${ncyc}
  cd $DIRN
  seriesTab -in ../peaks_list.tab -out ${FNAME}_max_standard.ser -list ../ft2_file.ls -max
  seriesTab -in ../peaks_list.tab -out ${FNAME}_max_dx1_dy1.ser -list ../ft2_file.ls -max -dx 1 -dy 1
  seriesTab -in ../peaks_list.tab -out ${FNAME}_sum_dx1_dy1.ser -list ../ft2_file.ls -sum -dx 1 -dy 1
  cp ${FNAME}_max_standard.ser ../peak_lists
  cd ..
end
</source>

= Analyse in relax =

== making a spin file from SPARKY list ==
relax does not yet has the possibility to read spins from a sparky file. [https://gna.org/support/?3044 See support request].

So we create one.

<source lang="bash">
set ATOMS=`tail -n+4 peaks_list.tab | awk '{print $7}'`
set SCRIPT=relax_2_spins.py

foreach I (`seq 1 ${#ATOMS}`)
set ATOM=${ATOMS[$I]}; set SPIN=`echo $ATOM | sed -e "s/N-HN//g"`; set RESN=`echo $SPIN | sed -e "s/[0-9]*//g"`; set RESI=`echo $SPIN | sed -e "s/[A-Za-z]//g"`
echo $ATOM $SPIN $RESN $RESI
echo "spin.create(spin_name='N', spin_num=$I, res_name='$RESN', res_num=$RESI, mol_name=None)" >> $SCRIPT
end

cat $SCRIPT
</source>

== Prepare directory for relax run ==
Then we make a directory ready for relax
<source lang="bash">
mkdir ../relax
cp exp_parameters.txt ../relax
cp exp_parameters_sort.txt ../relax
cp -r peak_lists* ../relax
cp peaks_list.tab ../relax
cp relax_2_spins.py ../relax
cd ../relax
</source>

== See unique parameters ==
<source lang="bash">
tail -n +2 exp_parameters.txt | awk '{print $3}' | sort -k1,1n | uniq
tail -n +2 exp_parameters.txt | awk '{print $4}' | sort -k1,1n | uniq
tail -n +2 exp_parameters.txt | awk '{print $5}' | sort -k1,1n | uniq
tail -n +2 exp_parameters.txt | awk '{print $6}' | sort -k1,1n | uniq
tail -n +2 exp_parameters.txt | awk '{print $7}' | sort -k1,1n | uniq
tail -n +2 exp_parameters.txt | awk '{print $8}' | sort -k1,1n | uniq
</source>

= See also =
[[Category:Tutorials]]