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.
set OUT=$PWD/exp_parameters.txt
echo "# DIRN I deltadof2 dpwr2slock ncyc trim ss sfrqapod_rmsd" > $OUT
foreach I (`seq 1 ${#FIDS}`)
set FID=${FIDS[$I]}; set DIRN=`dirname $FID`
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`
set apodrmsd=`showApod test.ft2 | grep "REMARK Automated Noise Std Dev in Processed Data:" | awk '{print $9}'`echo "$DIRN $I $deltadof2 $dpwr2slock $ncyc $trim $ss $sfrq$apodrmsd" >> $OUT
</source>= Get the process helper scripts =Go into the '''scripts''' directory and download these scripts to there.# [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#convert_all.com | convert_all.com]] # [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#fft_all.com | fft_all.com]] # [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#CPMG_2_convert_and_process.sh | CPMG_2_convert_and_process.sh ]] # [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#CPMG_3_fft_all.sh | CPMG_3_fft_all.sh]] # [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#NMRPipe_to_Sparky.sh | NMRPipe_to_Sparky.sh]] # [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#sparky_add.sh | sparky_add.sh]] # [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#stPeakList.pl | stPeakList.pl]] Then make them executablesort -b -k 3,3n -k 4,4n -k 5, and add to PATH5n exp_parameters.<source lang="bash"txt >cd scripts# Change shelltcsh# Make them executablechmod +x *.sh *.com *.pl# Add scripts to PATHsetenv PATH ${PWD}:${PATH}# Go back to previous directorycd .exp_parameters_sort.txt
</source>
== Change format to NMRPipe ==
<source lang="bash">
set FIDSCWD=$PWDset DIRS=`cat fid_files.ls| sed 's/\/fid//g'`set DIRN=`dirname cd ${FIDSDIRS[1]}`varian $DIRN
</source>
# 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 $DIRNecho $DIRNcp -f $DIRN1/fid.com .cp -f $DIRN1/nmrproc.com ../fid.com./nmrproc.comcd ..end</source> == Convert NMRPipe to Sparky ==Next we also want to convert them to SPARKY format.<source lang="bash">set FTS=`ls -v -d -1 */*.ft2` foreach FT ($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}.ucsfend</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.tabcat 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 =
Now it is time to convert all the fid from varian format to NMRPipe with the script [[Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved_scripts#CPMG_2_convert_and_process== Preparation ===== Prepare directory for relax run ===Then we make a directory ready for relax<source lang="bash">mkdir .sh | CPMG_2_convert_and_process.sh]] /relaxcp exp_parameters.txt ../relaxcp exp_parameters_sort.txt ../relaxcp -r peak_lists* ../relaxcp peaks_list.tab ../relaxcd ../relax</source>