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.
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 apod_rmsd" > $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`
set apodrmsd=`showApod test.ft2 | grep "REMARK Automated Noise Std Dev in Processed Data:" | awk '{print $9}'`
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]].