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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458987
</blockquote>
The data is recorded as FID interleaved
= Preparation =
You want to make a working dir, with different folders
<source lange="text">
peak_lists
spectrometer_data
scripts
</source>
You can create the folders by
<source lange="text">
mkdir peak_lists spectrometer_data scripts
</source>
In the folder '''spectrometer_data''' should be the files: '''fid''' and '''procpar''' as the output from recording fid interleaved on Varian.<br>
In the folder '''peak_lists''' should contain SPARKY list in [[SPARKY_list | SPARKY list format]].
In the folder '''scripts''' we put scripts which help us processing the files.
= Get the process helper scripts =
<source lange="bash">
cd scripts
# Change shell
tcsh
# Set array of scripts to download
set SCRIPTS="CPMG_1_sort_pseudo3D_initialize_files.sh CPMG_2_convert_and_process.sh CPMG_3_fft_all.sh convert_all.com fft_all.com sparky_add.sh stPeakList.pl NMRPipe_to_Sparky.sh"
# Download scripts
foreach SCRIPT ( ${SCRIPTS} )
curl https://raw.github.com/nmr-relax/relax_scripts/master/shell_scripts/$SCRIPT -o $SCRIPT
end
# Make them executable
chmod +x *.sh *.com *.pl
# Go back to previous directory
cd ..
</source>
= Extract interleaved spectra, process to NMRPipe and do spectral processing =
== Extract interleaved and change format to NMRPipe ==
<source lange="bash">
# Copy data
cp -r spectrometer_data spectrometer_data_processed
# sort_pseudo3D and initialize files
cd spectrometer_data_processed
CPMG_1_sort_pseudo3D_initialize_files.sh
</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
# Click 'Save script' to make 'fid.com' file, and 'Quit', and run the next CPMG script
### Now it is time to convert all the fid from varian format.
<source lange="bash">
CPMG_2_convert_and_process.sh
</source>
== Spectral processing ==
# Now we need to spectral process the spectra.
# Process one of the files normally and the next script will copy the processing script to the other folder.
# [m]->Right-Click Process 2D->Basic 2D
# Save->Execute->Done; then; RClick File->Select File->test.ft2->Read/draw->Done
# If your spectra look reversed (i.e. if your peaks do not seem to match your reference spectrum) it might be solved by changing to
# [m] '| nmrPipe -fn FT -neg \' to the script to the third lowest line.
# Save->Execute->Done. Then push [r] to refresh.
# Press [h], and find P0 and P1, and push [m], change parameters and update script
# The changes to '| nmrPipe -fn PS xxx \' should be the FIRST line (The proton dimension) with PS
# save/execute, push [r] (read) and the [e] (erase settings) to see result in NMRdraw
# And then run the next CPMG script
As suggested in the [[Manual | relax manaul]], section '''5.2.2 Spectral processing''', the spectral processing script could look like:
File: '''nmrproc.com'''
<source lange="bash">
#!/bin/csh
nmrPipe -in test.fid \
| nmrPipe -fn SOL \
| nmrPipe -fn GM -g1 5 -g2 10 -c 0.5 \
| nmrPipe -fn ZF -auto -size 8000 \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -p0 214.00 -p1 -21.00 -di -verb \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn ZF -auto -size 8000 \
| nmrPipe -fn FT -neg \
| nmrPipe -fn PS -p0 0.00 -p1 0.00 -di -verb \
| nmrPipe -fn TP \
| nmrPipe -fn POLY -auto \
| nmrPipe -fn EXT -left -sw \
-ov -out test.ft2
</source>
= See also =
[[Category:Tutorials]]
