Processing CEST Data: Difference between revisions
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# | # Have X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab) installed | ||
# Open a c-shell with “csh” and navigate to the directory with your ser file | # Open a c-shell with “csh” and navigate to the directory with your ser file | ||
# Open X11 | # Open X11 | ||
| Line 18: | Line 18: | ||
##| pipe2xyz –out fids/UBQ%03d.fid –y –ov | ##| pipe2xyz –out fids/UBQ%03d.fid –y –ov | ||
##/bin/rm –fr data/ | ##/bin/rm –fr data/ | ||
# Run the fid.com script you just saved. | # Run the [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fid.com fid.com] script you just saved. | ||
# Input file names and phase values into ftcpmg.com (follows this protocol) and run | # Input file names and phase values into [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/ftcpmg.com ftcpmg.com] (follows this protocol) and run | ||
# Open test spectrum in nmrDraw | # Open test spectrum in nmrDraw | ||
# Pick peaks and save the peak list | # Pick peaks and save the peak list | ||
# Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run | # Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/caddA.py addA.py]. | ||
# Run autoFit.tcl in the c-shell. | # Run [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/autoFit.tcl autoFit.tcl] in the c-shell. | ||
##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series | ##autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series | ||
# Run extract_profiles_bru.py (follows) | # Run [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/extract_profiles_bru.py extract_profiles_bru.py] (follows) | ||
##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/ | ##./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/ | ||
# Make sure the .out files are named like “A#N-HN.out” | # Make sure the .out files are named like “A#N-HN.out” | ||
# Then run ChemEx, check their tutorial | # Then run ChemEx, check their tutorial | ||
[[category: | Other Helpful Files: [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/calcFMFinput.py calcFMFinput.py] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/exp.cfg exp.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/fit.com fit.com] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/met.cfg met.cfg] [http://bionmr.unl.edu/files/misc/mediawikidownloads/CEST/par.cfg par.cfg] | ||
[[category:Needs_Updating]] <!--No idea what CEST Data is to link it correctly seems more like a protein file--> | |||
[[category:Data_Processing_and_Analysis]] | [[category:Data_Processing_and_Analysis]] | ||
Latest revision as of 00:04, 11 March 2022
Processing CEST Data
- Have X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab) installed
- Open a c-shell with “csh” and navigate to the directory with your ser file
- Open X11
- In the terminal type “bruker”
- Click “read parameters”
- Switch the F1 and F2 axes
- y should be real with N total and valid points
- z should be the 15N dimension
- zMODE Echo-Antiecho
- yMODE Real
- aq2D States
- Save the script. It should look like the script that follows this protocol.
- Add these lines:
- xyz2pipe –in fid/test%03d.fid –z –ri2c
- | pipe2xyz –out fids/UBQ%03d.fid –y –ov
- /bin/rm –fr data/
- Run the fid.com script you just saved.
- Input file names and phase values into ftcpmg.com (follows this protocol) and run
- Open test spectrum in nmrDraw
- Pick peaks and save the peak list
- Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run addA.py.
- Run autoFit.tcl in the c-shell.
- autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series
- Run extract_profiles_bru.py (follows)
- ./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/
- Make sure the .out files are named like “A#N-HN.out”
- Then run ChemEx, check their tutorial
Other Helpful Files: calcFMFinput.py exp.cfg fit.com met.cfg par.cfg