Processing CEST Data: Difference between revisions

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# 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
#      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: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]]

Revision as of 00:04, 11 March 2022

Processing CEST Data


  1. Have X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab) installed
  2. Open a c-shell with “csh” and navigate to the directory with your ser file
  3. Open X11
  4. In the terminal type “bruker”
  5. Click “read parameters”
  6. Switch the F1 and F2 axes
    1. y should be real with N total and valid points
    2. z should be the 15N dimension
    3. zMODE Echo-Antiecho
    4. yMODE Real
    5. aq2D States
  7. Save the script. It should look like the script that follows this protocol.
  8. Add these lines:
    1. xyz2pipe –in fid/test%03d.fid –z –ri2c
    2. | pipe2xyz –out fids/UBQ%03d.fid –y –ov
    3. /bin/rm –fr data/
  9. Run the fid.com script you just saved.
  10. Input file names and phase values into ftcpmg.com (follows this protocol) and run
  11. Open test spectrum in nmrDraw
  12. Pick peaks and save the peak list
  13. Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run addA.py.
  14. Run autoFit.tcl in the c-shell.
    1. autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series
  15. Run extract_profiles_bru.py (follows)
    1. ./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/
  16. Make sure the .out files are named like “A#N-HN.out”
  17. Then run ChemEx, check their tutorial
  1. Other Helpful Files: calcFMFinput.py exp.cfg fit.com met.cfg par.cfg