Processing CEST Data

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