Processing CEST Data

Processing CEST Data

1. Install X11, nmrPipe, Python >=2.7, and ChemEx (from the Kay lab)
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

       -	zMODE Echo-Antiecho
       -	yMODE Real
       -	aq2D States

1. Save the script. It should look like the script that follows this protocol.
2. 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/
3. Run the fid.com script you just saved.
4. Input file names and phase values into ftcpmg.com (follows this protocol) and run
5. Open test spectrum in nmrDraw
6. Pick peaks and save the peak list
7. Rename the peaks to their corresponding amino acid and residue #. Alternatively, create a peakList.txt with their IDs and run addASS.py.
8. Run autoFit.tcl in the c-shell.
   1. autoFit.tcl –specName fts/UBQ%03d.ft2 –inTab test.tab –series
9. Run extract_profiles_bru.py (follows)
   1. ./extract_profiles_bru.py –tbl nlin.tab –par fq3list –out fit/
10. Make sure the .out files are named like “A#N-HN.out”
11. Then run ChemEx, check their tutorial