! /buddha/rwb1002/samples/am/noesy/README

R.W.Broadhurst, Department of Biochemistry, University of Cambridge, U.K.
7/Jul/1994

THE DATA:

The spectrum in this directory is a 2D 1H-1H NOESY correlation, 
acquired on a Bruker am500 in sequential mode for d1 and using
TPPI for quadrature detection in d2.

FILE DESCRIPTIONS:

(1) tm9e6a.ser ! serial file from am500 (converted to amx format)

(2) tm9e6a.ser.par ! serial file decription

(3) tm9e6a.spc ! processed spectrum file

(4) tm9e6a.spc.par ! default description of processed spectrum file

(5) tm9e6a.spc.par.old ! referenced description file for spectrum

(6) tm9e6a_2dft.scr ! 2d processing control script file

(7) tm9e6a_d1.com ! command list for processing in d1

(8) tm9e6a_d2.com ! command list for processing in d2

(9) setup_plot2 ! a convenient setup for running plot2. To use
    this setup copy 'setup_plot2' to '.plot2'

FEATURES:

(1) How to deal with input data in amx format

(2) How to deal with am-type sequential data in d1

(3) How to deal with TPPI in d2

EXTRA COMMENTS: 

A way to go about phasing a 2D data set (if you don't already
know what the phase corrections should be):

(a) Process the spectrum first in d1 only.  This is done by
    editing the 2d processing control script file (tm9e6a_2dft.scr)
    and commenting out the d2 processing line (script 2 tm9e6a_d2.com)
    by placing a ! at the start of the line.  Then edit the command
    list for processing in d1 (tm9e6a_d1.com) and comment out the
    phase correction and baseline correction commands.

(b) Read this interferogram in to plot2 and look at the first row
    using the phasing routine.

(c) Find appropriate d1 phasing parameters by sliding the bars in
    the 'Phase Slice' window.  

(d) Reprocess in d1 to check phasing.  When this spectrum is read
    into plot2, remember to update the phase correction in the
    'Phase Slice' window back to 0 0.

(e) Decide on a d1 baseline correction (if needed) and reprocess
    again in d1.

(f) Now edit the 2d processing control script file again, setting
    the input to the .par file of the interferogram already
    processed in d1 (tm9e6a.spc.par) and sending the output to
    a new file	(tm9e6a2.spc.par).  This will save time when 
    processing in d2, building on the d1 processing already done
    rather than starting from the raw data each time, but may use
    up too much memory.  Comment out the d1 processing line 
    (script 1 tm9e6a_d1.com) and remove the comment from the d2 
    processing line (script 2 tm9e6a_d2.com).

(g) Process in d2 with the phase and baseline correction in the
    d2 command list (tm9e6a_d2.com) commented out.

(h) Read this spectrum into plot2 and choose columns to phase up.
    Usually it is best to choose two strong peaks remote in 
    chemical shift so that both zero and first order phase 
    corrections can be optimized.  To display the sum of two
    columns in the '1D Display' window put both columns in the
    'rows/columns:' box in the 'Select Slice' window, separated
    by a blank space (eg.  '120 1604').

(i) Reprocess in d2 with new phase correction and baseline 
    correction (if necessary).
