! /buddha/rwb1002/samples/README_phasing

R.W.Broadhurst, Department of Biochemistry, University of Cambridge, U.K.
13/Oct/1994

The best way to phase a spectrum is to know the phase correction
parameters in advance!  Experiments can be set up so that they
need a (0,0) or (90,0) phase correction in the acquisition
dimension d1 by modifying the receiver phase.  The phase correction
for indirect dimensions can be set, for example, to (90, -180) or
(180, -360) by correct choice of the initial value of the 
incremented delay.  A flat baseline in the indirect dimension
also tends to be a by product.   This method is outlined in

BAX_A, IKURA_M, KAY_LE & ZHU_G, J MAG RESON 91, 174 (1991)
	(for States)
ARCHER_SJ, BALDISSERI_DM & TORCHIA_DA, J MAG RESON 97, 602 (1992)
	(for TPPI)

However, if these procedures have not been followed, it is 
possible to phase your spectrum using the "process" and "plot2" 
programs in tandem.  An easier method using "plot1" will follow
when I have got to grips with that program!a

The example scripts used here come from the directory
/buddha/rwb1002/samples/am/noesy.

(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).




