Processing Bruker Magnitude 2D Experiments

The macros below are appropriate for processing experiments that are not phase-sensitive, including cosy, cosygs, cosy45gs, inv4gs and any others with MC2 parameter set to QF (found in the file called pulseprogram).

Using Arrayed Mode, processing can be done using a macro (below) or simply by entering the following commands using the command line.  

Users with the standard 2D version cannot use Arrayed Mode, and can process with a different macro (below).

See also: macros, 2D processing, displaying 2D data, sample data, processing Varian 2D data

Arrayed Mode processing from the command line

AR enter arrayed mode
IM import file called ser
S# set phase shift for sine multiplication to 0
MS  MS apply sine squared window function
FT no phasing is done
TD transpose data
MS MS apply sine squared window function
ZF zero-fill (may be repeated if needed)
FT  
SR these spectra need spectrum reverse
MC magnitude calculation
BC remove any DC and tilt in baseline
TD to view data with direct dimension horizontal
MH set minimum height to 1 (good starting guess for contour threshold; may need to adjust)
SS set scale
IP intensity plot

If the data is homonuclear and "square" (same number of data points in both dimensions), the spectrum can be symmetrized using the SY command.  Choose Spectral Parameters from the View menu and check the Number of Points in the 2 dimensions.  Additional zero-filling can be done during processing to make the data end up square, if symmetrizing is desired. 

Be sure to save the processed data.

Macro using Arrayed Mode

NUTSMACRO Magnitude data for NUTS-Professional
set array_on
ask filea
ga
set s# 0
bc ms ms ft 
;transpose data
td
ms ms zf ft sr mc bc
;transpose data
td
set mh 1
ss
ip
end

Note that NUTS remains in Arrayed Mode at the end of the macro.  The data can be symmetrized, if desired, provided it has the same number of data points in both dimensions.  Be sure to save the final data.

Macro without Arrayed Mode

Processing is done one 1 slice at a time, so the sequence of commands is done in a Link, which is repeated for each slice. 

Temporary files are written at each stage of processing, so the macro must reset the file names at each stage.  Be sure to save the final result.

NUTSMacro magnitude data
ask filea
ga		 Macro asks for FID to open
set sl 1
set s# 0		 window function used here is sine squared, applied with ms ms after setting s#=0
set filec ft1.2d  
ga bc ms ms ft bc sc in 1st dimension processing

GA reads in the first slice
BC removes DC offset of the 2 halves of the FID
MS MS applies sine squared  
BC after FT removes DC and tilt in baseline
SC saves the data
IN increments the slice counter
set filec td.2d
set filea ft1.2d
set sl 1
ga
td		 reset file names

transpose data
set filea td.2d
set filec ft2.2d
set sl 1
set lb 5		 reset file names
ga ms ms zf ft mc sr bc sc in 2nd dimension processing
this data requires spectrum reverse (SR) and magnitude calculation (MC)
set filea ft2.2d
set filec final.2d
set sl 1
ga
td		 reset file names

transpose data

 
set filea final.2d
ga
ss
set mh 1
ip
end		 open file data set

set contour threshold (MH = 1)

set scale, display intensity plot

The data can be symmetrized, if desired, provided it has the same number of data points in both dimensions.

Last updated: 7/3/00