Processing magnitude COSY data

COSY data can be acquired in any of several "flavors" and each must be processed differently.  This example applies to a magnitude COSY spectrum (not hypercomplex, not phase-sensitive).  Any magnitude data is processed in the same manner;  see hetcor processing.

Varian COSY spectrum of strychnine.
This data set can be downloaded, along with processing macros.

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 commands, displaying 2D data, sample data, processing 2D data

Arrayed Mode processing from the command line

IM import file called fid
AR enter arrayed mode
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 this spectrum needs spectrum reverse (may or may not be needed)
MC magnitude calculation
BC remove any DC offset and tilt in baseline
TD to view data with direct dimension horizontal
MH set minimum height to 1 (good starting guess for contour threshold)
SS set scale
IP intensity plot

If the data is "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 (with SA).

Macro using Arrayed Mode

NUTSMACRO Varian magnitude cosy data for NUTS-Professional
ask filea
ga
set array_on
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

Before running the macro, import the data with IM.  The macro start by prompting for a data file to open - select the translated NUTS file, which always starts with $.

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, or it will be overwritten the next time the macro is run.

NUTSMacro Varian  magnitude cosy
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 set name for temp file
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: 3/23/05