NUTS Help
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 phasesensitive). 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  zerofill (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 zerofilling 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).
NUTSMACRO Varian magnitude cosy data for NUTSProfessional 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 
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