Hypercomplex NOESY Data

Varian (and JEOL) acquires some phase-sensitive data (such as NOESY) as hypercomplex, meaning that 2 FIDs are acquired for each t1 time point, with a phase shift of one pulse in the sequence.  After FT in the direct dimension, the pairs of spectra are combined to create complex interferograms in the indirect dimension.

Varian phase-sensitive NOESY 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 commands using the command line, shown below.  

NUTS-Pro versions newer than May, 2002, include a modified arrayed mode for that allows phasing in both dimensions after processing.  Commands for processing are listed below.  

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, phasing 2D data

Arrayed Mode processing from the command line

Import the fid, then process using the following series of commands: 

PT set processing type to 2D_HyperComplex
AR enter arrayed mode (note that status bar says "pairwise complex arrayed mode"
S# set phase shift for sine multiplication to 90
MS  MS apply cosine squared window function
FT  
PH phase while viewing the first slice;  on exiting phase routine, the entire data set is phased
TD transpose data
MS MS  
ZF zero-fill (may be repeated if needed)
FT may require phasing;  see 2D phasing
SR may or may not be needed to make diagonal run in the conventional direction
TD to view data with direct dimension horizontal
MH set minimum height to 0.3 (good starting guess for contour threshold)
SS set scale
IP intensity plot

All quadrants of the data are retained, allowing phasing in both dimensions.  See details.  Be sure to save the processed data.  

Macro using Arrayed Mode  

NUTSMACRO Varian noesy in arrayed mode
; for hypercomplex data
ask fileimport
im
2f
pt 2D_hypercomplex,
2n,
set ARRAY_PAIRWISECOMPLEX
set s# 90
ms ms ft
; transpose
td
; process using zero-fill
ms ms zf ft
td
set mh 2
ss
ip
end

Note that the processed data have not been saved.  Phasing in one or both dimensions may be needed.  See 2D phasing. 

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. 

Before running the macro, import the data, FT and phase.  When the macro starts, it will ask for a file to open - select the translated file.  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 Hypercomplex 
ask filea
ga
set sl 1		 Before running macro, open data set, FT and phase 1st slice 

Macro asks for name of data set to open - supply translated file name
set filec ft1.2d
set s# 90		 window fcn will be cosine squared;  phase is set with S#
ga bc ms ms ft ps bc tr ia ga bc ms ms ft ps bc tr st in Link to process 1st dimension

GA reads in the first slice
BC removes DC offset of the 2 halves of the FID
MS MS applies cosine squared  
BC after FT removes DC and tilt in baseline
TR "tags" this to be the real half of the complex FID in t1
IA increments slice counter for File A
GA  reads in the next slice, which is processed same way
TR "tags" this to be the imaginary half of the complex FID in t1
ST saves the 2 halves, and IN increments the file pointers and loops to the beginning of the Link
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		 reset file names
set sl 1
ga ms ms zf ft sc in 		2nd dimension processing
set filea ft2.2d
set sl 1
ga
set mh .3
ip
end		 reset file names

set contour threshold (MH = 0.3), set scale, display intensity plot

This macro ends displaying data with the indirect dimension on the horizontal axis.  This is because usually some phasing is needed.  See 2D phasing.

Last updated: 3/23/05