Processing Varian HMBC data

Varian acquires HMBC data as hypercomplex, even though the data is not phase-sensitive, and a magnitude calculation is done at the end of processing.  In a hypercomplex experiment, 2 FIDs are acquired for each t1 time point, with a phase shift of one pulse.  After FT in the direct dimension, the real halves of each pair of spectra are combined to create complex interferograms in the indirect dimension.

Varian HMBC 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, displaying 2D data

Arrayed Mode processing from the command line

AR enter arrayed mode
IM import file called fid
S# set phase shift for sine multiplication to 45
MS  MS apply cosine squared window function
FT  
TR  TR  ST "tag" real half of each slice and store 
TD transpose data
MS MS  
ZF ZF zero-fill (experience has shown there is benefit from doing several ZFs, even 4 times)
FT  
MC magnitude calculation
BC remove any DC and tilt in baseline
TD to view data with direct dimension horizontal
MH set minimum height to 5 (good starting guess for contour threshold)
SS set scale
IP intensity plot

Be sure to save the processed data.

Macro using Arrayed Mode

NUTSMACRO Varian hmbc data (hypercomplex and magnitude) for NUTS-Professional
set array_on
ask filea
ga
set s# 45
;window fcn is sine-squared
bc ms ms ft 
; combine slices for hypercomplex data
tr tr st
;transpose data
td
;2nd dimension processing
;window fcn is sine-squared and we do one zero-fill
; magnitude calculation
ms ms zf ft mc bc
;transpose data
td
set mh 5
ss
ip
end

Note that NUTS remains in Arrayed Mode at the end of the macro.  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 Varian HMBC, hypercomplex and magnitude
ask filea
ga		 Macro asks for FID to open
set sl 1
set s# 45		 window function used here is sine squared, applied with ms ms after setting s#=45
set filec ft1.2d  
ga bc ms ms ft bc tr ia ga bc ms ms ft bc tr st in 1st dimension processing

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
set sl 1		 reset file names
ga ms ms zf ft mc bc sc in 2nd dimension processing
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 5
ip
end		 open file data set

set contour threshold (MH = 5)

set scale, display intensity plot

Last updated: 4/27/01