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Varian HMBC


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

ARenter arrayed mode
IMimport file called fid
S#set phase shift for sine multiplication to 45
MS  MSapply cosine squared window function
TR  TR  ST“tag” real half of each slice and store
TDtranspose data
ZF ZFzero-fill (experience has shown there is benefit from doing several ZFs, even 4 times)
MCmagnitude calculation
BCremove any DC and tilt in baseline
TDto view data with direct dimension horizontal
MHset minimum height to 5 (good starting guess for contour threshold)
SSset scale
IPintensity 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
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 in1st dimension processingGA reads in the first slice
BC removes DC offset of the 2 halves of the FID
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
reset file namestranspose data
set filea td.2d
set filec ft2.2d
set sl 1
reset file names
ga ms ms zf ft mc bc sc in2nd dimension processing
set filea ft2.2d
set filec final.2d
set sl 1
reset file namestranspose data


set filea final.2d
set mh 5
open file data setset contour threshold (MH = 5)

set scale, display intensity plot

Last updated: 4/27/01