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).
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|
|TR TR ST||“tag” real half of each slice and store|
|ZF ZF||zero-fill (experience has shown there is benefit from doing several ZFs, even 4 times)|
|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)|
Be sure to save the processed data.
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.
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|
|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 processingGA 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
|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 in||2nd 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