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Processing Varian gradient HMBC data

Processing Varian gradient HMBC data


Processing Varian gradient HMBC data

Varian g_hmbc data is a simple magnitude experiment, not phase sensitive and not hypercomplex.

Varian g_hmbc spectrum of sucrose.
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, sample data, processing Varian 2D data

Arrayed Mode processing from the command line

ARenter arrayed mode
IMimport file called fid
S#set phase shift for sine multiplication to 0
MS  MSapply sine squared window function
TDtranspose data
set line broadening to an appropriate value, apply EM (alternatively, sine squared can be used).
ZF ZFzero-fill (experience has shown there is benefit from doing several ZFs, even 4 times)
MCmagnitude calculation (alternatively, use M2)
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 g_hmbc data (magnitude) for NUTS-Professional set array_on ask filea ga set s# 0 set LB 5 bc ms ms ft  ;transpose data td em 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 g_hmbc, magnitude
ask filea
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 
ga bc ms ms ft bc sc in1st dimension processing

GA reads in the first slice
BC removes DC offset of the 2 halves of the FID
applies sine squared  
BC after FT removes DC and tilt in baseline
SC saves the data
IN increments the slice counter

set filec td.2d
set filea ft1.2d
set sl 1
reset file names

transpose data

set filea td.2d
set filec ft2.2d
set sl 1
set lb 5
reset file names
ga em zf ft mc bc sc in2nd dimension processing
set filea ft2.2d
set filec final.2d
set sl 1
reset file names

transpose data


set filea final.2d
set mh 5
open file data set

set contour threshold (MH = 5)

set scale, display intensity plot

Last updated: 7/20/04