Processing Varian HSQC data

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

Note that Varian's g-hsqc experiment is echo-antiecho, not hypercomplex, and must be processed differently.

Varian phase-sensitive HSQC 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.  

NUTS-Pro versions newer than May, 2002, include a modified arrayed mode for improved processing of hypercomplex data.  See details.

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

AR enter arrayed mode
IM import file called fid
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
TR  TR  ST "tag" real half of each slice and store 
TD transpose data
MS MS  
ZF zero-fill (may be repeated if needed)
FT may require phasing;  see 2D phasing
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.

Arrayed Mode processing using new PT feature (May, 2002)

Be sure you are not in arrayed mode, and open the data to be processed.

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 be needed to make diagonal run in the conventional direction
TD to view data with direct dimension horizontal
MH set minimum height to 3 (good starting guess for contour threshold)
SS set scale
IP intensity plot

All quadrants of the data are saved, allowing phasing in both dimensions.  Be sure to save the processed data.  To open the processed data at a later date, enter AR first, so that the data is sorted correctly when opened.

Macro using Arrayed Mode (does not use the new modified arrayed mode)

NUTSMACRO Varian hypercomplex HSQC processing for Arrayed Mode
;macro prompts for name of data set
; first, import, process and phase 1st slice

set array_on
ask FileA
ga
set s# 90
bc ms ms ft ps bc
; combine hypercomplex slices
tr tr st
;transpose data
td
ms ms zf ft 
td
set mh 4
ss
ip
end
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. 

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 Varian Hypercomplex HSQC 
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
IA increments slice counter for File A
TR "tags" this to be the real half of the complex FID in t1
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 filec final.2d
set sl 1
ga
td		 reset file names

transpose data
set filea final.2d
ga
ss
set mh 4
ip
end		 open final file

set scale, set contour threshold (MH = 4)

Last updated: 4/2/04