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Processing echo-antiecho data

Processing echo-antiecho data

NUTS Help

Processing "echo-antiecho" gradient data

These phase-sensitive gradient experiments are run such that each slice contains both sine and cosine terms in t1. This means that the data must be handled differently from hypercomplex data, in which odd numbered slices contain only cos t1 terms, and even numbered slices contain only sin t1 terms.  

Varian g-hsqc spectrum of sucrose.
This data set can be downloaded, along with processing macros.

The data are processed differently depending on whether or not Arrayed Mode (NUTS-Professional version only) is used.

To process this data, we FT and phase slice 1 and slice 2, then calculate the sum and the difference of them. Because the 2 slices are, respectively, (cos t1 + isin t1) and (cos t1isin t1), the sum gives you just cosine, and the difference gives you just sine.  Together, they comprise a complex "FID" in the indirect dimension.

This add/subtract process is handled with command C2 which works in Arrayed Mode only, but can be accomplished in non-arrayed mode using a combination of commands.  See below.

Phase correction in the direct dimension can be difficult, because the first slice may have little signal.  If a 1D spectrum was acquired when the 2D experiment was done, the phase correction can be determined using the 1D spectrum, and then applied to the 2D data using PS.  If not, phasing can be determined after processing.  See details.

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 which allows processing in both dimensions after FT.  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 

PT set processing type to 2D_EchoAntiecho
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  
C2 add/subtract pairs of spectra to create complex "fids" in indirect dimension
PH phase while viewing the first slice;  on exiting phase routine, the entire data set is phased.  If S/N is insufficient, skip phasing for now
TD transpose data
MS MS  
ZF zero-fill (may be repeated if needed)
FT may require phasing;  see 2D phasing
SR may or may not be needed to make diagonal run in the conventional direction
PH phase as described here
TD to view data with direct dimension horizontal; touch up phasing if needed (see 2D phasing)
MH set minimum height to 0.3 (good starting guess for contour threshold)
SS set scale
IP intensity plot

All quadrants of the data are retained, allowing phasing in both dimensions.  Be sure to save the processed data.  

Macro for processing using Arrayed Mode 

NUTSMACRO Varian g-hsqc in arrayed mode ; for echo-antiecho data ask fileimport im 2f pt 2D_echoantiecho, 2n, set ARRAY_PAIRWISECOMPLEX set s# 90 ms ms ft ; combine data c2 ; transpose td ; process using zero-fill ms ms zf ft td set mh 2 ss ip end

Phasing in one or both dimensions may be needed after processing.  See 2D phasing.  Note that data has not been saved.

Macro for processing without Arrayed Mode

Commands have been added to facilitate the addition/subtraction process. Two buffers, called B1 and B2, have been created. Typing B1 (or B2) copies the current data into Buffer 1 (or 2). Then typing B+ sums B1 + B2 and places the sum into the current data set. Similarly, B- does the same with the difference. However, by being a bit clever, it can be done without these commands.

Before running the macro, import the data with IM.  The macro start by prompting for a data file to open – select the translated NUTS file, which always starts with $.

It is recommended that users unfamiliar with 2D processing in NUTS begin by examining the explanation of HETCOR processing first, as many steps are the same and HETCOR is a simpler case. The processing required here differs from "normal" hypercomplex data only in the Link to process in the first dimension. It is recommended that users also read through the description of hypercomplex phase-sensitive 2D data.

NUTSMacro Varian echo-antiecho g_hsqc  determine phase correction before beginning
set s# 90
ask filea
ga
set filec ft1.2d
window function used here is cosine squared, applied with ms ms after setting s#=90

macro requests name of data set to be processed

  data are saved as Ixcos(wt1)+Iysin(wt1) and Ixcos(wt1)-Iysin(wt1)
We form the real half of the t1 complex pair from (slice 1 + slice 2) and the imaginar
y half from (slice 1 – slice 2)
ga zf b1 ia ga zf b2 b+ ms ms ft ps tr b- ms ms ft ps ti st in (Note that this Link appears in the macro all on one line)

GA reads in the first slice
ZF will zero-fill to the next higher power of 2
B1
loads it into buffer 1
IA increments the extension for fileA
GA ZF B2 reads in the next slice, zerofills and loads it into buffer 2
B+ adds the slices, then we apply window function, FT and phase
TR "tags" this to be the real half of the complex FID in t1
B- subtracts the contents of the buffers, then we apply window function, FT and phase

TI "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
set new file names and transpose data for processing in the second dimension
set filea td.2d
set sl 1
ga
set filec ft2.2d
read in transposed data, set file names

 

ga bc ms ms zf ft sr bc sc in process 2nd dimension with cosine squared, 1x zerofill and spectrum reverse
set filea ft2.2d
set sl 1
ga
set mh 4
ss
ip
end
reset file name, read in transformed data

set minimum height to 4 (good first guess)

set scale, draw intensity plot

Phasing can be done after running the macro.  See details

Last updated: 3/23/05