NUTS Help
Processing "echoantiecho" gradient data
These phasesensitive gradient experiments are run such that each slice contains both sine and cosine terms in t_{1}. This means that the data must be handled differently from hypercomplex data, in which odd numbered slices contain only cos t_{1} terms, and even numbered slices contain only sin t_{1} terms.
Varian ghsqc 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 (NUTSProfessional 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 t_{1} + isin t_{1}) and (cos t_{1}– isin t_{1}), 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 nonarrayed 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. NUTSPro 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
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  zerofill (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 ghsqc in arrayed mode ; for echoantiecho 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 zerofill 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 phasesensitive 2D data.
NUTSMacro Varian echoantiecho 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 I_{x}cos(wt_{1})+I_{y}sin(wt_{1}) and I_{x}cos(wt_{1})I_{y}sin(wt_{1}) We form the real half of the t_{1} 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 TI "tags" this to be the imaginary half of the complex FID in t_{1} 
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