SMILE and Data Processing

Auto Data Processing Scripts for PCA

Using SMILE processing to remove residual signals:

For NMRPipe v9.8 and higher, SIERRA-SMILE signal removal can now be accomplished by calling the basicSierra.com function:

basicSierra.com -in test.fid -ft orig.ft2 -out sierra.ft2 \ 
-reg 2.12 2.07 27.0 25.0 -tdN 6 \ 
-procArgs -xP0 auto, -xEXT1 3.5ppm -xEXTXN -1.5 ppm \ 
-xBASEARG POLY,auto ord=4 yP0 -90

where -reg specifies the ¹H and ¹³C ppm bounds for SMILE removal and -tdN specifies the baseline correction order applied to the excipient signal

(To install NMRPipe, go to https://www.ibbr.umd.edu/nmrpipe/install.html.)

An in depth overview of of the SMILE removal process is detailed below:

An explicit processing script can be found here: smile_subtract.txt (rename smile_subtract.com)

1. Process data normally:

#!/bin/csh

nmrPipe -in test.fid \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.50 -end 0.95 -pow 2 -elb 0.0 -glb 0.0 -c 0.5 \
| nmrPipe -fn ZF -zf 1 -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 $ -p1 0.0 -di \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.50 -end 0.95 -pow 1 -elb 0.0 -glb 0.0 -c 0.5 \
| nmrPipe -fn ZF -zf 2 -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 90.0 -p1 0.0 -di \
| nmrPipe -fn TP \
| nmrPipe -fn POLY -auto -ord 0 -verb \
  -out orig.ft2 -ov

2. Apply baseline correction in the indirect dimension:

Apply baseline correction in the indirect dimension if needed. As an alternative to the usual method of baseline correction "nmrPipe -fn POLY -auto ...", the "tdBaseline1D.com" utility can baseline correct a spectrum by replacing one or more points at the start of the time-domain data. The "-n ..." parameter specifies the number of points to replace, so that setting "-n 1" will apply a constant baseline correction, and setting higher values will correct for curved baselines.

nmrPipe -in orig.ft2 -fn TP -out tmp.ft2 -ov
tdBaseline1D.com -in tmp.ft2 -out base.ft2 -n $
/bin/rm -f tmp.ft2

3. Reprocess the baseline corrected data with SMILE (set -report 2 to save SMILE peak table):

nmrPipe -in base.ft2 \
| nmrPipe -fn HT \
| nmrPipe -fn PS -inv -hdr \
| nmrPipe -fn FT -inv \
| nmrPipe -fn ZF -inv \
| nmrPipe -fn SP -inv -hdr \
| nusPipe -fn SMILE -nDim 2 -maxIter 2048 -nSigma 2 -report 2 -sample None \
                    -xApod SP -xQ1 0.50 -xQ2 0.95 -xQ3 1 -xELB 0.0 -xGLB 0.0 \
                    -xT 100 -xP0 -90.0 -xP1 0.0 -scaling 1.0 \
| nmrPipe -fn ZF -zf 1 -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 -100.0 -p1 0.0 -di \
| nmrPipe -fn TP \
  -out smile.ft2 -ov

nmrPipe -in base.ft2 -out base.ft2 -inPlace -fn TP

4. Extract the relevant peaks from the SMILE peak table by setting the bounds around the peak of interest including attendant artifacts:

smile2tab.tcl -in smile.log -out smile.tab -ref orig.ft2

selectTab.tcl -in smile.tab -out small.tab -hdr -cond "X_PPM <= $downfield-¹H && X_PPM >= $upfield-¹H && Y_PPM <= $downfield-^₁₃C && Y_PPM >= $upfield-¹³C"

5. Process the simulated time-domain SMILE data:

set xT  = (`getParm -in orig.ft2 -parm NDTDSIZE -fmt %.0f -dim CUR_XDIM`)
set yT  = (`getParm -in orig.ft2 -parm NDTDSIZE -fmt %.0f -dim CUR_YDIM`)
set xN  = (`getParm -in smile.ft2 -parm NDFTSIZE -fmt %.0f -dim CUR_XDIM`)
set yN  = (`getParm -in smile.ft2 -parm NDFTSIZE -fmt %.0f -dim CUR_YDIM`)
set xP0 = (`getParm -in orig.ft2 -parm NDP0 -fmt %.1f -dim CUR_XDIM`)
set yP0 = (`getParm -in orig.ft2 -parm NDP0 -fmt %.1f -dim CUR_YDIM`)

echo ""
echo "SMILE Simulation: Time-Domain Size: $xT $yT Freq-Domain Size: $xN $yN"

simTimeND -in small.tab -tdd -nots -xP0 $xP0 -yP0 $yP0 \
  -xN               $xN  -yN               $yN  \
  -xT               $xT  -yT               $yT  \
  -xMODE            DQD  -yMODE  Echo-AntiEcho  \
  -xSW        12626.263  -ySW         5434.783  \
  -xOBS         900.162  -yOBS         226.349  \
  -xCAR           4.727  -yCAR          18.000  \
  -xLAB              1H  -yLAB             13C  \
  -ndim               2  -aq2D         Complex  \
  -out ./sim.fid -verb -ov

nmrPipe -in sim.fid \
| nmrPipe -fn SP -off 0.50 -end 0.95 -pow 2 -elb 10.0 -glb 0.0 -c 0.5 \
| nmrPipe -fn ZF -zf 1 -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 $xP0 -p1 0.0 -di \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.50 -end 0.95 -pow 1 -elb 0.0 -glb 0.0 -c 0.5 \
| nmrPipe -fn ZF -zf 2 -auto \
| nmrPipe -fn FT -verb \
| nmrPipe -fn PS -p0 $yP0 -p1 0.0 -di \
| nmrPipe -fn TP \
  -out sim.ft2 -ov

6. Scale simulated SMILE data using bounds set tightly around peak of interest and subtract from original measured data:

set c = (`findScale.tcl -in1 orig.ft2 -in2 sim.ft2 -roiArg -x X_AXIS $¹Hppm $¹Hppm -y Y_AXIS $¹³Cppm $¹³Cppm`)
echo $c
nmrPipe -in sim.ft2 -out sim.ft2 -inPlace -fn MULT -c $c

addNMR -in1 orig.ft2 -in2 sim.ft2 -out dif.ft2 -sub

sethdr orig.ft2  -title Measured
sethdr base.ft2  -title Baseline
sethdr smile.ft2 -title SMILE
sethdr sim.ft2   -title Simulated
sethdr dif.ft2   -title Difference

scale2D *.ft2

Links

Auto Data Processing Scripts for PCA

Using SMILE processing to remove residual signals: