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NMRPipe: a Comprehensive Software System for Biomolecular NMR
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  Frank Delaglio, Ph.D.

  Software Science Consultant
  325 Union Avenue #212
  Campbell CA 95008 USA


  Tel: 301 806-0867
  E-mail: delaglio@nmrscience.com



NMRPipe Processing Functions
BASE: Linear Baseline Corrections.

Flag Argument Default Description
 -nl xList None Baseline Node List (Valid Units: Pts Hz ppm %).
 -nw nw 0 Node Width +/- Pts.
 -first Include First Point of Data in Node List.
 -last Include Last Point of Data in Node List.

BASE applies a series of first-order baseline corrections over a set of baseline nodes. It is intended to remove baseline distortions in spectra, particularly in cases where automated baseline correction (POLY -auto) can't easily be used. The baseline node positions are held fixed for all vectors in the data, so the intent is that the selected node positions are in regions which are signal-free for all data vectors.

OPTIONS

-nw nodeWidth
This option specifies the number of points +/- from each baseline node which will be used in fitting the data to lines.

-nl nodeList
This option specifies the baseline positions, called nodes. By default, the positions are in points, with the first point being point 1. The positions can also be specified with labels Hz ppm %. When specifying a location with a unit label, there should be no spaces between the numerical value and the label.

For a given set of N baseline nodes, a series of N - 1 linear corrections will be applied between each node. The correction will be calculated by fitting a straight line between the points +/- nw at one node and the points +/- nw at the next node. The values of each straight line will then be subtracted from the original data. As such, only the points within the ranges of the given baseline nodes will be changed. For example, the following will apply a single linear correction between points 100 and 400; points 1 to 99 and points 400 and on will not be changed:

   | nmrPipe -fn BASE -nl 100 400 \
If we add another baseline node, and adjust the sizes of the nodes to +/- 3 points:
   | nmrPipe -fn BASE -nl 100 400 500 -nw 3 \
will subtract two straight lines from each vector in the data, adjusting points 100 to 500. At each vector, the first straight line will be calculated to fit the two points (x1,y1) and (x2,y2), and the second straight line will be calculated to fit the two points (x2,y2) and (x3,y3):
   x1 = 100
   y1 = average of intensities at points 100 +/- 3

   x2 = 400
   y2 = average of intensities at points 400 +/- 3

   x3 = 500
   y3 = average of intensities at points 500 +/- 3

-first
This option specifies that the last data point should be included as a node. It is equivalent to including "1" at the start of the -nl nodeList option.

-last
This option specifies that the last data point should be included as a node. It is equivalent to adding "100%" to the end of the -nl nodeList option.

EXAMPLES In the following example, each vector will be corrected by subtracting three straight lines. The first line will span from point 1 to the point at 10.5ppm. The second line will span from the point at 10.5ppm to the point at -0.5ppm. The third line will span from the point at -0.5ppm to the last point in the data.


nmrPipe -in test.fid \
| nmrPipe -fn SP -off 0.0 -end 0.95 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT \
| nmrPipe -fn BASE -first -last -nl 10.5ppm -0.5ppm -nw 3 \ 
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.0 -end 0.95 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -neg \
| nmrPipe -fn MC \
| nmrPipe -fn POLY -auto -ord 0 \
   -out test.ft2 -ov

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last updated: Jul 4, 2012 / big frank

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