NMRPipe seriesTab

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seriesTab can extract maximum values or the sum of regions in an NMRPipe-format spectral series, using an NMRPipe-format peak tables as input.

Usage

An example program usage is:

seriesTab -in peaks.dat -out peaks_0.ser -list files.list -sum -dx 1 -dy 1

peaks.dat contains the peak list with information of spectral position

VARS   INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s
 
    1   246.658    18.268    9.932  128.374 +7.000000e+05 W62NE1-W62HE1
    2   321.698    30.994    9.419  127.066 +7.000000e+05 L10N-L10HN
    3   320.089    55.737    9.430  124.523 +7.000000e+05 V6N-V6HN
...

files.list contains

test.ft2

Or create the files list by:

ls -v -d -1 */*.ft2 > files.list

For folders [0,1,2..,22] with extracted CPMG interleaved spectra, containing test.ft2

A call to function could be:

#! /bin/csh -f
set x = 0;
while ( $x <= 22 )
        cd $x
        seriesTab -in ../peaks.dat -out ../peaks_${x}.ser -list ../files.list -sum -dx 1 -dy 1
        cd ..
        @ x = $x + 1
end

The output is:

REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser
REMARK Mode: Summation Dimensions: 2
REMARK Input Region:    X +/- 1 X-ZF: 3
REMARK Analysis Region: X +/- 1
REMARK Input Region:    Y +/- 1 Y-ZF: 3
REMARK Analysis Region: Y +/- 1
 
VARS   INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s %7.4f
 
NULLVALUE -666
NULLSTRING *
 
    1   246.658    18.268    9.932  128.374 +1.851056e+06 W62NE1-W62HE1 1.0000
    2   321.698    30.994    9.419  127.066 +3.224387e+05 L10N-L10HN  1.0000
    3   320.089    55.737    9.430  124.523 +1.479366e+06 V6N-V6HN  1.0000

An input reader is wished, which is auto detected like a SPARKY list. The format is quite similar to this.
This is an export from CcpNmr Analysis

      Assignment         w1         w2       Height       Volume
    W62NE1-W62HE1    128.374      9.932   0.00E+00   0.00E+00 --
       L10N-L10HN    127.066      9.419   0.00E+00   0.00E+00 --
         V6N-V6HN    124.523      9.430   0.00E+00   0.00E+00 --

See also