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Created page with "== seriesTab == [http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html seriesTab] can extract Max Values or Sum of regions in an NMRPipe-format Spectral Series, using an N..."
== seriesTab ==
[http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html seriesTab] can extract Max Values or Sum of regions in an NMRPipe-format
Spectral Series, using an NMRPipe-format Peak Table as Input.
See homepage<br>
http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html
A call to the function could be:
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
<source lang="text">
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
...
</source>
'''files.list''' contains
<source lang="text">
test.ft2
</source>
For folders [0,1,2..,22] with extracted CPMG interleaved spectra, containing '''test.ft2'''
A call to function could be:
<source lang="bash">
#! /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
</source>
The output is:
<source lang="text">
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
</source>
An input reader is wished, which is auto detected like a SPARKY list. The
format is quite similar to this. <br>
This is an export from CcpNmr Analysis
<source lang="text">
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 --
</source>
[http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html seriesTab] can extract Max Values or Sum of regions in an NMRPipe-format
Spectral Series, using an NMRPipe-format Peak Table as Input.
See homepage<br>
http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html
A call to the function could be:
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
<source lang="text">
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
...
</source>
'''files.list''' contains
<source lang="text">
test.ft2
</source>
For folders [0,1,2..,22] with extracted CPMG interleaved spectra, containing '''test.ft2'''
A call to function could be:
<source lang="bash">
#! /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
</source>
The output is:
<source lang="text">
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
</source>
An input reader is wished, which is auto detected like a SPARKY list. The
format is quite similar to this. <br>
This is an export from CcpNmr Analysis
<source lang="text">
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 --
</source>
