Question

I have a 2D complex time domain set stored in ASCII format. I want to be able to process it using nmrPipe. Unfortunately I am running into trouble once I try to use txt2pipe.tcl macro from the nmrPipe package. By convention it assumes that the data is in frequency domain and is real. The conversion into the time domain can be achieved by setting the headers correctly, however the 2D acqusition mode not as easily (Comlex/States/Rance-Kay etc. ). Here is the header I use before FT'ing:

sethdr test.fid -ndim 2 -aq2D States -xFT Time -xMODE Complex \
        -xT 1024 -xN 512 -yFT Time -yMODE Complex -yT 256 -xN 128

Also the way the data is stored is as the following (with 4 spacing in between parameters):

1 1 1 Re[1,1] ! N-type

2 1 1 Re[1,1]

3 1 1 Re[1,1]

...

512 1 1 Re[1,1]

513 1 1 Im[1,1]

...

1024 1 1 Im[1,1]

1 2 1 Re[1,1]* ! P-type

2 2 1 Re[1,1]*

3 2 1 Re[1,1]*

...

512 2 1 Re[1,1]*

513 2 1 Im[1,1]*

...

1024 2 1 Im[1,1]*

. . .

1 256 1 Re[1,1]*

2 256 1 Re[1,1]*

3 256 1 Re[1,1]*

...

512 256 1 Re[1,1]*

513 256 1 Im[1,1]*

...

1024 256 1 Im[1,1]*

I would appreciate it if anyone can point me out whether there is something wrong with the header or the way the data is stored, or even whether it is possible to do with nmrDraw or not.

Thanks, Hasan Celik

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There are many ways to do this.

As described, this data happens already to be in the data order that an NMRPipe hypercomplex FID is stored. So, a simple approach might be to convert the data directly to binary, and add an appropriate NMRPipe header.

According to the info above, the data input has four columns (0 1 2 3) with the actual FID intensities in column 3. And the text file should have 1024*256 = 262144 lines.

For example, if the input text file is "fid.txt":

getCols fid.txt col.txt 3

txt2bin.tcl < col.txt > col.bin

bin2pipe -noIn -noOut \
  -xN              1024  -yN               256  \
  -xT               512  -yT               128  \
  -xMODE        Complex  -yMODE        Complex  \
  -xSW        10000.000  -ySW        10000.000  \
  -xOBS         500.000  -yOBS         500.000  \
  -xCAR           4.700  -yCAR           4.700  \
  -xLAB              F2  -yLAB              F1  \
  -ndim               2  -aq2D          States  \
  -out hdr.dat -verb -ov

cat hdr.dat col.bin > test.fid

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answered Dec 10 '09 at 00:34

delaglio
136●1

updated Dec 10 '09 at 07:00

Evgeny Fadeev
577●1

Thanks a lot for the help, Frank. It works as intended. - hasancelik (Dec 11 '09 at 07:06)

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