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Re: [nmrpipe] N15 HSQC_IPAP scripts

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  • Frank Delaglio
    IPAP conversion and processing schemes can differ substantially based on: 1. Whether the data are gradient enhanced. 2. Whether the IP/AP loop is the innermost
    Message 1 of 4 , Apr 28, 2003
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      IPAP conversion and processing schemes can differ substantially
      based on:

      1. Whether the data are gradient enhanced.

      2. Whether the IP/AP loop is the innermost one of the pulse sequence,
      or the real/imaginary loop is the inner one.

      Generally, the nmrPipe function "COADD" is used to select or combine
      the IP/AP channels.

      I find it helpful to process the IP and AP channels separately,
      and then combine them after processing. This makes it possible
      to inspect the data to choose a scaling factor that will lead
      to the best IP/AP cancelation.

      The stand-alone program "addNMR" can also be used to re-combine
      processed IP or AP data.

      Some examples are below.


      Cheerful Regards,

      big fd

      -------------------------------------------------------------------------
      If the IP/AP channel is in the innermost loop, the selection or
      combination of AP/IP data should be done at the start of processing:

      nmrPipe -in ./test.fid \
      | nmrPipe -fn COADD -cList 1 -1.11 -axis Y -time \
      | nmrPipe -fn SP -off 0.4 -end 0.98 -pow 2.0 -c 1.0 \
      | nmrPipe -fn ZF -size 4096 \
      | nmrPipe -fn FT -verb \
      | nmrPipe -fn PS -p0 -80.0 -p1 -180.0 -di \
      | nmrPipe -fn EXT -x1 10ppm -xn 6.0ppm -sw \
      | nmrPipe -fn TP \
      | nmrPipe -fn SP -off 0.4 -end 0.98 -pow 1.0 -c 1 \
      | nmrPipe -fn ZF -size 4096 \
      | nmrPipe -fn FT -verb \
      | nmrPipe -fn PS -p0 -90 -p1 180.0 -di \
      | nmrPipe -fn CS -rs -1ppm -neg -sw \
      | nmrPipe -fn TP \
      -ov -out A-B.DAT

      -------------------------------------------------------------------------
      If the IP/AP loop is outside the real/imaginary loop, the selection
      of combination of AP/IP data should be done after the direct dimension
      is processed.

      Note that in this case, one IP/AP channel is 90 degrees out of phase
      with respect to the other:

      #!/bin/csh

      var2pipe -in ./fid -noaswap \
      -xN 1024 -yN 484 \
      -xT 512 -yT 242 \
      -xMODE Complex -yMODE Complex \
      -xSW 6999.738 -ySW 2000.000 \
      -xOBS 499.628 -yOBS 50.633 \
      -xCAR 4.773 -yCAR 118.860 \
      -xLAB HN -yLAB N \
      -ndim 2 -aq2D States \
      -out ./test.fid -verb -ov

      nmrPipe -in test.fid \
      | nmrPipe -fn SOL \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 177 -p1 0.0 -di \
      | nmrPipe -fn EXT -left -sw -verb \
      | nmrPipe -fn TP \
      | nmrPipe -fn COADD -cList 1 0 -time \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 0 -p1 0 -di \
      | nmrPipe -fn TP \
      | nmrPipe -fn POLY -auto \
      -verb -ov -out A.ft2

      nmrPipe -in test.fid \
      | nmrPipe -fn SOL \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 177 -p1 0.0 -di \
      | nmrPipe -fn EXT -left -sw -verb \
      | nmrPipe -fn TP \
      | nmrPipe -fn COADD -cList 0 1 -time \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 -90 -p1 0 -di \
      | nmrPipe -fn TP \
      | nmrPipe -fn POLY -auto \
      -verb -ov -out B.ft2

      addNMR -in1 A.ft2 -in2 B.ft2 -out A+B.ft2 -c1 1.0 -c2 1.25 -add
      addNMR -in1 A.ft2 -in2 B.ft2 -out A-B.ft2 -c1 1.0 -c2 1.25 -sub
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