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How does padding and shifting affect inverse transforming?

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  • Norma Pawley
    Greetings all, I have some data with odd phasing that was cured using the combination of a one-point shift followed by zero-order phase correction, as
    Message 1 of 9 , Dec 2, 2002
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      Greetings all,

      I have some data with odd phasing that was "cured" using the combination of a one-point shift followed by zero-order phase correction, as suggested in the manual.  Nice results are obtained when linear prediction is done in each dimension sequentially.

      On the other hand, when the N dimension is inverse transformed, linear-predicted and re-transformed, trouble ensues.  At point   43 in the Z (13C) dimension, the processed spectrum suddenly undergoes a shift in the proton dimension.  I assume the shift occurs at 43 since there were originally 42 planes.   The script used is shown below -- suggestions on how to fix are welcome.

      Thanks in advance,

      Norma Pawley

      #!/bin/csh

      xyz2pipe -in fid/new_hncaco%03d.fid -x  -verb       \
      | 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 53.8  -p1 0.0 -di             \
      | nmrPipe  -fn EXT -x1 5.5ppm -xn 10.5ppm -sw -verb \
      | pipe2xyz -out ft/test%03d.ft3 -x

      xyz2pipe -in ft/test%03d.ft3 -y -verb               \
      | nmrPipe  -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5  \
      | nmrPipe  -fn ZF -auto                             \
      | nmrPipe  -fn FT                                   \
      | nmrPipe  -fn PS -p0 181.0 -p1 0.0 -di             \
      | pipe2xyz -out ft/test%03d.ft3 -y -inPlace

      xyz2pipe -in ft/test%03d.ft3 -z -verb               \
      | nmrPipe  -fn ZF -pad 1                            \
      | nmrPipe  -fn RS -rs 1 -sw                         \
      | nmrPipe  -fn LP -fb                                    \
      | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 1    \
      | nmrPipe  -fn ZF -auto                             \
      | nmrPipe  -fn FT                                   \
      | nmrPipe  -fn PS -p0 27.2 -p1 -137.0 -di           \
      | nmrPipe  -fn POLY -auto -ord 0                    \
      | pipe2xyz -out ft/test%03d.ft3 -z -inPlace

      xyz2pipe -in ft/test%03d.ft3 -y -verb               \
      | nmrPipe  -fn HT  -auto                            \
      | nmrPipe  -fn PS  -inv -hdr                        \
      | nmrPipe  -fn FT  -inv                             \
      | nmrPipe  -fn ZF  -inv                             \
      | nmrPipe  -fn SP  -inv -hdr                        \
      | nmrPipe  -fn LP  -fb                              \
      | nmrPipe  -fn SP  -hdr                             \
      | nmrPipe  -fn ZF  -auto                            \
      | nmrPipe  -fn FT                                   \
      | nmrPipe  -fn PS  -hdr -di                         \
      | pipe2xyz -out ft/test%03d.ft3 -y -inPlace

    • Frank Delaglio
      xyz2pipe -in ft/test%03d.ft3 -z -verb ... The ZF/RS step at the start shifts the FID and introduces a zero as the first point in the FID. The
      Message 2 of 9 , Dec 3, 2002
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        xyz2pipe -in ft/test%03d.ft3 -z -verb \
        | nmrPipe -fn ZF -pad 1 \
        | nmrPipe -fn RS -rs 1 -sw \
        | nmrPipe -fn LP -fb \
        | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT \
        | nmrPipe -fn PS -p0 27.2 -p1 -137.0 -di \
        | nmrPipe -fn POLY -auto -ord 0 \
        | pipe2xyz -out ft/test%03d.ft3 -z -inPlace

        The ZF/RS step at the start shifts the FID and introduces a zero as the
        first point in the FID. The shift is equivalent to adding P1 of 360 later.
        But, the intensity of the first point of the FID is still "missing".

        The LP step extends the data; but the result might be somewhat
        distorted because of the missing intensity.

        Also, even without LP, the final result will be baseline distorted,
        because the actual phase correction is P1 = 360 - 137, which does
        not correspond exactly with a zero-order offset in the spectrum.

        A simple alternative might be as follows, although depending on the data,
        the automated baseline correction might not be beautiful:

        xyz2pipe -in ft/test%03d.ft3 -z -verb \
        | nmrPipe -fn LP -fb \
        | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT \
        | nmrPipe -fn PS -p0 27.2 -p1 223 -di \
        | nmrPipe -fn POLY -auto \
        | pipe2xyz -out ft/test%03d.ft3 -z -inPlace

        The best way to combat this problem is to set the delays carefully
        so that they always correspond to P1 of 0, 180, or 360.
      • Norma Pawley
        Greetings All, Is there a way to print peak labels from nmrDraw? (One web-site says no, but I m hoping they re wrong.) Currently, I m using snapshot, which is
        Message 3 of 9 , Jan 29, 2003
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          Greetings All,

          Is there a way to print peak labels from nmrDraw?  (One web-site says no, but I'm hoping they're wrong.) Currently, I'm using snapshot, which is a non-optimal solution.  I'd prefer not to use an additional program (such as pipp or Sparky), but will if necessary.

          Thanks in advance,

          Norma Pawley
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