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[Q] gnoesyChsqc Varian NMR data processing using NMRPipe

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  • solwind@biochem.yonsei.ac.kr
    Hi, I have got some wierd processed data as followed; A gnoesyChsqc experiment with a 13C,15N double labeled protein in D2O solution was performed using Varian
    Message 1 of 1 , Apr 24, 2001
      Hi,

      I have got some wierd processed data as followed;

      A gnoesyChsqc experiment with a 13C,15N double labeled protein in D2O
      solution was performed using Varian Inova 500.

      After the experiment, I checked the data using VNMR software, and
      everything is all right.

      However, I found out that spectra were folded when fid data were
      processed using nmrPipe.

      In the spectra, axis-X(HN) and axix-Z(13C) were correct.
      The axis-Y(1H) were folded at the 4.7ppm (probably the H2O
      resonance), so the region in -2~4.7 ppm located in down-field, the
      region in 4.7~12 ppm located in up-field.

      The used nmrPipe process files are followed.>

      #!/bin/csh
      var2pipe -in ./fid \
      -xN 1024 -yN 192 -zN 88 \
      -xT 512 -yT 96 -zT 44 \
      -xMODE Complex -yMODE States-TPPI -zMODE States-TPPI \
      -xSW 8000.000 -ySW 8000.000 -zSW 10057.833 \
      -xOBS 499.954 -yOBS 499.954 -zOBS 125.717 \
      -xCAR 4.773 -yCAR 4.773 -zCAR 37.276 \
      -xLAB HN -yLAB H1 -zLAB C13 \
      -ndim 3 -aq2D States \
      -out ./data2/test%03d.fid -verb -ov
      sleep 5


      xyz2pipe -in ./data/test%03d.fid -x -verb \
      | nmrPipe -fn SOL \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
      | nmrPipe -fn ZF -size 2048 \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 -72 -p1 0 \
      | nmrPipe -fn POLY -ord 0 -auto \
      | nmrPipe -fn EXT -x1 -2.0PPM -xn 6.5PPM -di -sw \
      | nmrPipe -fn TP \
      | nmrPipe -fn SP -off 0.45 -end 0.98 -pow 2 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -alt \
      | nmrPipe -fn PS -p0 -90.0 -p1 180.0 -di -sw \
      | nmrPipe -fn POLY -ord 0 -auto \
      | pipe2xyz -out ./ft2/testC%03d.ft2 -y -ov

      xyz2pipe -in ./ft2/testC%03d.ft2 -z -verb \
      | nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -alt \
      | nmrPipe -fn PS -p0 -90.0 -p1 180.0 -di \
      | nmrPipe -fn POLY -ord 0 -auto \
      | nmrPipe -fn REV \
      | pipe2xyz -out ./ft2/resultsC%03d.ft3 -z -inPlace

      Please let me know the origin of problem and fix the problem.

      Thank you.
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