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IPAP-processing

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  • LIU Changdong
    Dear all: I run IPAP-HSQC for measure RDC on Varian machine. After processed data using below script. the inphase spectrum is ok,but there is some strong
    Message 1 of 5 , Jan 8, 2009
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      Dear all:
      I run IPAP-HSQC for measure RDC on Varian machine. After processed data using below script. the inphase spectrum is ok,but there is  some strong artifical peak in the antiphase spectrum(please see pics in attachment) .I tried many times but no improvement. Please give some suggestions.
      Thanks in advance.

      Best
      #!/bin/csh

      nmrPipe -in test.fid \
      | nmrPipe -fn SOL \
      | nmrPipe -fn GM -g1 12 -g2 20 -c 0.5 \
      #| 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 127 -p1 0.0 -di \
      | nmrPipe -fn POLY  auto  \
      | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw  \
      | nmrPipe -fn TP \
      | nmrPipe -fn COADD -cList 1 0 -time \
      | nmrPipe -fn LP -fb -ord 16 -pred 76 \
      | nmrPipe -fn GM -g1 5 -g2 10 -c 1.0  \
      #| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -size 2048 \
      | 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 GM -g1 12 -g2 20 -c 0.5 \
      #| 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 127 -p1 0.0 -di \
      | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw  \
      | nmrPipe -fn POLY -auto   \
      | nmrPipe -fn TP \
      | nmrPipe -fn COADD -cList 0 1 -time \
      | nmrPipe -fn LP -fb -ord 16 -pred 76 \
      | nmrPipe -fn GM -g1 5 -g2 10 -c 1.0  \
      #| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -size 2048 \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 -87.8 -p1 0 -di \
      | 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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    • jamesswarbrick
      Hi there a few things you may have/could check .... 1) I d not do POLY in the real dimension til after you have processed the indirect especially if you are
      Message 2 of 5 , Jan 9, 2009
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        Hi there
        a few things you may have/could check ....

        1) I'd not do POLY in the real dimension 'til after you have processed
        the indirect especially if you are linear predicting etc
        and prob not POLY on the indirect. You are probably getting baseline
        distortion and doing POLY owing to ->
        2) you really using f1180='y' ?? as you have put the first point
        scaling as 1 (c=1.0) in the indirect dimension. If f1180='n' then you
        should have c=0.5 always otherwise you'll get streaky F1.
        3) do you really want to predict that many points? remember that the
        S/N is important in determining the peak centre and judging from the
        quality of your data think S/N is pretty important and if you predict
        the S/N may take a hit depending on the number of points. (Peak
        accuracy prop to SN/LW)
        4)perhaps use a simple cosine window in the indirect to keep the S/N
        up but maybe keep the Gaussian in the real - or at least not as harsh
        in the indirect say g1 15 g2 20? - which will still disguise your
        annoying homonuclear couplings :)
        5) you prob 'shouldn't' zero fill so much in the indirect but use a
        peak picker to curve fit over "real points", rather than over zero
        filled ones.
        but you see this....depending how you are going to peak pick I guess.
        6) you could even try removing the SOL and just use nmrPipe -fn POLY -time
        or nothing and see what it looks like.

        i.e. something like..

        nmrPipe -in test.fid \
        | nmrPipe -fn POLY -time \
        | nmrPipe -fn GM -g1 12 -g2 20 -c 0.5 \
        | nmrPipe -fn ZF -size 2048 \
        | nmrPipe -fn FT \
        | nmrPipe -fn PS -p0 127 -p1 0.0 -di \
        | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw \
        | nmrPipe -fn TP \
        | nmrPipe -fn COADD -cList 0 1 -time \
        #| nmrPipe -fn LP -fb -ord 16 -pred 76 \
        | nmrPipe -fn GM -g1 15 -g2 20 -c 0.5 \
        | nmrPipe -fn ZF -size 1024 \
        | nmrPipe -fn FT \
        | nmrPipe -fn PS -p0 -87.8 -p1 0 -di \
        | nmrPipe -fn TP \
        | nmrPipe -fn POLY -auto \
        -verb -ov -out B.ft2


        cheers
        James
        James Swarbrick PhD
        Lecturer in Medicinal Chemistry
        Monash University
        Parkville







        --- In nmrpipe@yahoogroups.com, LIU Changdong <dongyi2827@...> wrote:
        >
        > Dear all:
        > I run IPAP-HSQC for measure RDC on Varian machine. After processed
        data using below script. the inphase spectrum is ok,but there is some
        strong artifical peak in the antiphase spectrum(please see pics in
        attachment) .I tried many times but no improvement. Please give some
        suggestions.
        > Thanks in advance.
        >
        > Best
        > #!/bin/csh
        >
        > nmrPipe -in test.fid \
        > | nmrPipe -fn SOL \
        > | nmrPipe -fn GM -g1 12 -g2 20 -c 0.5 \
        > #| 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 127 -p1 0.0 -di \
        > | nmrPipe -fn POLY auto \
        > | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw \
        > | nmrPipe -fn TP \
        > | nmrPipe -fn COADD -cList 1 0 -time \
        > | nmrPipe -fn LP -fb -ord 16 -pred 76 \
        > | nmrPipe -fn GM -g1 5 -g2 10 -c 1.0 \
        > #| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
        > | nmrPipe -fn ZF -size 2048 \
        > | 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 GM -g1 12 -g2 20 -c 0.5 \
        > #| 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 127 -p1 0.0 -di \
        > | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw \
        > | nmrPipe -fn POLY -auto \
        > | nmrPipe -fn TP \
        > | nmrPipe -fn COADD -cList 0 1 -time \
        > | nmrPipe -fn LP -fb -ord 16 -pred 76 \
        > | nmrPipe -fn GM -g1 5 -g2 10 -c 1.0 \
        > #| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
        > | nmrPipe -fn ZF -size 2048 \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 -87.8 -p1 0 -di \
        > | 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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        >
      • jamil saad
        Try this macro. Use -cList 1 1 for inphase and -cList 1 -1 for antiphase.. ... #!/bin/sh nmrPipe -in 50-HN-IPAP-test.fid ... -out 50-HN-IPAP-test-AP.ft -verb
        Message 3 of 5 , Jan 12, 2009
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          Try this macro.
          Use -cList 1 1 for inphase and -cList 1 -1 for antiphase.
          ------------------------------------------
          #!/bin/sh

          nmrPipe -in 50-HN-IPAP-test.fid \
          | nmrPipe -fn COADD -axis Y -cList 1 1 \
          | nmrPipe -fn SOL \
          | nmrPipe -fn SP -off 0.4 -end 1.0 -pow 2 \
          | nmrPipe -fn ZF -size 2048 \
          | nmrPipe -fn FT -auto \
          | nmrPipe -fn PS -p0 -218 -p1 0 -di \
          | nmrPipe -fn EXT -x1 11ppm -xn 6.0ppm -sw \
          | nmrPipe -fn TP \
          | nmrPipe -fn SP -off 0.4 -pow 2 -end \
          | nmrPipe -fn ZF \
          | nmrPipe -fn FT -auto \
          | nmrPipe -fn PS -p0 -90 -p1 180 -di \
          | nmrPipe -fn TP \
           -out 50-HN-IPAP-test-AP.ft -verb -ov



          From: LIU Changdong <dongyi2827@...>
          To: nmrpipe@yahoogroups.com
          Sent: Friday, January 9, 2009 12:37:06 AM
          Subject: [nmrpipe] IPAP-processing

          Dear all:
          I run IPAP-HSQC for measure RDC on Varian machine. After processed data using below script. the inphase spectrum is ok,but there is  some strong artifical peak in the antiphase spectrum(please see pics in attachment) .I tried many times but no improvement. Please give some suggestions.
          Thanks in advance.

          Best
          #!/bin/csh

          nmrPipe -in test.fid \
          | nmrPipe -fn SOL \
          | nmrPipe -fn GM -g1 12 -g2 20 -c 0.5 \
          #| 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 127 -p1 0.0 -di \
          | nmrPipe -fn POLY  auto  \
          | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw  \
          | nmrPipe -fn TP \
          | nmrPipe -fn COADD -cList 1 0 -time \
          | nmrPipe -fn LP -fb -ord 16 -pred 76 \
          | nmrPipe -fn GM -g1 5 -g2 10 -c 1.0  \
          #| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
          | nmrPipe -fn ZF -size 2048 \
          | 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 GM -g1 12 -g2 20 -c 0.5 \
          #| 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 127 -p1 0.0 -di \
          | nmrPipe -fn EXT -x1 6.5ppm -xn 10.5ppm -sw  \
          | nmrPipe -fn POLY -auto   \
          | nmrPipe -fn TP \
          | nmrPipe -fn COADD -cList 0 1 -time \
          | nmrPipe -fn LP -fb -ord 16 -pred 76 \
          | nmrPipe -fn GM -g1 5 -g2 10 -c 1.0  \
          #| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
          | nmrPipe -fn ZF -size 2048 \
          | nmrPipe -fn FT \
          | nmrPipe -fn PS -p0 -87.8 -p1 0 -di \
          | 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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