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problem in gnoesyNhsqc spectrum

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  • yunjun wang
    Hello, I have problem in processing a 3d gnoesyNhsqc recorded in Varian 800 using NMRpipe (Linux version). The peaks in HN-H plane are symetrically folded
    Message 1 of 3 , Mar 6, 2000
      Hello,

      I have problem in processing a 3d gnoesyNhsqc recorded
      in Varian 800 using NMRpipe (Linux version). The peaks
      in HN-H plane are symetrically folded about the water
      position and the peaks in HN-N plane are not clear.
      The scripts I used are as follows:

      var2pipe -in ./fid \
      -xN 896 -yN 256 -zN 64 \
      -xT 448 -yT 128 -zT 32 \
      -xMODE Complex -yMODE Complex -zMODE Complex \
      -xSW 8800.00 -ySW 8800.00 -zSW 2000 \
      -xOBS 799.907 -yOBS 799.907 -zOBS 81.79 \
      -xCAR 4.7 -yCAR 4.7 -zCAR 115.00000 \
      -xLAB HN -yLAB H -zLAB N \
      -ndim 3 -aq2D States -aqORD 0 \
      #| nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr
      \
      | pipe2xyz -out pipe-fid/3d%03d.fid -x -ov -to 0 -verb

      ================================================
      #!/bin/csh
      nmrPipe -fn SOL -in ./pipe-fid/3d001.fid \
      | nmrPipe -fn POLY -time \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -verb \
      | nmrPipe -fn PS -p0 -5.0 -p1 0.0 -di \
      | nmrPipe -fn EXT -x1 10.5PPM -xn 5.7PPM -sw \
      | nmrPipe -fn TP \
      #| nmrPipe -fn LP -pred 64 \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
      | nmrPipe -fn FT -verb \
      | nmrPipe -fn PS -p0 211.0 -p1 0 -di \
      | nmrPipe -fn POLY -auto \
      | nmrPipe -fn EXT -x1 10.5PPM -xn -1.2PPM -sw \
      | nmrPipe -fn TP \
      | nmrPipe -fn POLY -auto \
      #| nmrPipe -fn TP \
      -ov -out XY022.ft2
      =====================================================
      xyz2pipe -in pipe-fid/3d%03d.fid -x -verb \
      | nmrPipe -fn SOL \
      | nmrPipe -fn SP -off 0.333 -end 0.99 -pow 1 -c 1.0
      \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT \
      | nmrPipe -fn PS -p0 -5.0 -p1 0.0 \
      | nmrPipe -fn EXT -x1 10.5PPM -xn 5.5PPM -di -sw \
      | pipe2xyz -out DAT/3d_%03d.DAT -x -ov
      # Processing of F2 dimension (N) without LP
      xyz2pipe -in DAT/3d_%03d.DAT -z -verb \
      | nmrPipe -fn SP -off 0.5 -end 0.97 -pow 1 -c 1.0 \
      | nmrPipe -fn ZF -size 64 \
      | nmrPipe -fn FT -di \
      | pipe2xyz -out DAT/3d_%03d.DAT -z -inPlace
      # Processing of F1 dimension (H) with LP
      xyz2pipe -in DAT/3d_%03d.DAT -mem 8Mb -y -verb

      =================================================

      Any suggestions are highly appreciated!

      Yunjun Wang
      Stanford University
      Dept Molecular Pharmacology
      phone 650 725 1811
      email yunjunwang@...



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    • spin@thr.med.umn.edu
      Hello, ... I believe gnoesyNhsqc.c in Varian ProteinPack is a gradient sensitivity enhanced pulse sequence. You might want to try to uncomment the above line
      Message 2 of 3 , Mar 6, 2000
        Hello,

        > #| nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr \

        I believe gnoesyNhsqc.c in Varian ProteinPack is a gradient sensitivity
        enhanced pulse sequence. You might want to try to uncomment the
        above line when converting the Varin FID to nmrPipe format.

        > -ndim 3 -aq2D States -aqORD 0 \

        And probably you want to replace the "-aqORD 0" flag with "-aqORD
        1" assuming you array your 3D experiment using the order
        "d3,d2,phase,phase2"

        Shou-Lin
        ---
        Shou-Lin Chang
        312 Church St. S.E.
        5-258 Basic Sciences & Biomedical Engineering Building
        Department of Biochemistry, Molecular Biology
        and Biophysics, Medical School
        University of Minnesota at Twin Cities TEL(LAB):(612)625-8611
        Minneapolis, MN 55455 FAX(LAB):(612)624-5121
        EMAIL: chang033@...

        On Mon, 6 Mar 2000, yunjun wang wrote:

        > From: yunjun wang <yunjunwang@...>
        >
        > Hello,
        >
        > I have problem in processing a 3d gnoesyNhsqc recorded
        > in Varian 800 using NMRpipe (Linux version). The peaks
        > in HN-H plane are symetrically folded about the water
        > position and the peaks in HN-N plane are not clear.
        > The scripts I used are as follows:
        >
        > var2pipe -in ./fid \
        > -xN 896 -yN 256 -zN 64 \
        > -xT 448 -yT 128 -zT 32 \
        > -xMODE Complex -yMODE Complex -zMODE Complex \
        > -xSW 8800.00 -ySW 8800.00 -zSW 2000 \
        > -xOBS 799.907 -yOBS 799.907 -zOBS 81.79 \
        > -xCAR 4.7 -yCAR 4.7 -zCAR 115.00000 \
        > -xLAB HN -yLAB H -zLAB N \
        > -ndim 3 -aq2D States -aqORD 0 \
        > #| nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr
        > \
        > | pipe2xyz -out pipe-fid/3d%03d.fid -x -ov -to 0 -verb
        >
        > ================================================
        > #!/bin/csh
        > nmrPipe -fn SOL -in ./pipe-fid/3d001.fid \
        > | nmrPipe -fn POLY -time \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT -verb \
        > | nmrPipe -fn PS -p0 -5.0 -p1 0.0 -di \
        > | nmrPipe -fn EXT -x1 10.5PPM -xn 5.7PPM -sw \
        > | nmrPipe -fn TP \
        > #| nmrPipe -fn LP -pred 64 \
        > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
        > | nmrPipe -fn FT -verb \
        > | nmrPipe -fn PS -p0 211.0 -p1 0 -di \
        > | nmrPipe -fn POLY -auto \
        > | nmrPipe -fn EXT -x1 10.5PPM -xn -1.2PPM -sw \
        > | nmrPipe -fn TP \
        > | nmrPipe -fn POLY -auto \
        > #| nmrPipe -fn TP \
        > -ov -out XY022.ft2
        > =====================================================
        > xyz2pipe -in pipe-fid/3d%03d.fid -x -verb \
        > | nmrPipe -fn SOL \
        > | nmrPipe -fn SP -off 0.333 -end 0.99 -pow 1 -c 1.0
        > \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 -5.0 -p1 0.0 \
        > | nmrPipe -fn EXT -x1 10.5PPM -xn 5.5PPM -di -sw \
        > | pipe2xyz -out DAT/3d_%03d.DAT -x -ov
        > # Processing of F2 dimension (N) without LP
        > xyz2pipe -in DAT/3d_%03d.DAT -z -verb \
        > | nmrPipe -fn SP -off 0.5 -end 0.97 -pow 1 -c 1.0 \
        > | nmrPipe -fn ZF -size 64 \
        > | nmrPipe -fn FT -di \
        > | pipe2xyz -out DAT/3d_%03d.DAT -z -inPlace
        > # Processing of F1 dimension (H) with LP
        > xyz2pipe -in DAT/3d_%03d.DAT -mem 8Mb -y -verb
        >
        > =================================================
        >
        > Any suggestions are highly appreciated!
        >
        > Yunjun Wang
        > Stanford University
        > Dept Molecular Pharmacology
        > phone 650 725 1811
        > email yunjunwang@...
        >
        >
        >
        > __________________________________________________
        > Do You Yahoo!?
        > Talk to your friends online with Yahoo! Messenger.
        > http://im.yahoo.com
        >
        > ------------------------------------------------------------------------
        > MAXIMIZE YOUR CARD, MINIMIZE YOUR RATE!
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        > ------------------------------------------------------------------------
        >
        >
      • yunjun wang
        Hello Shou-Lin Chang, You are right, I modified the scripts as you suggested and now they work very well. Many thanks for your kind help ! Yunjun Wang Stanford
        Message 3 of 3 , Mar 7, 2000
          Hello Shou-Lin Chang,

          You are right, I modified the scripts as you suggested
          and now they work very well.

          Many thanks for your kind help !

          Yunjun Wang
          Stanford University
          Dept. Molecular Pharmocology
          phone 650 725 1811
          email yunjunwang@...

          --- spin@... wrote:
          > Hello,
          >
          > > #| nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd
          > -noWr \
          >
          > I believe gnoesyNhsqc.c in Varian ProteinPack is a
          > gradient sensitivity
          > enhanced pulse sequence. You might want to try to
          > uncomment the
          > above line when converting the Varin FID to nmrPipe
          > format.
          >
          > > -ndim 3 -aq2D States -aqORD 0
          > \
          >
          > And probably you want to replace the "-aqORD 0" flag
          > with "-aqORD
          > 1" assuming you array your 3D experiment using the
          > order
          > "d3,d2,phase,phase2"
          >
          > Shou-Lin
          > ---
          > Shou-Lin Chang
          > 312 Church St. S.E.
          > 5-258 Basic Sciences & Biomedical Engineering
          > Building
          > Department of Biochemistry, Molecular Biology
          > and Biophysics, Medical School
          > University of Minnesota at Twin Cities
          > TEL(LAB):(612)625-8611
          > Minneapolis, MN 55455 FAX(LAB):(612)624-5121
          > EMAIL: chang033@...
          >
          > On Mon, 6 Mar 2000, yunjun wang wrote:
          >
          > > From: yunjun wang <yunjunwang@...>
          > >
          > > Hello,
          > >
          > > I have problem in processing a 3d gnoesyNhsqc
          > recorded
          > > in Varian 800 using NMRpipe (Linux version). The
          > peaks
          > > in HN-H plane are symetrically folded about the
          > water
          > > position and the peaks in HN-N plane are not
          > clear.
          > > The scripts I used are as follows:
          > >
          > > var2pipe -in ./fid \
          > > -xN 896 -yN 256 -zN 64 \
          > > -xT 448 -yT 128 -zT 32 \
          > > -xMODE Complex -yMODE Complex -zMODE Complex \
          > > -xSW 8800.00 -ySW 8800.00 -zSW 2000 \
          > > -xOBS 799.907 -yOBS 799.907 -zOBS 81.79 \
          > > -xCAR 4.7 -yCAR 4.7 -zCAR 115.00000 \
          > > -xLAB HN -yLAB H -zLAB N \
          > > -ndim 3 -aq2D States -aqORD 0
          > \
          > > #| nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd
          > -noWr
          > > \
          > > | pipe2xyz -out pipe-fid/3d%03d.fid -x -ov -to 0
          > -verb
          > >
          > > ================================================
          > > #!/bin/csh
          > > nmrPipe -fn SOL -in ./pipe-fid/3d001.fid \
          > > | nmrPipe -fn POLY -time \
          > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0
          > \
          > > | nmrPipe -fn ZF -auto \
          > > | nmrPipe -fn FT -verb \
          > > | nmrPipe -fn PS -p0 -5.0 -p1 0.0 -di \
          > > | nmrPipe -fn EXT -x1 10.5PPM -xn 5.7PPM -sw \
          > > | nmrPipe -fn TP \
          > > #| nmrPipe -fn LP -pred 64 \
          > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0
          > \
          > > | nmrPipe -fn FT -verb \
          > > | nmrPipe -fn PS -p0 211.0 -p1 0 -di \
          > > | nmrPipe -fn POLY -auto \
          > > | nmrPipe -fn EXT -x1 10.5PPM -xn -1.2PPM -sw
          > \
          > > | nmrPipe -fn TP \
          > > | nmrPipe -fn POLY -auto \
          > > #| nmrPipe -fn TP \
          > > -ov -out XY022.ft2
          > >
          >
          =====================================================
          > > xyz2pipe -in pipe-fid/3d%03d.fid -x -verb \
          > > | nmrPipe -fn SOL \
          > > | nmrPipe -fn SP -off 0.333 -end 0.99 -pow 1 -c
          > 1.0
          > > \
          > > | nmrPipe -fn ZF -auto \
          > > | nmrPipe -fn FT \
          > > | nmrPipe -fn PS -p0 -5.0 -p1 0.0 \
          > > | nmrPipe -fn EXT -x1 10.5PPM -xn 5.5PPM -di -sw
          > \
          > > | pipe2xyz -out DAT/3d_%03d.DAT -x -ov
          > > # Processing of F2 dimension (N) without LP
          > > xyz2pipe -in DAT/3d_%03d.DAT -z -verb \
          > > | nmrPipe -fn SP -off 0.5 -end 0.97 -pow 1 -c 1.0
          > \
          > > | nmrPipe -fn ZF -size 64 \
          > > | nmrPipe -fn FT -di \
          > > | pipe2xyz -out DAT/3d_%03d.DAT -z -inPlace
          > > # Processing of F1 dimension (H) with LP
          > > xyz2pipe -in DAT/3d_%03d.DAT -mem 8Mb -y -verb
          > >
          > > =================================================
          > >
          > > Any suggestions are highly appreciated!
          > >
          > > Yunjun Wang
          > > Stanford University
          > > Dept Molecular Pharmacology
          > > phone 650 725 1811
          > > email yunjunwang@...
          > >
          > >
          > >
          > > __________________________________________________
          > > Do You Yahoo!?
          > > Talk to your friends online with Yahoo! Messenger.
          > > http://im.yahoo.com
          > >
          > >
          >
          ------------------------------------------------------------------------
          > > MAXIMIZE YOUR CARD, MINIMIZE YOUR RATE!
          > > Get a NextCard Visa, in 30 seconds! Get rates as
          > low as
          > > 0.0% Intro or 9.9% Fixed APR and no hidden fees.
          > > Apply NOW!
          > >
          >
          http://click.egroups.com/1/2122/1/_/503776/_/952379901/
          > >
          >
          ------------------------------------------------------------------------
          > >
          > >
          >
          >
          __________________________________________________
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