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Re: [nmrpipe] Mirror Image in gNhsqcnoesyNhsqc

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  • Siddhartha Sarma
    Try y= states-tppi and z=rance/kay. it should work. cheers Siddhartha ... -- Siddhartha P. Sarma Assistant Professor Molecular Biophysics Unit Indian
    Message 1 of 8 , Mar 31, 2004
      Try y= states-tppi and z=rance/kay. it should work.

      cheers

      Siddhartha



      On Thu, 1 Apr 2004, Yufeng wrote:

      > Well, this time it's me ...
      >
      > I used BioPack on Vnmr6.1C for a gNhsqcnoesyNhsqc experiments and acquired a 3D H-N-N spectra.
      > But the xy or xz planes I processed are just mirrored image spectra along carrier frequencies.
      > I tried yMode=Complex/Rance-Kay zMode=complex/Rance-Kay to convert but it doesn't work. Processing
      > scripts use FT -auto options.
      >
      > Is this spectra a doubly sensitivity-enhanced one?
      >
      > Any hints appreciated.
      >
      > Yufeng
      >
      > = = = = = = = = = = = = = = = = = = = =
      >
      > Yufeng Tong
      > Dept. Physiol. & Biophys.
      > Case Western Reserve Univ.
      > Cleveland, Ohio 44106
      > Tel: (216)368-8654 (O)
      > _______________________________________________________________________________
      > Life is an everlasting game of Weiqi(igo, baduk).
      >
      >
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >
      >

      --
      Siddhartha P. Sarma
      Assistant Professor
      Molecular Biophysics Unit
      Indian Institute of Science
      Bangalore, Karnataka - 560 012
      INDIA

      Tel: 80-2932839
      80-2932713
      Fax: 80-3600535
    • Vitaliy Gorbatyuk
      It is a problem of nmrPipe. It seems nmrPipe can not transform properly an experiment collected with sensitivity enhanced mode in two dimesions, i.e.
      Message 2 of 8 , Apr 1, 2004
        It is a problem of nmrPipe. It seems nmrPipe can not transform properly an
        experiment collected with
        sensitivity enhanced mode in two dimesions, i.e. yMode=Rance-Kay and
        zMode=Rance-Kay do not
        do their job simultaneously. You may check it by running the script and see
        if nmrPipe invokes a macro
        for shuffling in both dimensions. My version of nmrPipe does it only for
        one dimension. So you need to
        shuffle manually for other dimension:

        var2pipe -in ./fid \
        -xN 1024 -yN 256 -zN 146 \
        -xT 512 -yT 128 -zT 73 \
        -xMODE Complex -yMODE Complex -zMODE Rance-Kay \
        -xSW 5767.0127 -ySW 5767.0127 -zSW 9269.9884 \
        -xOBS 599.3871 -yOBS 599.3871 -zOBS 150.7156 \
        -xCAR 4.716 -yCAR 4.716 -zCAR 40.75 \
        -xLAB 1H -yLAB 1Hind -zLAB 13C \
        -ndim 3 -aq2D States \
        | nmrPipe -fn MAC -macro $NMRTXT/var_ranceY.M -noRd -noWr \
        | pipe2xyz -out ./data/fid%03d.pipe -verb -ov

        Good luck,

        VG





        From: "Yufeng" <crystalatom@...>
        Reply-To: nmrpipe@yahoogroups.com
        To: "nmrpipe@yahoogroups.com" <nmrpipe@yahoogroups.com>
        Subject: [nmrpipe] Mirror Image in gNhsqcnoesyNhsqc
        Date: Thu, 1 Apr 2004 05:05:34 +0800

        Well, this time it's me ...

        I used BioPack on Vnmr6.1C for a gNhsqcnoesyNhsqc experiments and acquired a
        3D H-N-N spectra.
        But the xy or xz planes I processed are just mirrored image spectra along
        carrier frequencies.
        I tried yMode=Complex/Rance-Kay zMode=complex/Rance-Kay to convert but it
        doesn't work. Processing
        scripts use FT -auto options.

        Is this spectra a doubly sensitivity-enhanced one?

        Any hints appreciated.

        Yufeng

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

        Yufeng Tong
        Dept. Physiol. & Biophys.
        Case Western Reserve Univ.
        Cleveland, Ohio 44106
        Tel: (216)368-8654 (O)
        _______________________________________________________________________________
        Life is an everlasting game of Weiqi(igo, baduk).



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      • Frank Delaglio
        Hi All ... Yes, it s true that the conversion software can accept either -yMODE Rance-Kay or -zMODE Rance-Kay but not both together. Why? Because there is
        Message 3 of 8 , Apr 1, 2004
          Hi All ...

          Yes, it's true that the conversion software can accept either
          "-yMODE Rance-Kay" or "-zMODE Rance-Kay" but not both together.

          Why? Because there is not one single shuffling scheme that is suitable
          for this special double-enhanced data.

          In some cases, a combination of the usual Y-axis and Z-axis shuffling
          scripts will work. In other cases we've seen, we had to make a special
          compostite script "ranceYZ.M", as used below ...

          cheerful regards,
          f

          var2pipe -in ./fid -aqORD 1 \
          -xN 1024 -yN 256 -zN 72 \
          -xT 512 -yT 128 -zT 36 \
          -xMODE Complex -yMODE Complex -zMODE Complex \
          -xSW 6999.738 -ySW 5500.000 -zSW 4199.916 \
          -xOBS 600.046 -yOBS 600.046 -zOBS 150.888 \
          -xCAR 4.630 -yCAR 4.630 -zCAR 46.327 \
          -xLAB H-acq -yLAB H-ind -zLAB C \
          -ndim 3 -aq2D States \
          | nmrPipe -fn MAC -macro $NMRTXT/var_ranceYZ.M -noRd -noWr \
          | nmrPipe -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr \
          | pipe2xyz -out ./data/test%03d.fid -verb -to 0



          On Thu, 1 Apr 2004, Vitaliy Gorbatyuk wrote:

          > It is a problem of nmrPipe. It seems nmrPipe can not transform properly an
          > experiment collected with
          > sensitivity enhanced mode in two dimesions, i.e. yMode=Rance-Kay and
          > zMode=Rance-Kay do not
          > do their job simultaneously. You may check it by running the script and see
          > if nmrPipe invokes a macro
          > for shuffling in both dimensions. My version of nmrPipe does it only for
          > one dimension. So you need to
          > shuffle manually for other dimension:
          >
          > var2pipe -in ./fid \
          > -xN 1024 -yN 256 -zN 146 \
          > -xT 512 -yT 128 -zT 73 \
          > -xMODE Complex -yMODE Complex -zMODE Rance-Kay \
          > -xSW 5767.0127 -ySW 5767.0127 -zSW 9269.9884 \
          > -xOBS 599.3871 -yOBS 599.3871 -zOBS 150.7156 \
          > -xCAR 4.716 -yCAR 4.716 -zCAR 40.75 \
          > -xLAB 1H -yLAB 1Hind -zLAB 13C \
          > -ndim 3 -aq2D States \
          > | nmrPipe -fn MAC -macro $NMRTXT/var_ranceY.M -noRd -noWr \
          > | pipe2xyz -out ./data/fid%03d.pipe -verb -ov
          >
          > Good luck,
          >
          > VG
          >
          >
          >
          >
          >
          > From: "Yufeng" <crystalatom@...>
          > Reply-To: nmrpipe@yahoogroups.com
          > To: "nmrpipe@yahoogroups.com" <nmrpipe@yahoogroups.com>
          > Subject: [nmrpipe] Mirror Image in gNhsqcnoesyNhsqc
          > Date: Thu, 1 Apr 2004 05:05:34 +0800
          >
          > Well, this time it's me ...
          >
          > I used BioPack on Vnmr6.1C for a gNhsqcnoesyNhsqc experiments and acquired a
          > 3D H-N-N spectra.
          > But the xy or xz planes I processed are just mirrored image spectra along
          > carrier frequencies.
          > I tried yMode=Complex/Rance-Kay zMode=complex/Rance-Kay to convert but it
          > doesn't work. Processing
          > scripts use FT -auto options.
          >
          > Is this spectra a doubly sensitivity-enhanced one?
          >
          > Any hints appreciated.
          >
          > Yufeng
          >
          > = = = = = = = = = = = = = = = = = = = =
          >
          > Yufeng Tong
          > Dept. Physiol. & Biophys.
          > Case Western Reserve Univ.
          > Cleveland, Ohio 44106
          > Tel: (216)368-8654 (O)
          > _______________________________________________________________________________
          > Life is an everlasting game of Weiqi(igo, baduk).
          >
          >
          >
          > ------------------------ Yahoo! Groups Sponsor ---------------------~-->
          > Buy Ink Cartridges or Refill Kits for your HP, Epson, Canon or Lexmark
          > Printer at MyInks.com. Free s/h on orders $50 or more to the US &
          > Canada.
          > http://www.c1tracking.com/l.asp?cid=5511
          > http://us.click.yahoo.com/mOAaAA/3exGAA/qnsNAA/cEYolB/TM
          > ---------------------------------------------------------------------~->
          >
          >
          > Yahoo! Groups Links
          >
          > <*> To visit your group on the web, go to:
          > http://groups.yahoo.com/group/nmrpipe/
          >
          > <*> To unsubscribe from this group, send an email to:
          > nmrpipe-unsubscribe@yahoogroups.com
          >
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          > access.
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          > Yahoo! Groups Links
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        • Yufeng
          Thanks Frank & Vitaliy, I tried but the result seems to be the same. If you have time, could you please have a look at
          Message 4 of 8 , Apr 1, 2004
            Thanks Frank & Vitaliy,

            I tried but the result seems to be the same.
            If you have time, could you please have a look at

            http://mbalster.cwru.edu/questions/gNhsqcnoesyNhsqc.fid/

            the .tgz file is the gzipped tarball of the data and scripts under that directory.

            others are self-explaining.

            Yufeng



            ======= 2004-04-02 06:24:53 You wrote =======

            >
            >Hi All ...
            >
            >Yes, it's true that the conversion software can accept either
            >"-yMODE Rance-Kay" or "-zMODE Rance-Kay" but not both together.
            >
            >Why? Because there is not one single shuffling scheme that is suitable
            >for this special double-enhanced data.
            >
            >In some cases, a combination of the usual Y-axis and Z-axis shuffling
            >scripts will work. In other cases we've seen, we had to make a special
            >compostite script "ranceYZ.M", as used below ...
            >
            >cheerful regards,
            >f
            >
            >var2pipe -in ./fid -aqORD 1 \
            > -xN 1024 -yN 256 -zN 72 \
            > -xT 512 -yT 128 -zT 36 \
            > -xMODE Complex -yMODE Complex -zMODE Complex \
            > -xSW 6999.738 -ySW 5500.000 -zSW 4199.916 \
            > -xOBS 600.046 -yOBS 600.046 -zOBS 150.888 \
            > -xCAR 4.630 -yCAR 4.630 -zCAR 46.327 \
            > -xLAB H-acq -yLAB H-ind -zLAB C \
            > -ndim 3 -aq2D States \
            >| nmrPipe -fn MAC -macro $NMRTXT/var_ranceYZ.M -noRd -noWr \
            >| nmrPipe -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr \
            >| pipe2xyz -out ./data/test%03d.fid -verb -to 0
            >
            >
            >

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

            Yufeng Tong
            Dept. Physiol. & Biophys.
            Case Western Reserve Univ.
            Cleveland, Ohio 44106
            Tel: (216)368-8654 (O)
            _______________________________________________________________________________
            Life is an everlasting game of Weiqi(igo, baduk).
          • Mark Maciejewski
            Yufeng, I think one of the problems you are having is that you ran your array as phase,phase2 rather than the more traditional phase2,phase. I also believe
            Message 5 of 8 , Apr 2, 2004
              Yufeng,

              I think one of the problems you are having is that you ran your array as phase,phase2 rather than the more traditional phase2,phase. I also believe that the gNhsqcnoesyhsqc is only sensitivity-enhanced in a single dimension, although I am not positive about this as I have never run it before. Having the phase values arrayed backwards would cause the ymode to be sensitivity enhanced while the zmode to be states-tppi. When I process your spectra in this way the mirror-images disappear. However, I seem to have a rather strange phasing problem with my spectra and the spectra appears to be folded. With a carrier at 111 ppm in N the folding does not suprise me, but I don't understand why I cannot get a good phase.

              Hope this helps somewhat.

              Mark

              Yufeng wrote:
              Thanks Frank & Vitaliy,
              
              I tried but the result seems to be the same. 
              If you have time, could you please have a look at 
              
              http://mbalster.cwru.edu/questions/gNhsqcnoesyNhsqc.fid/
              
              the .tgz file is the gzipped tarball of the data and scripts under that directory.
              
              others are self-explaining.
              
              Yufeng
              
              	
              
              ======= 2004-04-02 06:24:53 You wrote =======
              
                
              Hi All ...
              
              Yes, it's true that the conversion software can accept either 
              "-yMODE Rance-Kay" or "-zMODE Rance-Kay" but not both together.
              
              Why? Because there is not one single shuffling scheme that is suitable
              for this special double-enhanced data.
              
              In some cases, a combination of the usual Y-axis and Z-axis shuffling
              scripts will work.  In other cases we've seen, we had to make a special
              compostite script "ranceYZ.M", as used below ...
              
              cheerful regards,
              f
              
              var2pipe -in ./fid  -aqORD 1 \
               -xN              1024  -yN               256  -zN                72  \
               -xT               512  -yT               128  -zT                36  \
               -xMODE        Complex  -yMODE        Complex  -zMODE        Complex  \
               -xSW         6999.738  -ySW         5500.000  -zSW         4199.916  \
               -xOBS         600.046  -yOBS         600.046  -zOBS         150.888  \
               -xCAR           4.630  -yCAR           4.630  -zCAR          46.327  \
               -xLAB           H-acq  -yLAB           H-ind  -zLAB               C  \
               -ndim               3  -aq2D          States                         \
              | nmrPipe -fn MAC -macro $NMRTXT/var_ranceYZ.M -noRd -noWr \
              | nmrPipe -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr  \
              | pipe2xyz -out ./data/test%03d.fid -verb -to 0
              
              
              
                  
              = = = = = = = = = = = = = = = = = = = =
              
              Yufeng Tong
              Dept. Physiol. & Biophys.
              Case Western Reserve Univ.
              Cleveland, Ohio 44106
              Tel: (216)368-8654 (O)
              _______________________________________________________________________________
              Life is an everlasting game of Weiqi(igo, baduk).
              
              
              
               
              Yahoo! Groups Links
              
              <*> To visit your group on the web, go to:
                   http://groups.yahoo.com/group/nmrpipe/
              
              <*> To unsubscribe from this group, send an email to:
                   nmrpipe-unsubscribe@yahoogroups.com
              
              <*> Your use of Yahoo! Groups is subject to:
                   http://docs.yahoo.com/info/terms/
               
              
                

            • Frank Delaglio
              Hey Mark, good contribution, thanks. Now, about folding and phase distortion. here are some comments: Cheerful Regards, big fd 1. FT -alt: is not uncommon in
              Message 6 of 8 , Apr 2, 2004
                Hey Mark, good contribution, thanks.

                Now, about "folding" and phase distortion. here are some comments:

                Cheerful Regards,

                big fd

                1. FT -alt: is not uncommon in states-tppi experiments to require
                sign-alternation of the points before FT. Sometimes this step is
                accommodated in the pulse sequence, sometimes not. The result
                is a spectrum that is left/right swapped, which sometimes can
                look like a folding problem. Using "FT -alt" is the cure.

                2. The 15N NOE experiments often have a long delay in the indirect proton
                dimension. In many cases I've seen, the delay is carefully set to
                be equal to one dwell, so that the phase will be P0=-180 P1=360.

                This one-point delay (i.e. missing first point) causes a zero-order
                baseline distorsion, which can be fixed by using "POLY -auto -ord 0"
                after the FT.

                Note that in some cases, the delay may have been set much longer.
                This is not good for several reasons.

                * nmrDraw phase sliders only go to +/- 360 degrees.
                If needed, you can increase the ranges in "Proc/Phase Settings"

                * P1 > 360 will cause sinusoid baseline distortions.

                * If the delay is not a multiple of 1/2 dwell, the phase of folded
                peaks will be distorted. So, in practice, if your P1 is other than
                0, 180, or 360, you should expect that folded peaks will be out of
                phase.

                On Fri, 2 Apr 2004, Mark Maciejewski wrote:

                > Yufeng,
                >
                > I think one of the problems you are having is that you ran your array as
                > phase,phase2 rather than the more traditional phase2,phase. I also
                > believe that the gNhsqcnoesyhsqc is only sensitivity-enhanced in a
                > single dimension, although I am not positive about this as I have never
                > run it before. Having the phase values arrayed backwards would cause the
                > ymode to be sensitivity enhanced while the zmode to be states-tppi. When
                > I process your spectra in this way the mirror-images disappear. However,
                > I seem to have a rather strange phasing problem with my spectra and the
                > spectra appears to be folded. With a carrier at 111 ppm in N the folding
                > does not suprise me, but I don't understand why I cannot get a good phase.
                >
                > Hope this helps somewhat.
                >
                > Mark
                >
                > Yufeng wrote:
                >
                > >Thanks Frank & Vitaliy,
                > >
                > >I tried but the result seems to be the same.
                > >If you have time, could you please have a look at
                > >
                > >http://mbalster.cwru.edu/questions/gNhsqcnoesyNhsqc.fid/
                > >
                > >the .tgz file is the gzipped tarball of the data and scripts under that directory.
                > >
                > >others are self-explaining.
                > >
                > >Yufeng
                > >
                > >
                > >
                > >======= 2004-04-02 06:24:53 You wrote =======
                > >
                > >
                > >
                > >>Hi All ...
                > >>
                > >>Yes, it's true that the conversion software can accept either
                > >>"-yMODE Rance-Kay" or "-zMODE Rance-Kay" but not both together.
                > >>
                > >>Why? Because there is not one single shuffling scheme that is suitable
                > >>for this special double-enhanced data.
                > >>
                > >>In some cases, a combination of the usual Y-axis and Z-axis shuffling
                > >>scripts will work. In other cases we've seen, we had to make a special
                > >>compostite script "ranceYZ.M", as used below ...
                > >>
                > >>cheerful regards,
                > >>f
                > >>
                > >>var2pipe -in ./fid -aqORD 1 \
                > >> -xN 1024 -yN 256 -zN 72 \
                > >> -xT 512 -yT 128 -zT 36 \
                > >> -xMODE Complex -yMODE Complex -zMODE Complex \
                > >> -xSW 6999.738 -ySW 5500.000 -zSW 4199.916 \
                > >> -xOBS 600.046 -yOBS 600.046 -zOBS 150.888 \
                > >> -xCAR 4.630 -yCAR 4.630 -zCAR 46.327 \
                > >> -xLAB H-acq -yLAB H-ind -zLAB C \
                > >> -ndim 3 -aq2D States \
                > >>| nmrPipe -fn MAC -macro $NMRTXT/var_ranceYZ.M -noRd -noWr \
                > >>| nmrPipe -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr \
                > >>| pipe2xyz -out ./data/test%03d.fid -verb -to 0
                > >>
                > >>
                > >>
                > >>
                > >>
                > >
                > >= = = = = = = = = = = = = = = = = = = =
                > >
                > >Yufeng Tong
                > >Dept. Physiol. & Biophys.
                > >Case Western Reserve Univ.
                > >Cleveland, Ohio 44106
                > >Tel: (216)368-8654 (O)
                > >_______________________________________________________________________________
                > >Life is an everlasting game of Weiqi(igo, baduk).
                > >
                > >
                > >
                > >
                > >Yahoo! Groups Links
                > >
                > >
                > >
                > >
                > >
                > >
                > >
                >
                >
              • Shaheen Shojania
                Yufeng, Try the following script on your data: #!/bin/csh var2pipe -in ../fid -noaswap -aqORD 1 -xN 1024 -yN 64 -zN
                Message 7 of 8 , Apr 26, 2004
                  Yufeng,

                  Try the following script on your data:

                  #!/bin/csh

                  var2pipe -in ../fid -noaswap -aqORD 1\
                  -xN 1024 -yN 64 -zN 64 \
                  -xT 512 -yT 32 -zT 32 \
                  -xMODE Complex -yMODE Complex -zMODE States-TPPI \
                  -xSW 8000.000 -ySW 1400.000 -zSW 1400.021 \
                  -xOBS 599.885 -yOBS 60.792 -zOBS 60.792 \
                  -xCAR 4.821 -yCAR 111.222 -zCAR 111.222 \
                  -xLAB HN -yLAB N15 -zLAB 15N \
                  -ndim 3 -aq2D States \
                  | nmrPipe -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr \
                  | pipe2xyz -out ../data/fid/test%03d.fid -verb -to 0 -ov

                  I already tried it out on your data and it seems to work.

                  Good luck,

                  Shaheen


                  ________________________________________________________________

                  Shaheen Shojania
                  Department of Chemistry TEL: (204) 474-6697
                  University of Manitoba FAX: (204) 474-7608
                  316 Parker Building E-MAIL: umshoja0@...
                  144 Dysart Road
                  Winnipeg, MB
                  R3T 2N2
                  ________________________________________________________________
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