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processing DE-H(C)CH-TOCSY

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  • michal.respondek
    Dear All, I have a 3D double sensitivity enhanced hcch-tocsy acquired on Varian. So far I have been processing the spectra using: var2pipe -in ./fid -noaswap
    Message 1 of 6 , Oct 2, 2008
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      Dear All,
      I have a 3D double sensitivity enhanced hcch-tocsy acquired on Varian.
      So far I have been processing the spectra using:

      var2pipe -in ./fid -noaswap -aqORD 1 \
      -xN 2048 -yN 144 -zN 128 \
      -xT 1024 -yT 72 -zT 64 \
      -xMODE Complex -yMODE Complex -zMODE Complex \
      -xSW 8000.000 -ySW 8398.068 -zSW 12070.006 \
      -xOBS 599.875 -yOBS 599.875 -zOBS 150.843 \
      -xCAR 4.662 -yCAR 4.820 -zCAR 37.146 \
      -xLAB H1 -yLAB Hind -zLAB C13 \
      -ndim 3 -aq2D States \
      | nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr \
      | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr \
      | pipe2xyz -out data/test%03d.fid -verb -ov

      with good results. Now I got new proteinpack and here my problem
      starts. I cannot process XZ plane. XY looks good, but XZ look awful
      nothing like a regular 2D plane. I have tried using some protocols
      from NANUC library, but it did not help. Does anybody knows what kind
      of problem it could be or does anybody knows how to process
      DE-H(C)CH-TOCSY acquired on varian. I have seen some example scripts
      here but they did not help me either.
      here is the nmrproc file I use:
      for XY
      nmrPipe -in data/test001.fid \
      | 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 -79.0 -p1 0.0 -di \
      | nmrPipe -fn TP \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -neg \
      | nmrPipe -fn PS -p0 0 -p1 0 -di \
      -verb -ov -out test.ft2

      and for XZ

      $NMRTXT/ext.xz.com data/test%03d.fid xz001.fid

      nmrPipe -in xz001.fid \
      | 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 -79 -p1 0.0 -di -verb \
      | nmrPipe -fn TP \
      | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
      | nmrPipe -fn ZF -auto \
      | nmrPipe -fn FT -neg \
      | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb \
      -out testxz.ft2 -ov
    • DeRose, Eugene (NIH/NIEHS)
      Have you tried selecting Rance-Kay for ­yMODE and using the ranceZ.M macro, e.g., var2pipe -in ./fid -noaswap -xN 1024 -yN 160
      Message 2 of 6 , Oct 2, 2008
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        Re: [nmrpipe] processing DE-H(C)CH-TOCSY Have you tried selecting Rance-Kay for –yMODE and using the ranceZ.M macro, e.g.,

        var2pipe -in ./fid -noaswap  \
          -xN              1024  -yN               160  -zN                36  \
          -xT               512  -yT                80  -zT                18  \
          -xMODE        Complex  -yMODE      Rance-Kay  -zMODE        Complex  \
          -xSW         8401.596  -ySW        10557.477  -zSW         3770.384  \
          -xOBS         599.705  -yOBS         150.821  -zOBS         150.821  \
          -xCAR           4.773  -yCAR          35.000  -zCAR          20.000  \
          -xLAB               H  -yLAB            CACB  -zLAB               C  \
          -ndim               3  -aq2D          States                         \
        | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr                  \
        | pipe2xyz -out data/test%03d.fid -verb -ov

        In addition, is the array variable set to ‘phase,phase2’, requiring that –aqORD be set to 1.  The default is –aqORD 0, corresponding to array=’phase2,phase’.

        Eugene DeRose, Ph.D.
        NIEHS NMR Laboratory Manager
        Global Health Sector
        SRA International, Inc.
        Contractor to NIEHS/DIR
        National Institute of Environmental Health Sciences
        Research Triangle Park, NC 27709
        919.541.1981 voice
        919.541.5707 fax
        derose@...
        www.niehs.nih.gov
        www.sra.com
        Enhancing Human Health Around the World Everyday
        --

         


        On 10/2/08 11:48 AM, "michal.respondek" <michal.respondek@...> wrote:


         

        Dear All,
        I have a 3D double sensitivity enhanced hcch-tocsy acquired on Varian.
        So far I have been processing the spectra using:
         
        var2pipe -in ./fid -noaswap -aqORD 1 \
         -xN              2048  -yN               144  -zN               128  \
         -xT              1024  -yT                72  -zT                64  \
         -xMODE        Complex  -yMODE        Complex  -zMODE        Complex  \
         -xSW         8000.000  -ySW         8398.068  -zSW        12070.006  \
         -xOBS         599.875  -yOBS         599.875  -zOBS         150.843  \
         -xCAR           4.662  -yCAR           4.820  -zCAR          37.146  \
         -xLAB              H1  -yLAB            Hind  -zLAB             C13  \
         -ndim               3  -aq2D          States                         \
        | nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr                  \
        | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr                  \
        | pipe2xyz -out data/test%03d.fid -verb -ov

        with good results. Now I got new proteinpack and here my problem
        starts. I cannot process XZ plane. XY looks good, but XZ look awful
        nothing like a regular 2D plane. I have tried using some protocols
        from NANUC library, but it did not help. Does anybody knows what kind
        of problem it could be or does anybody knows how to process
        DE-H(C)CH-TOCSY acquired on varian. I have seen some example scripts
        here but they did not help me either.
        here is the nmrproc file I use:
         for XY
        nmrPipe -in data/test001.fid \
        | 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 -79.0  -p1 0.0 -di              \
        | nmrPipe  -fn TP                                     \
        | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5   \
        | nmrPipe  -fn ZF -auto                               \
        | nmrPipe  -fn FT -neg                                   \
        | nmrPipe  -fn PS -p0 0 -p1 0 -di                \
         -verb -ov -out test.ft2

        and for XZ

        $NMRTXT/ext.xz.com data/test%03d.fid xz001.fid

        nmrPipe -in xz001.fid \
        | 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 -79  -p1 0.0 -di -verb             \
        | nmrPipe  -fn TP                                       \
        | nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5      \
        | nmrPipe  -fn ZF -auto                                 \
        | nmrPipe  -fn FT -neg                                      \
        | nmrPipe  -fn PS -p0 0.0 -p1 0.0 -di -verb             \
         -out testxz.ft2 -ov

         
            

      • michal.respondek
        I have tried that one, it is exactly the one from the NANUC library. Still no improvement, but anyway Thank You Eugene for replying. ... macro, ... 128 ...
        Message 3 of 6 , Oct 2, 2008
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          I have tried that one, it is exactly the one from the NANUC library.
          Still no improvement, but anyway Thank You Eugene for replying.




          --- In nmrpipe@yahoogroups.com, "DeRose, Eugene (NIH/NIEHS)"
          <derose@...> wrote:
          >
          > Have you tried selecting Rance-Kay for ­yMODE and using the ranceZ.M
          macro,
          > e.g.,
          >
          > var2pipe -in ./fid -noaswap \
          > -xN 1024 -yN 160 -zN 36 \
          > -xT 512 -yT 80 -zT 18 \
          > -xMODE Complex -yMODE Rance-Kay -zMODE Complex \
          > -xSW 8401.596 -ySW 10557.477 -zSW 3770.384 \
          > -xOBS 599.705 -yOBS 150.821 -zOBS 150.821 \
          > -xCAR 4.773 -yCAR 35.000 -zCAR 20.000 \
          > -xLAB H -yLAB CACB -zLAB C \
          > -ndim 3 -aq2D States \
          > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr \
          > | pipe2xyz -out data/test%03d.fid -verb -ov
          >
          > In addition, is the array variable set to Œphase,phase2¹, requiring that
          > ­aqORD be set to 1. The default is ­aqORD 0, corresponding to
          > array=¹phase2,phase¹.
          >
          > Eugene DeRose, Ph.D.
          > NIEHS NMR Laboratory Manager
          > Global Health Sector
          > SRA International, Inc.
          > Contractor to NIEHS/DIR
          > National Institute of Environmental Health Sciences
          > Research Triangle Park, NC 27709
          > 919.541.1981 voice
          > 919.541.5707 fax
          > derose@...
          > www.niehs.nih.gov
          > www.sra.com
          > Enhancing Human Health Around the World Everyday
          > --
          >
          >
          >
          >
          > On 10/2/08 11:48 AM, "michal.respondek" <michal.respondek@...>
          > wrote:
          >
          > >
          > >
          > >
          > > Dear All,
          > > I have a 3D double sensitivity enhanced hcch-tocsy acquired on Varian.
          > > So far I have been processing the spectra using:
          > >
          > > var2pipe -in ./fid -noaswap -aqORD 1 \
          > > -xN 2048 -yN 144 -zN
          128 \
          > > -xT 1024 -yT 72 -zT
          64 \
          > > -xMODE Complex -yMODE Complex -zMODE
          Complex \
          > > -xSW 8000.000 -ySW 8398.068 -zSW
          12070.006 \
          > > -xOBS 599.875 -yOBS 599.875 -zOBS
          150.843 \
          > > -xCAR 4.662 -yCAR 4.820 -zCAR
          37.146 \
          > > -xLAB H1 -yLAB Hind -zLAB
          C13 \
          > > -ndim 3 -aq2D States
          \
          > > | nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr
          \
          > > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr
          \
          > > | pipe2xyz -out data/test%03d.fid -verb -ov
          > >
          > > with good results. Now I got new proteinpack and here my problem
          > > starts. I cannot process XZ plane. XY looks good, but XZ look awful
          > > nothing like a regular 2D plane. I have tried using some protocols
          > > from NANUC library, but it did not help. Does anybody knows what kind
          > > of problem it could be or does anybody knows how to process
          > > DE-H(C)CH-TOCSY acquired on varian. I have seen some example scripts
          > > here but they did not help me either.
          > > here is the nmrproc file I use:
          > > for XY
          > > nmrPipe -in data/test001.fid \
          > > | 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 -79.0 -p1 0.0 -di \
          > > | nmrPipe -fn TP \
          > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
          > > | nmrPipe -fn ZF -auto \
          > > | nmrPipe -fn FT -neg \
          > > | nmrPipe -fn PS -p0 0 -p1 0 -di \
          > > -verb -ov -out test.ft2
          > >
          > > and for XZ
          > >
          > > $NMRTXT/ext.xz.com data/test%03d.fid xz001.fid
          > >
          > > nmrPipe -in xz001.fid \
          > > | 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 -79 -p1 0.0 -di -verb \
          > > | nmrPipe -fn TP \
          > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
          > > | nmrPipe -fn ZF -auto \
          > > | nmrPipe -fn FT -neg \
          > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb \
          > > -out testxz.ft2 -ov
          > >
          > >
          > >
          >
        • Ryan McKay
          Hi there, What is the seqfil you re using? e.g. ghcch_tocsy or ghcch_tocsyA? R On 2-Oct-08, at 3:57 PM, michal.respondek wrote: I have tried that one, it is
          Message 4 of 6 , Oct 6, 2008
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            Hi there,

            What is the seqfil you're using?

            e.g. ghcch_tocsy or ghcch_tocsyA?

            R

            On 2-Oct-08, at 3:57 PM, michal.respondek wrote:

            I have tried that one, it is exactly the one from the NANUC library.
            Still no improvement, but anyway Thank You Eugene for replying. 

            --- In nmrpipe@yahoogroups .com, "DeRose, Eugene (NIH/NIEHS)"
            <derose@...> wrote:
            >
            > Have you tried selecting Rance-Kay for yMODE and using the ranceZ.M
            macro,
            > e.g.,
            > 
            > var2pipe -in ./fid -noaswap \
            > -xN 1024 -yN 160 -zN 36 \
            > -xT 512 -yT 80 -zT 18 \
            > -xMODE Complex -yMODE Rance-Kay -zMODE Complex \
            > -xSW 8401.596 -ySW 10557.477 -zSW 3770.384 \
            > -xOBS 599.705 -yOBS 150.821 -zOBS 150.821 \
            > -xCAR 4.773 -yCAR 35.000 -zCAR 20.000 \
            > -xLAB H -yLAB CACB -zLAB C \
            > -ndim 3 -aq2D States \
            > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ. M -noRd -noWr \
            > | pipe2xyz -out data/test%03d. fid -verb -ov
            > 
            > In addition, is the array variable set to Œphase,phase2¹ , requiring that
            > aqORD be set to 1. The default is aqORD 0, corresponding to
            > array=¹phase2, phase¹.
            > 
            > Eugene DeRose, Ph.D.
            > NIEHS NMR Laboratory Manager
            > Global Health Sector
            > SRA International, Inc.
            > Contractor to NIEHS/DIR
            > National Institute of Environmental Health Sciences
            > Research Triangle Park, NC 27709
            > 919.541.1981 voice
            > 919.541.5707 fax
            > derose@...
            > www.niehs.nih. gov
            > www.sra.com
            > Enhancing Human Health Around the World Everyday
            > -- 
            > 
            > 
            > 
            > 
            > On 10/2/08 11:48 AM, "michal.respondek" <michal.respondek@ ...>
            > wrote:
            > 
            > > 
            > > 
            > > 
            > > Dear All,
            > > I have a 3D double sensitivity enhanced hcch-tocsy acquired on Varian.
            > > So far I have been processing the spectra using:
            > > 
            > > var2pipe -in ./fid -noaswap -aqORD 1 \
            > > -xN 2048 -yN 144 -zN 
            128 \
            > > -xT 1024 -yT 72 -zT 
            64 \
            > > -xMODE Complex -yMODE Complex -zMODE 
            Complex \
            > > -xSW 8000.000 -ySW 8398.068 -zSW 
            12070.006 \
            > > -xOBS 599.875 -yOBS 599.875 -zOBS 
            150.843 \
            > > -xCAR 4.662 -yCAR 4.820 -zCAR 
            37.146 \
            > > -xLAB H1 -yLAB Hind -zLAB 
            C13 \
            > > -ndim 3 -aq2D States 
            \
            > > | nmrPipe -fn MAC -macro $NMRTXT/ranceY. M -noRd -noWr 
            \
            > > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ. M -noRd -noWr 
            \
            > > | pipe2xyz -out data/test%03d. fid -verb -ov
            > > 
            > > with good results. Now I got new proteinpack and here my problem
            > > starts. I cannot process XZ plane. XY looks good, but XZ look awful
            > > nothing like a regular 2D plane. I have tried using some protocols
            > > from NANUC library, but it did not help. Does anybody knows what kind
            > > of problem it could be or does anybody knows how to process
            > > DE-H(C)CH-TOCSY acquired on varian. I have seen some example scripts
            > > here but they did not help me either.
            > > here is the nmrproc file I use:
            > > for XY
            > > nmrPipe -in data/test001. fid \
            > > | 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 -79.0 -p1 0.0 -di \
            > > | nmrPipe -fn TP \
            > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
            > > | nmrPipe -fn ZF -auto \
            > > | nmrPipe -fn FT -neg \
            > > | nmrPipe -fn PS -p0 0 -p1 0 -di \
            > > -verb -ov -out test.ft2
            > > 
            > > and for XZ
            > > 
            > > $NMRTXT/ext. xz.com data/test%03d. fid xz001.fid
            > > 
            > > nmrPipe -in xz001.fid \
            > > | 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 -79 -p1 0.0 -di -verb \
            > > | nmrPipe -fn TP \
            > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
            > > | nmrPipe -fn ZF -auto \
            > > | nmrPipe -fn FT -neg \
            > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb \
            > > -out testxz.ft2 -ov
            > > 
            > > 
            > >
            >



            ------------------------------------------------------------------------------------

            Ryan T. McKay, Ph.D. -     Scientific Director

            NANUC - Canada's National High Field NMR Centre

            Room 105                           Email:  ryan@...

            NANUC Bld.                        Phone: (780) 492-2700

            University of Alberta            Fax:     (780) 492-9174

            Edmonton, Alberta              Cell:     (780) 920-8871

            Canada T6G 2E1                AIM:     ryanmckaynmr

                                 http://www.nanuc.ca






          • michal.respondek
            Hi, the seqfil we used is ghcch_tocsy. Though It would be interesting to see the processing scripts for both of the seqfil.
            Message 5 of 6 , Oct 7, 2008
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              Hi, the seqfil we used is ghcch_tocsy.
              Though It would be interesting to see the processing scripts for both
              of the seqfil.


              --- In nmrpipe@yahoogroups.com, Ryan McKay <ryan@...> wrote:
              >
              > Hi there,
              >
              > What is the seqfil you're using?
              >
              > e.g. ghcch_tocsy or ghcch_tocsyA?
              >
              > R
              >
              > On 2-Oct-08, at 3:57 PM, michal.respondek wrote:
              >
              > I have tried that one, it is exactly the one from the NANUC library.
              > Still no improvement, but anyway Thank You Eugene for replying.
              >
              > --- In nmrpipe@yahoogroups.com, "DeRose, Eugene (NIH/NIEHS)"
              > <derose@> wrote:
              > >
              > > Have you tried selecting Rance-Kay for yMODE and using the ranceZ.M
              > macro,
              > > e.g.,
              > >
              > > var2pipe -in ./fid -noaswap \
              > > -xN 1024 -yN 160 -zN 36 \
              > > -xT 512 -yT 80 -zT 18 \
              > > -xMODE Complex -yMODE Rance-Kay -zMODE Complex \
              > > -xSW 8401.596 -ySW 10557.477 -zSW 3770.384 \
              > > -xOBS 599.705 -yOBS 150.821 -zOBS 150.821 \
              > > -xCAR 4.773 -yCAR 35.000 -zCAR 20.000 \
              > > -xLAB H -yLAB CACB -zLAB C \
              > > -ndim 3 -aq2D States \
              > > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr \
              > > | pipe2xyz -out data/test%03d.fid -verb -ov
              > >
              > > In addition, is the array variable set to Œphase,phase2¹, requiring
              > that
              > > aqORD be set to 1. The default is aqORD 0, corresponding to
              > > array=¹phase2,phase¹.
              > >
              > > Eugene DeRose, Ph.D.
              > > NIEHS NMR Laboratory Manager
              > > Global Health Sector
              > > SRA International, Inc.
              > > Contractor to NIEHS/DIR
              > > National Institute of Environmental Health Sciences
              > > Research Triangle Park, NC 27709
              > > 919.541.1981 voice
              > > 919.541.5707 fax
              > > derose@
              > > www.niehs.nih.gov
              > > www.sra.com
              > > Enhancing Human Health Around the World Everyday
              > > --
              > >
              > >
              > >
              > >
              > > On 10/2/08 11:48 AM, "michal.respondek" <michal.respondek@>
              > > wrote:
              > >
              > > >
              > > >
              > > >
              > > > Dear All,
              > > > I have a 3D double sensitivity enhanced hcch-tocsy acquired on
              > Varian.
              > > > So far I have been processing the spectra using:
              > > >
              > > > var2pipe -in ./fid -noaswap -aqORD 1 \
              > > > -xN 2048 -yN 144 -zN
              > 128 \
              > > > -xT 1024 -yT 72 -zT
              > 64 \
              > > > -xMODE Complex -yMODE Complex -zMODE
              > Complex \
              > > > -xSW 8000.000 -ySW 8398.068 -zSW
              > 12070.006 \
              > > > -xOBS 599.875 -yOBS 599.875 -zOBS
              > 150.843 \
              > > > -xCAR 4.662 -yCAR 4.820 -zCAR
              > 37.146 \
              > > > -xLAB H1 -yLAB Hind -zLAB
              > C13 \
              > > > -ndim 3 -aq2D States
              > \
              > > > | nmrPipe -fn MAC -macro $NMRTXT/ranceY.M -noRd -noWr
              > \
              > > > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ.M -noRd -noWr
              > \
              > > > | pipe2xyz -out data/test%03d.fid -verb -ov
              > > >
              > > > with good results. Now I got new proteinpack and here my problem
              > > > starts. I cannot process XZ plane. XY looks good, but XZ look awful
              > > > nothing like a regular 2D plane. I have tried using some protocols
              > > > from NANUC library, but it did not help. Does anybody knows what
              > kind
              > > > of problem it could be or does anybody knows how to process
              > > > DE-H(C)CH-TOCSY acquired on varian. I have seen some example
              > scripts
              > > > here but they did not help me either.
              > > > here is the nmrproc file I use:
              > > > for XY
              > > > nmrPipe -in data/test001.fid \
              > > > | 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 -79.0 -p1 0.0 -di \
              > > > | nmrPipe -fn TP \
              > > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
              > > > | nmrPipe -fn ZF -auto \
              > > > | nmrPipe -fn FT -neg \
              > > > | nmrPipe -fn PS -p0 0 -p1 0 -di \
              > > > -verb -ov -out test.ft2
              > > >
              > > > and for XZ
              > > >
              > > > $NMRTXT/ext.xz.com data/test%03d.fid xz001.fid
              > > >
              > > > nmrPipe -in xz001.fid \
              > > > | 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 -79 -p1 0.0 -di -verb \
              > > > | nmrPipe -fn TP \
              > > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
              > > > | nmrPipe -fn ZF -auto \
              > > > | nmrPipe -fn FT -neg \
              > > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb \
              > > > -out testxz.ft2 -ov
              > > >
              > > >
              > > >
              > >
              >
              >
              >
              >
              >
              >
              ------------------------------------------------------------------------------------
              > Ryan T. McKay, Ph.D. - Scientific Director
              > NANUC - Canada's National High Field NMR Centre
              > Room 105 Email: ryan@...
              > NANUC Bld. Phone: (780) 492-2700
              > University of Alberta Fax: (780) 492-9174
              > Edmonton, Alberta Cell: (780) 920-8871
              > Canada T6G 2E1 AIM: ryanmckaynmr
              > http://www.nanuc.ca
              >
            • Ryan McKay
              Hi there, Take the 3D script from the NANUC NMRPipe script library and try this for the fid.com It was contributed by Tara Sprules (Eastern Canadian NMR
              Message 6 of 6 , Oct 14, 2008
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                Hi there,

                Take the 3D script from the NANUC NMRPipe script library and try this for the fid.com

                It was contributed by Tara Sprules (Eastern Canadian NMR Centre@McGill).


                Quote Below:
                Thanks! This was the one that finally worked, once I added -aqORD 1.

                FYI: I recorded my expt on varian, using array phase,phase2 (with
                phase=1,2 and phase2=1,2).

                Tara

                On Tue, 2 Dec 2003, [euc-kr] Á¤Áø¿ø wrote:

                Hi,

                please try this script.

                -----------

                #!/bin/csh

                var2pipe -in ./fid -swap  \
                 -xN              1024  -yN               100  -zN                96  \
                 -xT               512  -yT                50  -zT                48  \
                 -xMODE        Complex  -yMODE Complex         -zMODE  Complex        \
                 -xSW         8000.000  -ySW         8000.000  -zSW         9427.292  \
                 -xOBS         499.863  -yOBS         499.863  -zOBS         125.694  \
                 -xCAR           4.773  -yCAR           4.773  -zCAR          37.599  \
                 -xLAB              H1  -yLAB              H1  -zLAB             C13  \
                 -ndim               3  -aq2D          States                         \
                | nmrPipe -fn MAC -macro $NMRTXT/var_ranceY.M -noRd -noWr \
                | nmrPipe  -fn MAC -macro $NMRTXT/var_ranceZ.M -noRd -noWr \
                | pipe2xyz -out ./data/test%03d.fid -verb -ov



                On 7-Oct-08, at 2:22 AM, michal.respondek wrote:

                Hi, the seqfil we used is ghcch_tocsy.
                Though It would be interesting to see the processing scripts for both
                of the seqfil.

                --- In nmrpipe@yahoogroups .com, Ryan McKay <ryan@...> wrote:
                >
                > Hi there,
                > 
                > What is the seqfil you're using?
                > 
                > e.g. ghcch_tocsy or ghcch_tocsyA?
                > 
                > R
                > 
                > On 2-Oct-08, at 3:57 PM, michal.respondek wrote:
                > 
                > I have tried that one, it is exactly the one from the NANUC library.
                > Still no improvement, but anyway Thank You Eugene for replying.
                > 
                > --- In nmrpipe@yahoogroups .com, "DeRose, Eugene (NIH/NIEHS)"
                > <derose@> wrote:
                > >
                > > Have you tried selecting Rance-Kay for yMODE and using the ranceZ.M
                > macro,
                > > e.g.,
                > >
                > > var2pipe -in ./fid -noaswap \
                > > -xN 1024 -yN 160 -zN 36 \
                > > -xT 512 -yT 80 -zT 18 \
                > > -xMODE Complex -yMODE Rance-Kay -zMODE Complex \
                > > -xSW 8401.596 -ySW 10557.477 -zSW 3770.384 \
                > > -xOBS 599.705 -yOBS 150.821 -zOBS 150.821 \
                > > -xCAR 4.773 -yCAR 35.000 -zCAR 20.000 \
                > > -xLAB H -yLAB CACB -zLAB C \
                > > -ndim 3 -aq2D States \
                > > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ. M -noRd -noWr \
                > > | pipe2xyz -out data/test%03d. fid -verb -ov
                > >
                > > In addition, is the array variable set to Œphase,phase2¹ , requiring 
                > that
                > > aqORD be set to 1. The default is aqORD 0, corresponding to
                > > array=¹phase2, phase¹.
                > >
                > > Eugene DeRose, Ph.D.
                > > NIEHS NMR Laboratory Manager
                > > Global Health Sector
                > > SRA International, Inc.
                > > Contractor to NIEHS/DIR
                > > National Institute of Environmental Health Sciences
                > > Research Triangle Park, NC 27709
                > > 919.541.1981 voice
                > > 919.541.5707 fax
                > > derose@
                > > www.niehs.nih. gov
                > > www.sra.com
                > > Enhancing Human Health Around the World Everyday
                > > --
                > >
                > >
                > >
                > >
                > > On 10/2/08 11:48 AM, "michal.respondek" <michal.respondek@ >
                > > wrote:
                > >
                > > >
                > > >
                > > >
                > > > Dear All,
                > > > I have a 3D double sensitivity enhanced hcch-tocsy acquired on 
                > Varian.
                > > > So far I have been processing the spectra using:
                > > >
                > > > var2pipe -in ./fid -noaswap -aqORD 1 \
                > > > -xN 2048 -yN 144 -zN
                > 128 \
                > > > -xT 1024 -yT 72 -zT
                > 64 \
                > > > -xMODE Complex -yMODE Complex -zMODE
                > Complex \
                > > > -xSW 8000.000 -ySW 8398.068 -zSW
                > 12070.006 \
                > > > -xOBS 599.875 -yOBS 599.875 -zOBS
                > 150.843 \
                > > > -xCAR 4.662 -yCAR 4.820 -zCAR
                > 37.146 \
                > > > -xLAB H1 -yLAB Hind -zLAB
                > C13 \
                > > > -ndim 3 -aq2D States
                > \
                > > > | nmrPipe -fn MAC -macro $NMRTXT/ranceY. M -noRd -noWr
                > \
                > > > | nmrPipe -fn MAC -macro $NMRTXT/ranceZ. M -noRd -noWr
                > \
                > > > | pipe2xyz -out data/test%03d. fid -verb -ov
                > > >
                > > > with good results. Now I got new proteinpack and here my problem
                > > > starts. I cannot process XZ plane. XY looks good, but XZ look awful
                > > > nothing like a regular 2D plane. I have tried using some protocols
                > > > from NANUC library, but it did not help. Does anybody knows what 
                > kind
                > > > of problem it could be or does anybody knows how to process
                > > > DE-H(C)CH-TOCSY acquired on varian. I have seen some example 
                > scripts
                > > > here but they did not help me either.
                > > > here is the nmrproc file I use:
                > > > for XY
                > > > nmrPipe -in data/test001. fid \
                > > > | 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 -79.0 -p1 0.0 -di \
                > > > | nmrPipe -fn TP \
                > > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
                > > > | nmrPipe -fn ZF -auto \
                > > > | nmrPipe -fn FT -neg \
                > > > | nmrPipe -fn PS -p0 0 -p1 0 -di \
                > > > -verb -ov -out test.ft2
                > > >
                > > > and for XZ
                > > >
                > > > $NMRTXT/ext. xz.com data/test%03d. fid xz001.fid
                > > >
                > > > nmrPipe -in xz001.fid \
                > > > | 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 -79 -p1 0.0 -di -verb \
                > > > | nmrPipe -fn TP \
                > > > | nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
                > > > | nmrPipe -fn ZF -auto \
                > > > | nmrPipe -fn FT -neg \
                > > > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb \
                > > > -out testxz.ft2 -ov
                > > >
                > > >
                > > >
                > >
                > 
                > 
                > 
                > 
                > 
                >
                ------------ --------- --------- --------- --------- --------- -
                > Ryan T. McKay, Ph.D. - Scientific Director
                > NANUC - Canada's National High Field NMR Centre
                > Room 105 Email: ryan@...
                > NANUC Bld. Phone: (780) 492-2700
                > University of Alberta Fax: (780) 492-9174
                > Edmonton, Alberta Cell: (780) 920-8871
                > Canada T6G 2E1 AIM: ryanmckaynmr
                > http://www.nanuc. ca
                >



                ------------------------------------------------------------------------------------

                Ryan T. McKay, Ph.D. -     Scientific Director

                NANUC - Canada's National High Field NMR Centre

                Room 105                           Email:  ryan@...

                NANUC Bld.                        Phone: (780) 492-2700

                University of Alberta            Fax:     (780) 492-9174

                Edmonton, Alberta              Cell:     (780) 920-8871

                Canada T6G 2E1                AIM:     ryanmckaynmr

                                     http://www.nanuc.ca






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