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Re: [nmrpipe] JEOL Delta data conversion

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  • Frank Delaglio
    Do you have any more details about the type of experiment you are working with? The processing scheme will depend on acquisition mode. Most example schemes are
    Message 1 of 5 , Jan 28, 2010
      Do you have any more details about the type of experiment
      you are working with?

      The processing scheme will depend on acquisition mode.
      Most example schemes are for hypercomplex data formats,
      typically States or States-TPPI.

      However, maybe your data are older-style TPPI or Absolute-value
      (Magnitude mode) data, which each require somewhat different
      processing schemes.




      Quoting simon sham <ssham44@...>:

      > Hi,
      > I have tried to convert a JEOL Delta 2D data file to nmrpipe format
      > and processed them. I know nmrpipe can convert the data. For
      > whatever reasons, the spectrum did not look quite right.
      > Are there any special parameters that I need to know about when
      > converting/processing the data?
      >  
      > Thanks for your insight,
      >  
      > Simon
      >
      >
      >
    • simon sham
      Hi all nmrpipers, The JEOL pulse sequence is HMBC_pfg.ex2: #!/bin/csh # X-Axis Size after DF Adjustment: 2027 Complex Points. delta2pipe -in
      Message 2 of 5 , Feb 2, 2010
        Hi all nmrpipers,

        The JEOL pulse sequence is HMBC_pfg.ex2:
        #!/bin/csh

        # X-Axis Size after DF Adjustment: 2027 Complex Points.

        delta2pipe -in /home/sham/stevenlee/stevenlee_hmqc_011210-1.jdf \
          \
          -df -dfVal 19.750000 -trVal 7.998047e-01  \
          -xN              4096  -yN               512  \
          -xT              2048  -yT               256  \
          -xMODE        Complex  -yMODE        Real  \
          -xSW         3006.976  -ySW         1511.396  \
          -xOBS         300.530  -yOBS          75.568  \
          -xCAR           4.001  -yCAR         115.000  \
          -xLAB              1H  -yLAB             13C  \
          -ndim               2  -aq2D          States  \
          -out test.fid -verb -ov

        sleep 5#!/bin/csh

        nmrPipe -in /home/sham/stevenlee/test.fid \
        |nmrPipe -fn SP -off 0.166 -end 0.98 -pow -c 1.0\
        |nmrPipe -fn ZF -auto  \
        |nmrPipe -fn FT -auto  \
        |nmrPipe -fn PS -p0 123.0 -p1 0.0 -di \
        |nmrPipe -fn POLY -auto \
        |nmrPipe -fn TP \
        |nmrPipe -fn SP -off 0.166 -end 0.98 -pow 1 -c 1 \
        |nmrPipe -fn ZF -auto            \
        |nmrPipe -fn FT -auto            \
        |nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb  \
        |nmrPipe -fn TP                 \
        |nmrPipe -out hmbc.ft2 -ov

        Thanks in advance for your help.

        Simon

        This is what I have in my processing com:



        The quadrature modes in both dimension in the pulse sequence:
        collect COMPLEX, OBS REAL, IRR, NTYPE:

        This is what I have in my fid.com:








        --- On Thu, 1/28/10, Frank Delaglio <delaglio@...> wrote:

        From: Frank Delaglio <delaglio@...>
        Subject: Re: [nmrpipe] JEOL Delta data conversion
        To: nmrpipe@yahoogroups.com
        Date: Thursday, January 28, 2010, 4:50 PM

         



        Do you have any more details about the type of experiment
        you are working with?

        The processing scheme will depend on acquisition mode.
        Most example schemes are for hypercomplex data formats,
        typically States or States-TPPI.

        However, maybe your data are older-style TPPI or Absolute-value
        (Magnitude mode) data, which each require somewhat different
        processing schemes.

        Quoting simon sham <ssham44@yahoo. com>:

        > Hi,
        > I have tried to convert a JEOL Delta 2D data file to nmrpipe format
        > and processed them. I know nmrpipe can convert the data. For
        > whatever reasons, the spectrum did not look quite right.
        > Are there any special parameters that I need to know about when
        > converting/processi ng the data?
        >  
        > Thanks for your insight,
        >  
        > Simon
        >
        >
        >


      • Frank Delaglio
        try magnitude mode -- none of this format was available when delta2pipe was developed, so the program does not recognize this type of data ... let us know what
        Message 3 of 5 , Feb 2, 2010
          try magnitude mode -- none of this format was available when
          delta2pipe was developed, so the program does not recognize
          this type of data ... let us know what happens ...

          delta2pipe -in stevenlee_hmqc_011210-1.jdf \
          -df -dfVal 19.750000 -trVal 7.998047e-01 \
          -xN 4096 -yN 512 \
          -xT 2048 -yT 512 \
          -xMODE Complex -yMODE Real \
          -xSW 3006.976 -ySW 1511.396 \
          -xOBS 300.530 -yOBS 75.568 \
          -xCAR 4.001 -yCAR 115.000 \
          -xLAB 1H -yLAB 13C \
          -ndim 2 -aq2D Magnitude \
          -out test.fid -verb -ov


          nmrPipe -in test.fid \
          |nmrPipe -fn SP \
          |nmrPipe -fn ZF -auto \
          |nmrPipe -fn FT \
          |nmrPipe -fn TP \
          |nmrPipe -fn SP \
          |nmrPipe -fn ZF -auto \
          |nmrPipe -fn FT \
          |nmrPipe -fn MC -verb \
          |nmrPipe -fn TP \
          |nmrPipe -out hmbc.ft2 -ov

          Quoting simon sham <ssham44@...>:

          > Hi all nmrpipers,
          >
          > The JEOL pulse sequence is HMBC_pfg.ex2:
          > #!/bin/csh
          >
          > # X-Axis Size after DF Adjustment: 2027 Complex Points.
          >
          > delta2pipe -in /home/sham/stevenlee/stevenlee_hmqc_011210-1.jdf \
          >   \
          >   -df -dfVal 19.750000 -trVal 7.998047e-01  \
          >   -xN              4096  -yN               512  \
          >   -xT              2048  -yT               256  \
          >   -xMODE        Complex  -yMODE        Real  \
          >   -xSW         3006.976  -ySW         1511.396  \
          >   -xOBS         300.530  -yOBS          75.568  \
          >   -xCAR           4.001  -yCAR         115.000  \
          >   -xLAB              1H  -yLAB             13C  \
          >   -ndim               2  -aq2D          States  \
          >   -out test.fid -verb -ov
          >
          > sleep 5#!/bin/csh
          >
          > nmrPipe -in /home/sham/stevenlee/test.fid \
          > |nmrPipe -fn SP -off 0.166 -end 0.98 -pow -c 1.0\
          > |nmrPipe -fn ZF -auto  \
          > |nmrPipe -fn FT -auto  \
          > |nmrPipe -fn PS -p0 123.0 -p1 0.0 -di \
          > |nmrPipe -fn POLY -auto \
          > |nmrPipe -fn TP \
          > |nmrPipe -fn SP -off 0.166 -end 0.98 -pow 1 -c 1 \
          > |nmrPipe -fn ZF -auto            \
          > |nmrPipe -fn FT -auto            \
          > |nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb  \
          > |nmrPipe -fn TP                 \
          > |nmrPipe -out hmbc.ft2 -ov
          >
          > Thanks in advance for your help.
          >
          > Simon
          >
          > This is what I have in my processing com:
          >
          >
          >
          > The quadrature modes in both dimension in the pulse sequence:
          > collect COMPLEX, OBS REAL, IRR, NTYPE:
          >
          > This is what I have in my fid.com:
          >
          >
          >
          >
          >
          >
          >
          >
          > --- On Thu, 1/28/10, Frank Delaglio <delaglio@...> wrote:
          >
          > From: Frank Delaglio <delaglio@...>
          > Subject: Re: [nmrpipe] JEOL Delta data conversion
          > To: nmrpipe@yahoogroups.com
          > Date: Thursday, January 28, 2010, 4:50 PM
          >
          >
          >
          >
          >
          >
          >
          >  
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          > Do you have any more details about the type of experiment
          >
          > you are working with?
          >
          >
          >
          > The processing scheme will depend on acquisition mode.
          >
          > Most example schemes are for hypercomplex data formats,
          >
          > typically States or States-TPPI.
          >
          >
          >
          > However, maybe your data are older-style TPPI or Absolute-value
          >
          > (Magnitude mode) data, which each require somewhat different
          >
          > processing schemes.
          >
          >
          >
          > Quoting simon sham <ssham44@yahoo. com>:
          >
          >
          >
          >> Hi,
          >
          >> I have tried to convert a JEOL Delta 2D data file to nmrpipe format
          >
          >> and processed them. I know nmrpipe can convert the data. For
          >
          >> whatever reasons, the spectrum did not look quite right.
          >
          >> Are there any special parameters that I need to know about when
          >
          >> converting/processi ng the data?
          >
          >>  
          >
          >> Thanks for your insight,
          >
          >>  
          >
          >> Simon
          >
          >>
          >
          >>
          >
          >>
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
          >
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          >
          >
        • simon sham
          Frank, Thanks for your help. In the 13C dimension, there are two sets of mirror signals at the 13C offset frequency.   Simon ... From: Frank Delaglio
          Message 4 of 5 , Feb 2, 2010
            Frank,
            Thanks for your help. In the 13C dimension, there are two sets of mirror signals at the 13C offset frequency.
             
            Simon

            --- On Tue, 2/2/10, Frank Delaglio <delaglio@...> wrote:

            From: Frank Delaglio <delaglio@...>
            Subject: Re: [nmrpipe] JEOL Delta data conversion
            To: nmrpipe@yahoogroups.com
            Date: Tuesday, February 2, 2010, 2:32 PM

             


            try magnitude mode -- none of this format was available when
            delta2pipe was developed, so the program does not recognize
            this type of data ... let us know what happens ...

            delta2pipe -in stevenlee_hmqc_ 011210-1. jdf \
            -df -dfVal 19.750000 -trVal 7.998047e-01 \
            -xN 4096 -yN 512 \
            -xT 2048 -yT 512 \
            -xMODE Complex -yMODE Real \
            -xSW 3006.976 -ySW 1511.396 \
            -xOBS 300.530 -yOBS 75.568 \
            -xCAR 4.001 -yCAR 115.000 \
            -xLAB 1H -yLAB 13C \
            -ndim 2 -aq2D Magnitude \
            -out test.fid -verb -ov

            nmrPipe -in test.fid \
            |nmrPipe -fn SP \
            |nmrPipe -fn ZF -auto \
            |nmrPipe -fn FT \
            |nmrPipe -fn TP \
            |nmrPipe -fn SP \
            |nmrPipe -fn ZF -auto \
            |nmrPipe -fn FT \
            |nmrPipe -fn MC -verb \
            |nmrPipe -fn TP \
            |nmrPipe -out hmbc.ft2 -ov

            Quoting simon sham <ssham44@yahoo. com>:

            > Hi all nmrpipers,
            >
            > The JEOL pulse sequence is HMBC_pfg.ex2:
            > #!/bin/csh
            >
            > # X-Axis Size after DF Adjustment: 2027 Complex Points.
            >
            > delta2pipe -in /home/sham/stevenle e/stevenlee_ hmqc_011210- 1.jdf \
            >   \
            >   -df -dfVal 19.750000 -trVal 7.998047e-01  \
            >   -xN              4096  -yN               512  \
            >   -xT              2048  -yT               256  \
            >   -xMODE        Complex  -yMODE        Real  \
            >   -xSW         3006.976  -ySW         1511.396  \
            >   -xOBS         300.530  -yOBS          75.568  \
            >   -xCAR           4.001  -yCAR         115.000  \
            >   -xLAB              1H  -yLAB             13C  \
            >   -ndim               2  -aq2D          States  \
            >   -out test.fid -verb -ov
            >
            > sleep 5#!/bin/csh
            >
            > nmrPipe -in /home/sham/stevenle e/test.fid \
            > |nmrPipe -fn SP -off 0.166 -end 0.98 -pow -c 1.0\
            > |nmrPipe -fn ZF -auto  \
            > |nmrPipe -fn FT -auto  \
            > |nmrPipe -fn PS -p0 123.0 -p1 0.0 -di \
            > |nmrPipe -fn POLY -auto \
            > |nmrPipe -fn TP \
            > |nmrPipe -fn SP -off 0.166 -end 0.98 -pow 1 -c 1 \
            > |nmrPipe -fn ZF -auto            \
            > |nmrPipe -fn FT -auto            \
            > |nmrPipe -fn PS -p0 0.0 -p1 0.0 -di -verb  \
            > |nmrPipe -fn TP                 \
            > |nmrPipe -out hmbc.ft2 -ov
            >
            > Thanks in advance for your help.
            >
            > Simon
            >
            > This is what I have in my processing com:
            >
            >
            >
            > The quadrature modes in both dimension in the pulse sequence:
            > collect COMPLEX, OBS REAL, IRR, NTYPE:
            >
            > This is what I have in my fid.com:
            >
            >
            >
            >
            >
            >
            >
            >
            > --- On Thu, 1/28/10, Frank Delaglio <delaglio@nmrscience .com> wrote:
            >
            > From: Frank Delaglio <delaglio@nmrscience .com>
            > Subject: Re: [nmrpipe] JEOL Delta data conversion
            > To: nmrpipe@yahoogroups .com
            > Date: Thursday, January 28, 2010, 4:50 PM
            >
            >
            >
            >
            >
            >
            >
            >  
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            > Do you have any more details about the type of experiment
            >
            > you are working with?
            >
            >
            >
            > The processing scheme will depend on acquisition mode.
            >
            > Most example schemes are for hypercomplex data formats,
            >
            > typically States or States-TPPI.
            >
            >
            >
            > However, maybe your data are older-style TPPI or Absolute-value
            >
            > (Magnitude mode) data, which each require somewhat different
            >
            > processing schemes.
            >
            >
            >
            > Quoting simon sham <ssham44@yahoo. com>:
            >
            >
            >
            >> Hi,
            >
            >> I have tried to convert a JEOL Delta 2D data file to nmrpipe format
            >
            >> and processed them. I know nmrpipe can convert the data. For
            >
            >> whatever reasons, the spectrum did not look quite right.
            >
            >> Are there any special parameters that I need to know about when
            >
            >> converting/processi ng the data?
            >
            >>  
            >
            >> Thanks for your insight,
            >
            >>  
            >
            >> Simon
            >
            >>
            >
            >>
            >
            >>
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >
            >


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