Loading ...
Sorry, an error occurred while loading the content.

Problems processing HMBC phase sensitive using Echo-Antiecho gradient selection

Expand Messages
  • Rosa Fayos
    Dear nmrpipe group, When I process the experiment HMBC (pulse sequence hmbcetgpl2nd ), acquired in Magnitud Mode. I get the expected spectrum but twice in
    Message 1 of 8 , Apr 3, 2008
    • 0 Attachment

      Dear nmrpipe group,


      When I process the experiment HMBC (pulse sequence  "hmbcetgpl2nd"), acquired in Magnitud Mode.
      I get the expected spectrum but twice in the indirect dimension.

      I have read old messages about processing this kind of experiments and it seems I need to pre-process the data first, adding or substracting the data.

      My queston is, how could I do this?
      Thank you very much in advance,

      -Rosa

      The scripts I am using are below:


      #!/bin/csh
      bruk2pipe -in ./ser  \
        -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
        -xN              4096  -yN                512  \
        -xT              2048  -yT                512  \
        -xMODE           DQD   -yMODE             Real \
        -xSW         12820.51  -ySW           34246.575 \
        -xOBS         800.33   -yOBS          201.243 \
        -xCAR           4.72    -yCAR           71.0  \
        -xLAB           1H     -yLAB             13C  \
        -ndim            2     -aq2D           Magnitude  \
        -out ./test.fid -verb -ov


      to process:

       nmrPipe -in test.fid \
      | nmrPipe -fn SP \
      | nmrPipe -fn ZF -size 4096 \
      | nmrPipe -fn FT -auto \
      | nmrPipe -fn TP  \
      | nmrPipe -fn SP \
      | nmrPipe -fn ZF -size 4096 \
      | nmrPipe -fn FT -real -neg\
      | nmrPipe -fn MC  \
      | nmrPipe -fn TP \
      | nmrPipe -out test.ft2 -ov



      Enviado desde Correo Yahoo!
      Disfruta de una bandeja de entrada más inteligente..
    • Siddhartha Sarma
      Your -aq2D should be complex (States) in the conversion script. You could also try the FT -auto option in the indirect dimension. The rest should be okay.
      Message 2 of 8 , Apr 3, 2008
      • 0 Attachment
        Your -aq2D should be complex (States) in the conversion script.

        You could also try the FT -auto option in the indirect dimension.


        The rest should be okay.


        Siddhartha


        On Thu, 3 Apr 2008, Rosa Fayos wrote:

        >
        > Dear nmrpipe group,
        >
        >
        > When I process the experiment HMBC (pulse sequence "hmbcetgpl2nd"), acquired in Magnitud Mode.
        > I get the expected spectrum but twice in the indirect dimension.
        >
        > I have read old messages about processing this kind of experiments and it seems I need to pre-process the data first, adding or substracting the data.
        >
        > My queston is, how could I do this?
        > Thank you very much in advance,
        >
        > -Rosa
        >
        > The scripts I am using are below:
        >
        >
        > #!/bin/csh
        > bruk2pipe -in ./ser \
        > -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
        > -xN 4096 -yN 512 \
        > -xT 2048 -yT 512 \
        > -xMODE DQD -yMODE Real \
        > -xSW 12820.51 -ySW 34246.575 \
        > -xOBS 800.33 -yOBS 201.243 \
        > -xCAR 4.72 -yCAR 71.0 \
        > -xLAB 1H -yLAB 13C \
        > -ndim 2 -aq2D Magnitude \
        > -out ./test.fid -verb -ov
        >
        >
        > to process:
        >
        > nmrPipe -in test.fid \
        > | nmrPipe -fn SP \
        > | nmrPipe -fn ZF -size 4096 \
        > | nmrPipe -fn FT -auto \
        > | nmrPipe -fn TP \
        > | nmrPipe -fn SP \
        > | nmrPipe -fn ZF -size 4096 \
        > | nmrPipe -fn FT -real -neg\
        > | nmrPipe -fn MC \
        > | nmrPipe -fn TP \
        > | nmrPipe -out test.ft2 -ov
        >
        >
        >
        > ---------------------------------
        >
        > Enviado desde Correo Yahoo!
        > Disfruta de una bandeja de entrada más inteligente..
        >
        >

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

        Tel: 80-22932839
        Fax: 80-23600535

        --
        This message has been scanned for viruses and
        dangerous content by MailScanner, and is
        believed to be clean.
      • Rosa Fayos
        Thank you Siddhartha for your quick answer. I have tried setting States in -aq2D and FT -auto in the indirect dimension but I keep getting the spectrum
        Message 3 of 8 , Apr 3, 2008
        • 0 Attachment
          Thank you Siddhartha for your quick answer.
          I have tried  setting States in -aq2D and FT -auto in the indirect dimension but I keep getting the spectrum "doubled" in the indirect dimension, the upper half part is the image of the bottom half part in the indirect dimension.

          -Rosa


          Siddhartha Sarma <sidd@...> escribió:

          Your -aq2D should be complex (States) in the conversion script.

          You could also try the FT -auto option in the indirect dimension.

          The rest should be okay.

          Siddhartha

          On Thu, 3 Apr 2008, Rosa Fayos wrote:

          >
          > Dear nmrpipe group,
          >
          >
          > When I process the experiment HMBC (pulse sequence "hmbcetgpl2nd" ), acquired in Magnitud Mode.
          > I get the expected spectrum but twice in the indirect dimension.
          >
          > I have read old messages about processing this kind of experiments and it seems I need to pre-process the data first, adding or substracting the data.
          >
          > My queston is, how could I do this?
          > Thank you very much in advance,
          >
          > -Rosa
          >
          > The scripts I am using are below:
          >
          >
          > #!/bin/csh
          > bruk2pipe -in ./ser \
          > -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
          > -xN 4096 -yN 512 \
          > -xT 2048 -yT 512 \
          > -xMODE DQD -yMODE Real \
          > -xSW 12820.51 -ySW 34246.575 \
          > -xOBS 800.33 -yOBS 201.243 \
          > -xCAR 4.72 -yCAR 71.0 \
          > -xLAB 1H -yLAB 13C \
          > -ndim 2 -aq2D Magnitude \
          > -out ./test.fid -verb -ov
          >
          >
          > to process:
          >
          > nmrPipe -in test.fid \
          > | nmrPipe -fn SP \
          > | nmrPipe -fn ZF -size 4096 \
          > | nmrPipe -fn FT -auto \
          > | nmrPipe -fn TP \
          > | nmrPipe -fn SP \
          > | nmrPipe -fn ZF -size 4096 \
          > | nmrPipe -fn FT -real -neg\
          > | nmrPipe -fn MC \
          > | nmrPipe -fn TP \
          > | nmrPipe -out test.ft2 -ov
          >
          >
          >
          > ------------ --------- --------- ---
          >
          > Enviado desde Correo Yahoo!
          > Disfruta de una bandeja de entrada más inteligente. .
          >
          >

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

          Tel: 80-22932839
          Fax: 80-23600535

          --
          This message has been scanned for viruses and
          dangerous content by MailScanner, and is
          believed to be clean.




          ¿Con Mascota por primera vez? - Sé un mejor Amigo
          Entra en Yahoo! Respuestas.

        • Scott E. Norris
          This can happen if you have the wrong number of D0 in your acquisition. The pulse programs contains 2 D0, is that what you have defined in the parameters?
          Message 4 of 8 , Apr 3, 2008
          • 0 Attachment
            Re: [nmrpipe] Problems processing HMBC phase sensitive usi
            This can happen if you have the wrong number of D0 in your acquisition. The pulse programs contains 2 D0, is that what you have defined in the parameters?

            Scott Norris
            FDA/CBER

            Thank you Siddhartha for your quick answer.
            I have tried  setting States in -aq2D and FT -auto in the indirect dimension but I keep getting the spectrum "doubled" in the indirect dimension, the upper half part is the image of the bottom half part in the indirect dimension.

            -Rosa


            Siddhartha Sarma <sidd@...> escribió:

            Your -aq2D should be complex (States) in the conversion script.

            You could also try the FT -auto option in the indirect dimension.

            The rest should be okay.

            Siddhartha

            On Thu, 3 Apr 2008, Rosa Fayos wrote:

            >
            > Dear nmrpipe group,
            >
            >
            > When I process the experiment HMBC (pulse sequence "hmbcetgpl2nd"), acquired in Magnitud Mode.
            > I get the expected spectrum but twice in the indirect dimension.
            >
            > I have read old messages about processing this kind of experiments and it seems I need to pre-process the data first, adding or substracting the data.
            >
            > My queston is, how could I do this?
            > Thank you very much in advance,
            >
            > -Rosa
            >
            > The scripts I am using are below:
            >
            >
            > #!/bin/csh
            > bruk2pipe -in ./ser \
            > -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
            > -xN 4096 -yN 512 \
            > -xT 2048 -yT 512 \
            > -xMODE DQD -yMODE Real \
            > -xSW 12820.51 -ySW 34246.575 \
            > -xOBS 800.33 -yOBS 201.243 \
            > -xCAR 4.72 -yCAR 71.0 \
            > -xLAB 1H -yLAB 13C \
            > -ndim 2 -aq2D Magnitude \
            > -out ./test.fid -verb -ov
            >
            >
            > to process:
            >
            > nmrPipe -in test.fid \
            > | nmrPipe -fn SP \
            > | nmrPipe -fn ZF -size 4096 \
            > | nmrPipe -fn FT -auto \
            > | nmrPipe -fn TP \
            > | nmrPipe -fn SP \
            > | nmrPipe -fn ZF -size 4096 \
            > | nmrPipe -fn FT -real -neg\
            > | nmrPipe -fn MC \
            > | nmrPipe -fn TP \
            > | nmrPipe -out test.ft2 -ov
            >
            >
            >
            > ---------------------------------
            >
            > Enviado desde Correo Yahoo!
            > Disfruta de una bandeja de entrada más inteligente..
            >
            >

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

            Tel: 80-22932839
            Fax: 80-23600535

            --
            This message has been scanned for viruses and
            dangerous content by MailScanner, and is
            believed to be clean.

             


            ¿Con Mascota por primera vez? - Sé un mejor Amigo
            Entra en Yahoo! Respuestas.
                                                                         


            -- 
            
            Scott Norris
            CBER/OVRR/DBPAP/LB
            301-496-0837
            "He that lies down with dogs shall rise up with fleas"
                                                    Benjamin Franklin
          • Frank Delaglio
            Here s the usual way to convert and process Magnitude-mode spectra. -yN and -yT will generally be the same -yMODE Real -aq2D Magnitude During processing, use
            Message 5 of 8 , Apr 3, 2008
            • 0 Attachment
              Here's the usual way to convert and process Magnitude-mode spectra.

              -yN and -yT will generally be the same
              -yMODE Real
              -aq2D Magnitude

              During processing, use ordinary FT, do not delete the imaginaries
              after the direct dimension is transformed. If the indirect dimension
              is reversed in the result, use "FT -neg" there instead of "FT".

              bruk2pipe -in ./ser \
              -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719 \
              -xN 4096 -yN 512 \
              -xT 2048 -yT 512 \
              -xMODE DQD -yMODE Real \
              -xSW 12820.51 -ySW 34246.575 \
              -xOBS 800.33 -yOBS 201.243 \
              -xCAR 4.72 -yCAR 71.0 \
              -xLAB 1H -yLAB 13C \
              -ndim 2 -aq2D Magnitude \
              -out ./test.fid -verb -ov

              nmrPipe -in test.fid \
              | nmrPipe -fn SP \
              | nmrPipe -fn ZF -size 4096 \
              | nmrPipe -fn FT -auto \
              | nmrPipe -fn TP \
              | nmrPipe -fn SP \
              | nmrPipe -fn ZF -size 4096 \
              | nmrPipe -fn FT -neg \
              | nmrPipe -fn MC \
              | nmrPipe -fn TP \
              | nmrPipe -out test.ft2 -ov

              Quoting "Scott E. Norris" <sen@...>:

              > This can happen if you have the wrong number of D0 in your acquisition.
              > The pulse programs contains 2 D0, is that what you have defined in the
              > parameters?
              >
              > Scott Norris
              > FDA/CBER
              >
              >> Thank you Siddhartha for your quick answer.
              >> I have tried setting States in -aq2D and FT -auto in the indirect
              >> dimension but I keep getting the spectrum "doubled" in the indirect
              >> dimension, the upper half part is the image of the bottom half
              >> part in the indirect dimension.
              >>
              >> -Rosa
              >>
              >>
              >> Siddhartha Sarma <sidd@...> escribió:
              >>
              >>
              >> Your -aq2D should be complex (States) in the conversion script.
              >>
              >> You could also try the FT -auto option in the indirect dimension.
              >>
              >> The rest should be okay.
              >>
              >> Siddhartha
              >>
              >> On Thu, 3 Apr 2008, Rosa Fayos wrote:
              >>
              >>>
              >>> Dear nmrpipe group,
              >>>
              >>>
              >>> When I process the experiment HMBC (pulse sequence
              >>> "hmbcetgpl2nd"), acquired in Magnitud Mode.
              >>> I get the expected spectrum but twice in the indirect dimension.
              >>>
              >>> I have read old messages about processing this kind of experiments
              >>> and it seems I need to pre-process the data first, adding or
              >>> substracting the data.
              >>>
              >>> My queston is, how could I do this?
              >>> Thank you very much in advance,
              >>>
              >>> -Rosa
              >>>
              >>> The scripts I am using are below:
              >>>
              >>>
              >>> #!/bin/csh
              >>> bruk2pipe -in ./ser \
              >>> -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
              >>> -xN 4096 -yN 512 \
              >>> -xT 2048 -yT 512 \
              >>> -xMODE DQD -yMODE Real \
              >>> -xSW 12820.51 -ySW 34246.575 \
              >>> -xOBS 800.33 -yOBS 201.243 \
              >>> -xCAR 4.72 -yCAR 71.0 \
              >>> -xLAB 1H -yLAB 13C \
              >>> -ndim 2 -aq2D Magnitude \
              >>> -out ./test.fid -verb -ov
              >>>
              >>>
              >>> to process:
              >>>
              >>> nmrPipe -in test.fid \
              >>> | nmrPipe -fn SP \
              >>> | nmrPipe -fn ZF -size 4096 \
              >>> | nmrPipe -fn FT -auto \
              >>> | nmrPipe -fn TP \
              >>> | nmrPipe -fn SP \
              >>> | nmrPipe -fn ZF -size 4096 \
              >>> | nmrPipe -fn FT -real -neg\
              >>> | nmrPipe -fn MC \
              >>> | nmrPipe -fn TP \
              >>> | nmrPipe -out test.ft2 -ov
              >>>
              >>>
              >>>
              >>> ---------------------------------
              >>>
              >>> Enviado desde Correo Yahoo!
              >>> Disfruta de una bandeja de entrada más inteligente..
              >>>
              >>>
              >>
              >> --
              >> Siddhartha P. Sarma
              >> Associate Professor
              >> Molecular Biophysics Unit
              >> Indian Institute of Science
              >> Bangalore, Karnataka - 560 012
              >> INDIA
              >>
              >> Tel: 80-22932839
              >> Fax: 80-23600535
              >>
              >> --
              >> This message has been scanned for viruses and
              >> dangerous content by MailScanner, and is
              >> believed to be clean.
              >>
              >>
              >>
              >>
              >>
              >> ¿Con Mascota por primera vez? - Sé un mejor Amigo
              >> <http://es.rd.yahoo.com/evt:51361/*http://es.answers.yahoo.com/dir/index;_ylc=X3oDMTE4ZWhyZjU0BF9TAzIxMTQ3MTQzMjIEc2VjA0Jhbm5lcgRzbGsDQWNxdWlzaXRpb24-?link=over&sid=XXXXXXXX>Entra en Yahoo!
              >> Respuestas.
              >>
              >>
              >
              >
              > --
              > Scott Norris
              > CBER/OVRR/DBPAP/LB
              > 301-496-0837
              > "He that lies down with dogs shall rise up with fleas"
              > Benjamin Franklin
            • Rosa Fayos
              Yes, the ND0 was set to 2, and when I process the spectrum with xwinnmr or topspin it looks fine, thank you for your email, -Rosa --- El jue, 3/4/08, Scott E.
              Message 6 of 8 , Apr 4, 2008
              • 0 Attachment


                Yes, the ND0 was set to 2, and when I process the spectrum with xwinnmr or topspin it looks fine,
                thank you for your email,

                -Rosa




                --- El jue, 3/4/08, Scott E. Norris <sen@...> escribió:
                De: Scott E. Norris <sen@...>
                Asunto: Re: [nmrpipe] Problems processing HMBC phase sensitive using Echo-Antiecho gradient selection
                Para: nmrpipe@yahoogroups.com
                Fecha: jueves, 3 abril, 2008 2:46

                This can happen if you have the wrong number of D0 in your acquisition. The pulse programs contains 2 D0, is that what you have defined in the parameters?

                Scott Norris
                FDA/CBER

                Thank you Siddhartha for your quick answer.
                I have tried  setting States in -aq2D and FT -auto in the indirect dimension but I keep getting the spectrum "doubled" in the indirect dimension, the upper half part is the image of the bottom half part in the indirect dimension.

                -Rosa


                Siddhartha Sarma <sidd@.... ernet.in> escribió:

                Your -aq2D should be complex (States) in the conversion script.

                You could also try the FT -auto option in the indirect dimension.

                The rest should be okay.

                Siddhartha

                On Thu, 3 Apr 2008, Rosa Fayos wrote:

                >
                > Dear nmrpipe group,
                >
                >
                > When I process the experiment HMBC (pulse sequence "hmbcetgpl2nd"), acquired in Magnitud Mode.
                > I get the expected spectrum but twice in the indirect dimension.
                >
                > I have read old messages about processing this kind of experiments and it seems I need to pre-process the data first, adding or substracting the data.
                >
                > My queston is, how could I do this?
                > Thank you very much in advance,
                >
                > -Rosa
                >
                > The scripts I am using are below:
                >
                >
                > #!/bin/csh
                > bruk2pipe -in ./ser \
                > -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
                > -xN 4096 -yN 512 \
                > -xT 2048 -yT 512 \
                > -xMODE DQD -yMODE Real \
                > -xSW 12820.51 -ySW 34246.575 \
                > -xOBS 800.33 -yOBS 201.243 \
                > -xCAR 4.72 -yCAR 71.0 \
                > -xLAB 1H -yLAB 13C \
                > -ndim 2 -aq2D Magnitude \
                > -out ./test.fid -verb -ov
                >
                >
                > to process:
                >
                > nmrPipe -in test.fid \
                > | nmrPipe -fn SP \
                > | nmrPipe -fn ZF -size 4096 \
                > | nmrPipe -fn FT -auto \
                > | nmrPipe -fn TP \
                > | nmrPipe -fn SP \
                > | nmrPipe -fn ZF -size 4096 \
                > | nmrPipe -fn FT -real -neg\
                > | nmrPipe -fn MC \
                > | nmrPipe -fn TP \
                > | nmrPipe -out test.ft2 -ov
                >
                >
                >
                > ------------ --------- --------- ---
                >
                > Enviado desde Correo Yahoo!
                > Disfruta de una bandeja de entrada más inteligente. .
                >
                >

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

                Tel: 80-22932839
                Fax: 80-23600535

                --
                This message has been scanned for viruses and
                dangerous content by MailScanner, and is
                believed to be clean.

                 


                ¿Con Mascota por primera vez? - Sé un mejor Amigo
                Entra en Yahoo! Respuestas.
                                                                             


                -- 
                Scott Norris
                CBER/OVRR/DBPAP/ LB
                301-496-0837
                "He that lies down with dogs shall rise up with fleas"
                                                        Benjamin Franklin



                ¿Con Mascota por primera vez? - Sé un mejor Amigo
                Entra en Yahoo! Respuestas.
              • Rosa Fayos
                Yes, that is the way I´ve tried to convert and process the spectrum but I keep getting the doubled spectrum in the indirect dimension, Thanks, -Rosa --- El
                Message 7 of 8 , Apr 4, 2008
                • 0 Attachment


                  Yes, that is the way I´ve tried to convert and process the spectrum but I keep getting the "doubled" spectrum in the indirect dimension,
                  Thanks,
                  -Rosa


                  --- El jue, 3/4/08, Frank Delaglio <delaglio@...> escribió:
                  De: Frank Delaglio <delaglio@...>
                  Asunto: Re: [nmrpipe] Problems processing HMBC phase sensitive using Echo-Antiecho gradient selection
                  Para: nmrpipe@yahoogroups.com
                  Fecha: jueves, 3 abril, 2008 6:19



                  Here's the usual way to convert and process Magnitude-mode spectra.

                  -yN and -yT will generally be the same
                  -yMODE Real
                  -aq2D Magnitude

                  During processing, use ordinary FT, do not delete the imaginaries
                  after the direct dimension is transformed. If the indirect dimension
                  is reversed in the result, use "FT -neg" there instead of "FT".

                  bruk2pipe -in ./ser \
                  -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719 \
                  -xN 4096 -yN 512 \
                  -xT 2048 -yT 512 \
                  -xMODE DQD -yMODE Real \
                  -xSW 12820.51 -ySW 34246.575 \
                  -xOBS 800.33 -yOBS 201.243 \
                  -xCAR 4.72 -yCAR 71.0 \
                  -xLAB 1H -yLAB 13C \
                  -ndim 2 -aq2D Magnitude \
                  -out ./test.fid -verb -ov

                  nmrPipe -in test.fid \
                  | nmrPipe -fn SP \
                  | nmrPipe -fn ZF -size 4096 \
                  | nmrPipe -fn FT -auto \
                  | nmrPipe -fn TP \
                  | nmrPipe -fn SP \
                  | nmrPipe -fn ZF -size 4096 \
                  | nmrPipe -fn FT -neg \
                  | nmrPipe -fn MC \
                  | nmrPipe -fn TP \
                  | nmrPipe -out test.ft2 -ov

                  Quoting "Scott E. Norris" <sen@.... nih.gov>:

                  > This can happen if you have the wrong number of D0 in your acquisition.
                  > The pulse programs contains 2 D0, is that what you have defined in the
                  > parameters?
                  >
                  > Scott Norris
                  > FDA/CBER
                  >
                  >> Thank you Siddhartha for your quick answer.
                  >> I have tried setting States in -aq2D and FT -auto in the indirect
                  >> dimension but I keep getting the spectrum "doubled" in the indirect
                  >> dimension, the upper half part is the image of the bottom half
                  >> part in the indirect dimension.
                  >>
                  >> -Rosa
                  >>
                  >>
                  >> Siddhartha Sarma <sidd@.... ernet.in> escribió:
                  >>
                  >>
                  >> Your -aq2D should be complex (States) in the conversion script.
                  >>
                  >> You could also try the FT -auto option in the indirect dimension.
                  >>
                  >> The rest should be okay.
                  >>
                  >> Siddhartha
                  >>
                  >> On Thu, 3 Apr 2008, Rosa Fayos wrote:
                  >>
                  >>>
                  >>> Dear nmrpipe group,
                  >>>
                  >>>
                  >>> When I process the experiment HMBC (pulse sequence
                  >>> "hmbcetgpl2nd" ), acquired in Magnitud Mode.
                  >>> I get the expected spectrum but twice in the indirect dimension.
                  >>>
                  >>> I have read old messages about processing this kind of experiments
                  >>> and it seems I need to pre-process the data first, adding or
                  >>> substracting the data.
                  >>>
                  >>> My queston is, how could I do this?
                  >>> Thank you very much in advance,
                  >>>
                  >>> -Rosa
                  >>>
                  >>> The scripts I am using are below:
                  >>>
                  >>>
                  >>> #!/bin/csh
                  >>> bruk2pipe -in ./ser \
                  >>> -bad 0.0 -aswap -AMX -decim 1560 -dspfvs 20 -grpdly 67.9867858886719\
                  >>> -xN 4096 -yN 512 \
                  >>> -xT 2048 -yT 512 \
                  >>> -xMODE DQD -yMODE Real \
                  >>> -xSW 12820.51 -ySW 34246.575 \
                  >>> -xOBS 800.33 -yOBS 201.243 \
                  >>> -xCAR 4.72 -yCAR 71.0 \
                  >>> -xLAB 1H -yLAB 13C \
                  >>> -ndim 2 -aq2D Magnitude \
                  >>> -out ./test.fid -verb -ov
                  >>>
                  >>>
                  >>> to process:
                  >>>
                  >>> nmrPipe -in test.fid \
                  >>> | nmrPipe -fn SP \
                  >>> | nmrPipe -fn ZF -size 4096 \
                  >>> | nmrPipe -fn FT -auto \
                  >>> | nmrPipe -fn TP \
                  >>> | nmrPipe -fn SP \
                  >>> | nmrPipe -fn ZF -size 4096 \
                  >>> | nmrPipe -fn FT -real -neg\
                  >>> | nmrPipe -fn MC \
                  >>> | nmrPipe -fn TP \
                  >>> | nmrPipe -out test.ft2 -ov
                  >>>
                  >>>
                  >>>
                  >>> ------------ --------- --------- ---
                  >>>
                  >>> Enviado desde Correo Yahoo!
                  >>> Disfruta de una bandeja de entrada más inteligente. .
                  >>>
                  >>>
                  >>
                  >> --
                  >> Siddhartha P. Sarma
                  >> Associate Professor
                  >> Molecular Biophysics Unit
                  >> Indian Institute of Science
                  >> Bangalore, Karnataka - 560 012
                  >> INDIA
                  >>
                  >> Tel: 80-22932839
                  >> Fax: 80-23600535
                  >>
                  >> --
                  >> This message has been scanned for viruses and
                  >> dangerous content by MailScanner, and is
                  >> believed to be clean.
                  >>
                  >>
                  >>
                  >>
                  >>
                  >> ¿Con Mascota por primera vez? - Sé un mejor Amigo
                  >> <http://es.rd. yahoo.com/ evt:51361/ *http://es. answers.yahoo. com/dir/index; _ylc=X3oDMTE4ZWh yZjU0BF9TAzIxMTQ 3MTQzMjIEc2VjA0J hbm5lcgRzbGsDQWN xdWlzaXRpb24- ?link=over& sid=XXXXXXXX>Entra en Yahoo!
                  >> Respuestas.
                  >>
                  >>
                  >
                  >
                  > --
                  > Scott Norris
                  > CBER/OVRR/DBPAP/ LB
                  > 301-496-0837
                  > "He that lies down with dogs shall rise up with fleas"
                  > Benjamin Franklin




                  ¿Con Mascota por primera vez? - Sé un mejor Amigo
                  Entra en Yahoo! Respuestas.
                • afowler13
                  Hi Rosa, Here s what I got to work for processing HMBC from our AvanceII; the pulse program was hmbcgplpndqf, so slightly different than yours. Note that both
                  Message 8 of 8 , Apr 16, 2008
                  • 0 Attachment
                    Hi Rosa,

                    Here's what I got to work for processing HMBC from our AvanceII; the
                    pulse program was hmbcgplpndqf, so slightly different than yours. Note
                    that both dimensions use complex FT and that the imaginaries are not
                    deleted in the direct dimension phasing.

                    fid.com:

                    #!/bin/csh

                    bruk2pipe -in ./ser \
                    -bad 0.0 -aswap -DMX -decim 1664 -dspfvs 20 -grpdly 67.9841613769531 \
                    -xN 4096 -yN 200 \
                    -xT 2048 -yT 200 \
                    -xMODE DQD -yMODE TPPI \
                    -xSW 12019.231 -ySW 44642.857 \
                    -xOBS 800.224 -yOBS 201.236 \
                    -xCAR 4.773 -yCAR 102.555 \
                    -xLAB 1H -yLAB 13C \
                    -ndim 2 -aq2D States \
                    -out ./test.fid -verb -ov

                    nmrproc.com:

                    #!/bin/csh

                    # note 2nd dimension FT does NOT use -real flag or the spectrum
                    # will be shifted in a strange way. Ignore the warning.
                    # need to optimize indirect window to reduce wings.

                    nmrPipe -in test.fid \
                    | nmrPipe -fn SP -off 0.35 -end 1.00 -pow 2 -c 0.5 \
                    | nmrPipe -fn ZF -auto \
                    | nmrPipe -fn FT -auto \
                    | nmrPipe -fn PS -p0 0.00 -p1 0.00 -verb \
                    | nmrPipe -fn TP \
                    | nmrPipe -fn SP -off 0.4 -end 1.0 -pow 2 -c 1.0 \
                    | nmrPipe -fn ZF -size 1024 \
                    | nmrPipe -fn FT -neg \
                    | nmrPipe -fn MC -di -verb \
                    | nmrPipe -fn TP \
                    | nmrPipe -fn POLY -auto -ord 1 \
                    -ov -out test.ft2

                    Hope this helps.
                    Cheers,
                    Andrew
                  Your message has been successfully submitted and would be delivered to recipients shortly.