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Coversion of BRUKER data

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  • Per Eugen Kristiansen
    I am trying to convert BRUKER data to NMRpipe format, but do always end up with about 70 datapoints that are ~0 in the fid s. Is there a way that i can easilly
    Message 1 of 6 , Jun 12, 2005
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      I am trying to convert BRUKER data to NMRpipe format, but do always end up
      with about 70 datapoints that are ~0 in the fid's. Is there a way that i can
      easilly avoid this?
      What am i doing wrong?

      Per Eugen Kristiansen
    • Atom Crystal
      post your acqus and convert script. possibly problem related to Bruker s decim and dspfvs. ... http://us.click.yahoo.com/RzSHvD/UOnJAA/79vVAA/cEYolB/TM ...
      Message 2 of 6 , Jun 12, 2005
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        post your acqus and convert script. possibly problem
        related to Bruker's decim and dspfvs.

        --- Per Eugen Kristiansen <eugen@...> wrote:

        > I am trying to convert BRUKER data to NMRpipe
        > format, but do always end up
        > with about 70 datapoints that are ~0 in the fid's.
        > Is there a way that i can
        > easilly avoid this?
        > What am i doing wrong?
        >
        > Per Eugen Kristiansen
        >
        >
        >
        >
        >
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      • Per Eugen Kristiansen
        Hi Sending an example of the fid i have truble converting from bruker to NMRpipe. The script was obtained by the bruker program. The script in the tar file
        Message 3 of 6 , Jun 13, 2005
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          Hi

          Sending an example of the fid i have truble converting from bruker to
          NMRpipe. The script was obtained by the bruker program. The script in the
          tar file does actually not work on my machine, as neither the DECIM value or
          the dspfvs value are recognized as valid values when the script is runing.

          If someone could help me ensure a way to obatain a script that would
          translate the fid in a good way it would be appreciated.

          Per Eugen
          From: "Atom Crystal" <crystalatom@...>
          To: <nmrpipe@yahoogroups.com>
          Sent: Sunday, June 12, 2005 7:41 PM
          Subject: Re: [nmrpipe] Coversion of BRUKER data


          > post your acqus and convert script. possibly problem
          > related to Bruker's decim and dspfvs.
          >
          > --- Per Eugen Kristiansen <eugen@...> wrote:
          >
          >> I am trying to convert BRUKER data to NMRpipe
          >> format, but do always end up
          >> with about 70 datapoints that are ~0 in the fid's.
          >> Is there a way that i can
          >> easilly avoid this?
          >> What am i doing wrong?
          >>
          >> Per Eugen Kristiansen
          >>
          >>
          >>
          >>
          >>
          >> ------------------------ Yahoo! Groups Sponsor
          >>
          >>
          >>
          >> Yahoo! Groups Links
          >>
          >>
          >> nmrpipe-unsubscribe@yahoogroups.com
          >>
          >>
          >>
          >>
          >>
          >
          >
          > __________________________________________________
          > Do You Yahoo!?
          > Tired of spam? Yahoo! Mail has the best spam protection around
          > http://mail.yahoo.com
          >
          >
          >
          >
          >
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          >
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        • Frank Delaglio
          Get the latest version of NMRPipe, which has facilities for converting this newer type of DRU Bruker data ... you can identify this data by looking for GRPDLY
          Message 4 of 6 , Jun 13, 2005
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            Get the latest version of NMRPipe, which has facilities for
            converting this newer type of DRU Bruker data ... you can identify
            this data by looking for GRPDLY in the acq files ...


            On Mon, 13 Jun 2005, Per Eugen Kristiansen wrote:

            > Hi
            >
            > Sending an example of the fid i have truble converting from bruker to
            > NMRpipe. The script was obtained by the bruker program. The script in the
            > tar file does actually not work on my machine, as neither the DECIM value or
            > the dspfvs value are recognized as valid values when the script is runing.
            >
            > If someone could help me ensure a way to obatain a script that would
            > translate the fid in a good way it would be appreciated.
            >
            > Per Eugen
            > From: "Atom Crystal" <crystalatom@...>
            > To: <nmrpipe@yahoogroups.com>
            > Sent: Sunday, June 12, 2005 7:41 PM
            > Subject: Re: [nmrpipe] Coversion of BRUKER data
            >
            >
            > > post your acqus and convert script. possibly problem
            > > related to Bruker's decim and dspfvs.
            > >
            > > --- Per Eugen Kristiansen <eugen@...> wrote:
            > >
            > >> I am trying to convert BRUKER data to NMRpipe
            > >> format, but do always end up
            > >> with about 70 datapoints that are ~0 in the fid's.
            > >> Is there a way that i can
            > >> easilly avoid this?
            > >> What am i doing wrong?
            > >>
            > >> Per Eugen Kristiansen
            > >>
            > >>
            > >>
            > >>
            > >>
            > >> ------------------------ Yahoo! Groups Sponsor
            > >>
            > >>
            > >>
            > >> Yahoo! Groups Links
            > >>
            > >>
            > >> nmrpipe-unsubscribe@yahoogroups.com
            > >>
            > >>
            > >>
            > >>
            > >>
            > >
            > >
            > > __________________________________________________
            > > Do You Yahoo!?
            > > Tired of spam? Yahoo! Mail has the best spam protection around
            > > http://mail.yahoo.com
            > >
            > >
            > >
            > >
            > >
            > >
            > >
            > > Yahoo! Groups Links
            > >
            > >
            > >
            > >
            > >
            > >
            >
            >
            >
            >
            > Yahoo! Groups Links
            >
            >
            >
            >
            >
          • Ryan McKay
            Depending on the computer platform used to collect the data and the subsequent computer used to process you may need to set the -swap in the opening line. e.g.
            Message 5 of 6 , Jun 13, 2005
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              Depending on the computer platform used to collect the data and the subsequent computer used to process you may need to set the -swap in the opening line.

              e.g.
              bruk2pipe -in ./ser -bad 0.0 -noaswap -DMX -decim 16 -dspfvs 12  \


              Typically the "bruker" program will set the -decim etc. for you and get it correct(?).

              Ryan



              On Jun 13,, at 1:22 AM, Per Eugen Kristiansen wrote:

              <bruker.tar>






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

              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

              Security Certificate .p7s is included for address confirmation.




            • Ryan McKay
              I ran bruker on your data and got the following for the fid.com #!/bin/csh bruk2pipe -in ./fid -bad 0.0 -aswap -DMX -decim 2080 -dspfvs 20 - grpdly 68 -xN
              Message 6 of 6 , Jun 13, 2005
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                I ran "bruker" on your data and got the following for the fid.com

                #!/bin/csh

                bruk2pipe -in ./fid -bad 0.0 -aswap -DMX -decim 2080 -dspfvs 20 -grpdly 68  \
                  -xN             18432  \
                  -xT              9216  \
                  -xMODE            DQD  \
                  -xSW         9615.385  \
                  -xOBS         600.133  \
                  -xCAR           4.773  \
                  -xLAB              F3  \
                  -ndim               1  \
                  -out ./test.fid -verb -ov

                sleep 5


                I used the following processing scheme:

                ryan% more nmrproc.com
                #!/bin/csh


                nmrPipe -in test.fid \
                | nmrPipe -fn POLY -time                                       \
                | nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 1 -c 1.0    \
                | nmrPipe  -fn ZF -auto                               \
                | nmrPipe  -fn FT -auto                               \
                | nmrPipe  -fn PS -p0 0.00 -p1 0.00 -di -verb         \
                   -ov -out test.ft2

                And got a typical 1D spectra with a large water peak at ~4.9ppm and a singlet at 3.9ppm.

                Edge digital processing was also evident along with some very weak peaks in the 0.5 to 3ppm region.

                Looks like water suppression is the largest problem not processing.

                Best wishes,
                Ryan

                ps below is a screen capture of the 1D result (not sure if attachments are allowed).




                On Jun 13,, at 1:22 AM, Per Eugen Kristiansen wrote:

                <bruker.tar>






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

                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

                Security Certificate .p7s is included for address confirmation.




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