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Bruk2pipe with NUS data

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  • sette@...
    Hi all, I have a 3D acquired with Topspin 3.1 using 64 x 64 points for N15 and C13 reduced both to 25% with NUS. The strange thing happens with bruk2pipe that
    Message 1 of 7 , Mar 5, 2013
      Hi all,

      I have a 3D acquired with Topspin 3.1 using 64 x 64 points for N15 and
      C13 reduced both to 25% with NUS.
      The strange thing happens with bruk2pipe that says it's a 2D with 1024
      C13 points in F1. But in Bruker 3 dimensions appear in acquisition
      window.
      Is there a reason for this?

      Thanks,
      Marco



      Dr.Marco Sette, Ph.D.

      Department of Chemical Sciences and Technology
      University of Rome, "Tor Vergata"
      via della Ricerca Scientifica, 00133, Rome, Italy
      e-mail: sette@...
      e-mail: m77it@...
      Tel.: +39-0672594424
      Fax: +39-0672594328

      www.rete29aprile.it


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    • Matthew J. Whitley
      Hi Marco, I too was confused at first that the bruker-- pipe conversion macro wasn t getting the details of the acquired data correct when the data is acquired
      Message 2 of 7 , Mar 6, 2013
        Hi Marco,

        I too was confused at first that the bruker-->pipe conversion macro wasn't getting the details of the acquired data correct when the data is acquired in NUS mode in TopSpin 3.1.

        I believe this is happening because Bruker has changed the name of certain parameters in the newest version of TopSpin and in the newest versions of its standard pulse programs, and so NMRPipe doesn't know the correct parameters to look for.

        Whatever the cause, I have found that everything works fine when I manually changing the bruker-->pipe conversion script to correspond to what I know to be correct about the acquired data.
        For example, even though bruk2pipe thinks your data is 2D, you can change it manually to 3D processing by changing the "Dimension Count" (upper right column in the NMRPipe Conversion Utility window) to 3D and then updating the spectral widths, observed frequencies, centers, etc. to the proper values.

        Your particular results occurred because you have a grid of 64 x 64 = 4096 total pairs of indirect points, 25% of which makes 1024.

        Hope this helps, and good luck!

        Matthew
      • bigfdelaglio
        Hi All, Just as an added note, the latest NMRPipe schemes for 3D NUS data start by converting the FID as a 2D file, but with parameters filled in for all three
        Message 3 of 7 , Mar 6, 2013
          Hi All,

          Just as an added note, the latest NMRPipe schemes for 3D NUS data start
          by converting the FID as a 2D file, but with parameters filled in for
          all three dimensions. Then, a subsequent expansion script converts that
          result into a full 3D FID, with zeros for all the "missing" values.

          Cheerful Regards,

          f

          Quoting "Matthew J. Whitley" <matthew.j.whitley@...>:

          > Hi Marco,
          >
          > I too was confused at first that the bruker-->pipe conversion macro
          > wasn't getting the details of the acquired data correct when the
          > data is acquired in NUS mode in TopSpin 3.1.
          >
          > I believe this is happening because Bruker has changed the name of
          > certain parameters in the newest version of TopSpin and in the
          > newest versions of its standard pulse programs, and so NMRPipe
          > doesn't know the correct parameters to look for.
          >
          > Whatever the cause, I have found that everything works fine when I
          > manually changing the bruker-->pipe conversion script to correspond
          > to what I know to be correct about the acquired data.
          > For example, even though bruk2pipe thinks your data is 2D, you can
          > change it manually to 3D processing by changing the "Dimension
          > Count" (upper right column in the NMRPipe Conversion Utility window)
          > to 3D and then updating the spectral widths, observed frequencies,
          > centers, etc. to the proper values.
          >
          > Your particular results occurred because you have a grid of 64 x 64
          > = 4096 total pairs of indirect points, 25% of which makes 1024.
          >
          > Hope this helps, and good luck!
          >
          > Matthew
          >
          >
          >
        • sette@...
          Hi Matthew, thanks for your explanation. I used my own script to convert the 2D conversion file in a 3D conversion file but now is much more clear to me what
          Message 4 of 7 , Mar 6, 2013
            Hi Matthew,

            thanks for your explanation.
            I used my own script to convert the 2D conversion file in a 3D
            conversion file but now is much more clear to me what happens,
            especially the stranges 1024 points in F1.
            Thanks a lot !!!

            Frank, one question, everything on NUS is into the nusdemo2d and
            nusdemo3d directories or there are extra files, readme, tutorial on
            the web site?

            Cheers,
            Marco


            delaglio@... ha scritto:

            >
            > Hi All,
            >
            > Just as an added note, the latest NMRPipe schemes for 3D NUS data start
            > by converting the FID as a 2D file, but with parameters filled in for
            > all three dimensions. Then, a subsequent expansion script converts that
            > result into a full 3D FID, with zeros for all the "missing" values.
            >
            > Cheerful Regards,
            >
            > f
            >
            > Quoting "Matthew J. Whitley" <matthew.j.whitley@...>:
            >
            >> Hi Marco,
            >>
            >> I too was confused at first that the bruker-->pipe conversion macro
            >> wasn't getting the details of the acquired data correct when the
            >> data is acquired in NUS mode in TopSpin 3.1.
            >>
            >> I believe this is happening because Bruker has changed the name of
            >> certain parameters in the newest version of TopSpin and in the
            >> newest versions of its standard pulse programs, and so NMRPipe
            >> doesn't know the correct parameters to look for.
            >>
            >> Whatever the cause, I have found that everything works fine when I
            >> manually changing the bruker-->pipe conversion script to correspond
            >> to what I know to be correct about the acquired data.
            >> For example, even though bruk2pipe thinks your data is 2D, you can
            >> change it manually to 3D processing by changing the "Dimension
            >> Count" (upper right column in the NMRPipe Conversion Utility window)
            >> to 3D and then updating the spectral widths, observed frequencies,
            >> centers, etc. to the proper values.
            >>
            >> Your particular results occurred because you have a grid of 64 x 64
            >> = 4096 total pairs of indirect points, 25% of which makes 1024.
            >>
            >> Hope this helps, and good luck!
            >>
            >> Matthew
            >>
            >>
            >>
            >
            >
            >
            >



            Dr.Marco Sette, Ph.D.

            Department of Chemical Sciences and Technology
            University of Rome, "Tor Vergata"
            via della Ricerca Scientifica, 00133, Rome, Italy
            e-mail: sette@...
            e-mail: m77it@...
            Tel.: +39-0672594424
            Fax: +39-0672594328

            www.rete29aprile.it


            ----------------------------------------------------------------
            Invito da parte dell'Ateneo:
            Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del
            tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata
            codice fiscale: 80213750583 http://5x1000.uniroma2.it
          • k.kazimierczuk@cent.uw.edu.pl
            Hi Matthew, The current version of mddnmr is 2.5 and it can be downloaded from: http://mddnmr.spektrino.com/ http://mddnmr.spektrino.com/ Compressed sensing
            Message 5 of 7 , Feb 14
              Hi Matthew,

              The current version of mddnmr is 2.5 and it can be downloaded from:


              Compressed sensing algorithms of 2D/3D/4D IST and 2D/3D IRLS are included, MDD and Low-Rank.

              Cheers,
              Krzysztof Kazimierczuk
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