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Bruker NUS data processing using nmrPipe

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  • Weidong Hu
    Dear nmrPipe users,   We just installed a new Bruker 700 with NUS package. A user collected a 3D data set, but could not process the data since the MDD
    Message 1 of 7 , Feb 11, 2013
      Dear nmrPipe users,
       
      We just installed a new Bruker 700 with NUS package. A user collected a 3D data set, but could not process the data since the MDD processing package coming with Topspin 3.1 was a trial version, and expired after new year (Jan. 1st, 2013). I am wondering could we process the NUS 2D to 4D with nmrPipe, if so, could someone share the procedure how to do it?
       
      Thank you very much.
       
      Weidong
       
       
    • mattjwoa
      Hi Weidong, nmrPipe does not have MDD functionality to my knowledge, but it does have the capability of reconstructing spectra from non-uniformly sampled NMR
      Message 2 of 7 , Feb 19, 2013
        Hi Weidong,

        nmrPipe does not have MDD functionality to my knowledge, but it does have the capability of reconstructing spectra from non-uniformly sampled NMR data using a maximum entropy algorithm, which is just a different approach compared to MDD. The nmrPipe function is called MEM, and you can read all about it by searching MEM using Google or by reading the MEM man page.

        Alternatively, you can just download the MDD software directly and process the data offline from the spectrometer. I believe the current version of the mddnmr software is 2.2. There is also a web portal where you can submit data for spectral reconstruction by MDD:
        http://www.enmr.eu/webportal/mdd.html


        Hope this helps.

        Matthew


        --- In nmrpipe@yahoogroups.com, Weidong Hu <lakesu@...> wrote:
        >
        > Dear nmrPipe users,
        >  
        > We just installed a new Bruker 700 with NUS package. A user collected a 3D data set, but could not process the data since the MDD processing package coming with Topspin 3.1 was a trial version, and expired after new year (Jan. 1st, 2013). I am wondering could we process the NUS 2D to 4D with nmrPipe, if so, could someone share the procedure how to do it?
        >  
        > Thank you very much.
        >  
        > Weidong
        >  
        >  
        >
      • 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 3 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


          ----------------------------------------------------------------
          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
        • 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 4 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 5 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 6 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 7 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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