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Re: [nmrpipe] binary conversion from NTNMR

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  • Frank Delaglio
    what s your question??
    Message 1 of 8 , Nov 7, 2005
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      what's your question??


      On Fri, 4 Nov 2005, Loren Andreas wrote:

      > pipers,
      > I'm fairly new at this.
      > I am converting a 2D file aquired with the States method. (Collected in the order RIRI for each T1 point; The
      > first RI is for the virtual "real" and the second RI for the virtural "imaginary"). My script does not result in any
      > negative shifts in the NMR spectrum:
      >
      > bin2pipe -in AFG2d.mn5 -bo 2048 -ri -noswap \
      > -xN 2048 -yN 650 \
      > -xT 1024 -yT 650 \
      > -xMODE Complex -yMODE Complex \
      > -xSW 50000.00 -ySW 50000.0 \
      > -xOBS 150.991133 -yOBS 150.991133 \
      > -xCAR 0 -yCAR 0 \
      > -xLAB 13C -yLAB 13C \
      > -ndim 2 -aq2D states \
      > -out AFG2d.dat -verb -ov
      >
      > if I make -yN 1300, I get the following error:
      >
      > DATAIO File Read Error 0.
      > Request: 21299200 Actual: 5326848.
      >
      > I'm not sure what the proper format is in Pipe language.
      >
      > thanks in advance
      >
      > -Loren Andreas
      >
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >
      >
      >
      >
    • Frank Delaglio
      btw usually value for yN is 2x the value for yT ...
      Message 2 of 8 , Nov 7, 2005
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        btw usually value for "yN" is 2x the value for "yT" ...


        On Mon, 7 Nov 2005, Frank Delaglio wrote:

        >
        > what's your question??
        >
        >
        > On Fri, 4 Nov 2005, Loren Andreas wrote:
        >
        > > pipers,
        > > I'm fairly new at this.
        > > I am converting a 2D file aquired with the States method. (Collected in the order RIRI for each T1 point; The
        > > first RI is for the virtual "real" and the second RI for the virtural "imaginary"). My script does not result in any
        > > negative shifts in the NMR spectrum:
        > >
        > > bin2pipe -in AFG2d.mn5 -bo 2048 -ri -noswap \
        > > -xN 2048 -yN 650 \
        > > -xT 1024 -yT 650 \
        > > -xMODE Complex -yMODE Complex \
        > > -xSW 50000.00 -ySW 50000.0 \
        > > -xOBS 150.991133 -yOBS 150.991133 \
        > > -xCAR 0 -yCAR 0 \
        > > -xLAB 13C -yLAB 13C \
        > > -ndim 2 -aq2D states \
        > > -out AFG2d.dat -verb -ov
        > >
        > > if I make -yN 1300, I get the following error:
        > >
        > > DATAIO File Read Error 0.
        > > Request: 21299200 Actual: 5326848.
        > >
        > > I'm not sure what the proper format is in Pipe language.
        > >
        > > thanks in advance
        > >
        > > -Loren Andreas
        > >
        > >
        > >
        > >
        > > Yahoo! Groups Links
        > >
        > >
        > >
        > >
        > >
        > >
        > >
        >
        >
        >
        >
        > Yahoo! Groups Links
        >
        >
        >
        >
        >
        >
        >
        >
      • youngredg cheerful
        ... hi, I met problems when I wanted to tranfer arrayed data from varian inova to delta. They were automatically transfered to 1D data. However, in delta
        Message 3 of 8 , Nov 7, 2005
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          >
          > what's your question??
          >
          hi,
          I met problems when I wanted to tranfer arrayed data
          from varian inova to delta. They were automatically
          transfered to 1D data. However, in delta software, it
          said that when processing arrayed data, they should be
          automatically transfered to 2D data. My question is
          how to process nmr data which come from varian inova
          in jeol delta software.
          please help me
          cheers



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        • Loren Andreas
          I ll try to phrase this more clearly. When I make yN 2x yT, I get a read error that makes me think the program gas come to the end of the file. yT is the
          Message 4 of 8 , Nov 7, 2005
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            I'll try to phrase this more clearly. When I make yN 2x yT, I get a read error that makes me think the program gas
            come to the end of the file. yT is the correct number of time points, which makes me think that my script is
            reading the file incorrectly.

            So is there a different aquisition mode that I should use besides the preset states method when the ordering of the
            spectra in the binary file is RI(real)RI(imag) for each T1 point?

            thanks,
            Loren

            ----- Original Message -----
            From: Frank Delaglio <delaglio@...>
            Date: Monday, November 7, 2005 9:40 am
            Subject: Re: [nmrpipe] binary conversion from NTNMR
            >
            > btw usually value for "yN" is 2x the value for "yT" ...
            >
            >
            > On Mon, 7 Nov 2005, Frank Delaglio wrote:
            >
            > >
            > > what's your question??
            > >
            > >
            > > On Fri, 4 Nov 2005, Loren Andreas wrote:
            > >
            > > > pipers,
            > > > I'm fairly new at this.
            > > > I am converting a 2D file aquired with the States method.
            > (Collected in the order RIRI for each T1 point; The
            > > > first RI is for the virtual "real" and the second RI for the
            > virtural "imaginary"). My script does not result in any
            > > > negative shifts in the NMR spectrum:
            > > >
            > > > bin2pipe -in AFG2d.mn5 -bo 2048 -ri -noswap \
            > > > -xN 2048 -yN 650 \
            > > > -xT 1024 -yT 650 \
            > > > -xMODE Complex -yMODE Complex \
            > > > -xSW 50000.00 -ySW 50000.0 \
            > > > -xOBS 150.991133 -yOBS 150.991133 \
            > > > -xCAR 0 -yCAR 0 \
            > > > -xLAB 13C -yLAB 13C \
            > > > -ndim 2 -aq2D states \
            > > > -out AFG2d.dat -verb -ov
            > > >
            > > > if I make -yN 1300, I get the following error:
            > > >
            > > > DATAIO File Read Error 0.
            > > > Request: 21299200 Actual: 5326848.
            > > >
            > > > I'm not sure what the proper format is in Pipe language.
            > > >
            > > > thanks in advance
            > > >
            > > > -Loren Andreas
            > > >
            > > >
            > > >
            > > >
            > > > Yahoo! Groups Links
            > > >
            > > >
            > > >
            > > >
            > > >
            > > >
            > > >
            > >
            > >
            > >
            > >
            > > Yahoo! Groups Links
            > >
            > >
            > >
            > >
            > >
            > >
            > >
            > >
            >
            >
            > ------------------------ Yahoo! Groups Sponsor --------------------
            > ~-->
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          • Frank Delaglio
            Hi Loren, Probably, one or both X/Y sizes are wrong by 2x. The size of your input file should be: (bo) + (xN)*(yN)*(bytes per word) So, your input size of
            Message 5 of 8 , Nov 7, 2005
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              Hi Loren,

              Probably, one or both X/Y sizes are wrong by 2x.

              The size of your input file should be:

              (bo) + (xN)*(yN)*(bytes per word)

              So, your input size of 5326848 bytes is consistant with either:

              -xN 2048 -yN 650 \
              -xT 1024 -yT 325 \

              OR

              -xN 1024 -yN 1300 \
              -xT 512 -yT 650 \

              The xN yN parameters are the TOTAL NUMBER of 4-byte points stored
              in the file for the given dimension

              For states mode data, xT and yT will generally be half of the above
              values.


              On Mon, 7 Nov 2005, Loren Andreas wrote:

              > I'll try to phrase this more clearly. When I make yN 2x yT, I get a read error that makes me think the program gas
              > come to the end of the file. yT is the correct number of time points, which makes me think that my script is
              > reading the file incorrectly.
              >
              > So is there a different aquisition mode that I should use besides the preset states method when the ordering of the
              > spectra in the binary file is RI(real)RI(imag) for each T1 point?
              >
              > thanks,
              > Loren
              >
              > ----- Original Message -----
              > From: Frank Delaglio <delaglio@...>
              > Date: Monday, November 7, 2005 9:40 am
              > Subject: Re: [nmrpipe] binary conversion from NTNMR
              > >
              > > btw usually value for "yN" is 2x the value for "yT" ...
              > >
              > >
              > > On Mon, 7 Nov 2005, Frank Delaglio wrote:
              > >
              > > >
              > > > what's your question??
              > > >
              > > >
              > > > On Fri, 4 Nov 2005, Loren Andreas wrote:
              > > >
              > > > > pipers,
              > > > > I'm fairly new at this.
              > > > > I am converting a 2D file aquired with the States method.
              > > (Collected in the order RIRI for each T1 point; The
              > > > > first RI is for the virtual "real" and the second RI for the
              > > virtural "imaginary"). My script does not result in any
              > > > > negative shifts in the NMR spectrum:
              > > > >
              > > > > bin2pipe -in AFG2d.mn5 -bo 2048 -ri -noswap \
              > > > > -xN 2048 -yN 650 \
              > > > > -xT 1024 -yT 650 \
              > > > > -xMODE Complex -yMODE Complex \
              > > > > -xSW 50000.00 -ySW 50000.0 \
              > > > > -xOBS 150.991133 -yOBS 150.991133 \
              > > > > -xCAR 0 -yCAR 0 \
              > > > > -xLAB 13C -yLAB 13C \
              > > > > -ndim 2 -aq2D states \
              > > > > -out AFG2d.dat -verb -ov
              > > > >
              > > > > if I make -yN 1300, I get the following error:
              > > > >
              > > > > DATAIO File Read Error 0.
              > > > > Request: 21299200 Actual: 5326848.
              > > > >
              > > > > I'm not sure what the proper format is in Pipe language.
              > > > >
              > > > > thanks in advance
              > > > >
              > > > > -Loren Andreas
              > > > >
              > > > >
              > > > >
              > > > >
              > > > > Yahoo! Groups Links
              > > > >
              > > > >
              > > > >
              > > > >
              > > > >
              > > > >
              > > > >
              > > >
              > > >
              > > >
              > > >
              > > > Yahoo! Groups Links
              > > >
              > > >
              > > >
              > > >
              > > >
              > > >
              > > >
              > > >
              > >
              > >
              > > ------------------------ Yahoo! Groups Sponsor --------------------
              > > ~-->
              > > Get fast access to your favorite Yahoo! Groups. Make Yahoo! your
              > > home page
              > > http://us.click.yahoo.com/dpRU5A/wUILAA/yQLSAA/cEYolB/TM
              > > --------------------------------------------------------------------
              > > ~->
              > >
              > >
              > > Yahoo! Groups Links
              > >
              > >
              > >
              > >
              > >
              > >
              > >
              >
              >
              >
              >
              >
              >
              > Yahoo! Groups Links
              >
              >
              >
              >
              >
              >
              >
              >
            • Loren Andreas
              never mind. my problem was in POLY in xy.com thanks, the plot looks great! -L ... From: Frank Delaglio Date: Monday, November
              Message 6 of 8 , Nov 7, 2005
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                never mind. my problem was in POLY in xy.com

                thanks, the plot looks great!
                -L

                ----- Original Message -----
                From: Frank Delaglio <delaglio@...>
                Date: Monday, November 7, 2005 9:40 am
                Subject: Re: [nmrpipe] binary conversion from NTNMR
                >
                > btw usually value for "yN" is 2x the value for "yT" ...
                >
                >
                > On Mon, 7 Nov 2005, Frank Delaglio wrote:
                >
                > >
                > > what's your question??
                > >
                > >
                > > On Fri, 4 Nov 2005, Loren Andreas wrote:
                > >
                > > > pipers,
                > > > I'm fairly new at this.
                > > > I am converting a 2D file aquired with the States method.
                > (Collected in the order RIRI for each T1 point; The
                > > > first RI is for the virtual "real" and the second RI for the
                > virtural "imaginary"). My script does not result in any
                > > > negative shifts in the NMR spectrum:
                > > >
                > > > bin2pipe -in AFG2d.mn5 -bo 2048 -ri -noswap \
                > > > -xN 2048 -yN 650 \
                > > > -xT 1024 -yT 650 \
                > > > -xMODE Complex -yMODE Complex \
                > > > -xSW 50000.00 -ySW 50000.0 \
                > > > -xOBS 150.991133 -yOBS 150.991133 \
                > > > -xCAR 0 -yCAR 0 \
                > > > -xLAB 13C -yLAB 13C \
                > > > -ndim 2 -aq2D states \
                > > > -out AFG2d.dat -verb -ov
                > > >
                > > > if I make -yN 1300, I get the following error:
                > > >
                > > > DATAIO File Read Error 0.
                > > > Request: 21299200 Actual: 5326848.
                > > >
                > > > I'm not sure what the proper format is in Pipe language.
                > > >
                > > > thanks in advance
                > > >
                > > > -Loren Andreas
                > > >
                > > >
                > > >
                > > >
                > > > Yahoo! Groups Links
                > > >
                > > >
                > > >
                > > >
                > > >
                > > >
                > > >
                > >
                > >
                > >
                > >
                > > Yahoo! Groups Links
                > >
                > >
                > >
                > >
                > >
                > >
                > >
                > >
                >
                >
                > ------------------------ Yahoo! Groups Sponsor --------------------
                > ~-->
                > Get fast access to your favorite Yahoo! Groups. Make Yahoo! your
                > home page
                > http://us.click.yahoo.com/dpRU5A/wUILAA/yQLSAA/cEYolB/TM
                > --------------------------------------------------------------------
                > ~->
                >
                >
                > Yahoo! Groups Links
                >
                >
                >
                >
                >
                >
                >
              • Loren Andreas
                I had some problems with my email. At any rate, you ve answered my question, and everything seems to be working. thanks -Loren ... From: Frank Delaglio
                Message 7 of 8 , Nov 9, 2005
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                  I had some problems with my email. At any rate, you've answered my question, and everything seems to be
                  working.

                  thanks
                  -Loren

                  ----- Original Message -----
                  From: Frank Delaglio <delaglio@...>
                  Date: Monday, November 7, 2005 9:02 am
                  Subject: Re: [nmrpipe] binary conversion from NTNMR
                  >
                  > what's your question??
                  >
                  >
                  > On Fri, 4 Nov 2005, Loren Andreas wrote:
                  >
                  > > pipers,
                  > > I'm fairly new at this.
                  > > I am converting a 2D file aquired with the States method.
                  > (Collected in the order RIRI for each T1 point; The
                  > > first RI is for the virtual "real" and the second RI for the
                  > virtural "imaginary"). My script does not result in any
                  > > negative shifts in the NMR spectrum:
                  > >
                  > > bin2pipe -in AFG2d.mn5 -bo 2048 -ri -noswap \
                  > > -xN 2048 -yN 650 \
                  > > -xT 1024 -yT 650 \
                  > > -xMODE Complex -yMODE Complex \
                  > > -xSW 50000.00 -ySW 50000.0 \
                  > > -xOBS 150.991133 -yOBS 150.991133 \
                  > > -xCAR 0 -yCAR 0 \
                  > > -xLAB 13C -yLAB 13C \
                  > > -ndim 2 -aq2D states \
                  > > -out AFG2d.dat -verb -ov
                  > >
                  > > if I make -yN 1300, I get the following error:
                  > >
                  > > DATAIO File Read Error 0.
                  > > Request: 21299200 Actual: 5326848.
                  > >
                  > > I'm not sure what the proper format is in Pipe language.
                  > >
                  > > thanks in advance
                  > >
                  > > -Loren Andreas
                  > >
                  > >
                  > >
                  > >
                  > > Yahoo! Groups Links
                  > >
                  > >
                  > >
                  > >
                  > >
                  > >
                  > >
                  >
                  >
                  > ------------------------ Yahoo! Groups Sponsor --------------------
                  > ~-->
                  > Get fast access to your favorite Yahoo! Groups. Make Yahoo! your
                  > home page
                  > http://us.click.yahoo.com/dpRU5A/wUILAA/yQLSAA/cEYolB/TM
                  > --------------------------------------------------------------------
                  > ~->
                  >
                  >
                  > Yahoo! Groups Links
                  >
                  >
                  >
                  >
                  >
                  >
                  >
                  >
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