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Re: [nmrpipe] HMBC idiot

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  • Frank Delaglio
    oo! Well, perhaps its an idiot s HMBC, but it s surely a brilliant solution. Kids who want to try this at home: note that James has correctly combined the data
    Message 1 of 4 , Apr 11, 2006
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      oo!

      Well, perhaps its an idiot's HMBC, but it's surely a brilliant solution.

      Kids who want to try this at home: note that James has correctly
      combined the data after the MC ... the phased data in the time-domain
      would likely cancel through interference if added, but the magnitude
      data will not.

      -big fd

      On Tue, 11 Apr 2006, James Swarbrick wrote:

      > Hi there
      >
      > I stuffed up at my first HMBC spectra on a Varian Spectrometer the other day.
      > I arrayed using phase = 1,2 and I got some strange looking spectra.
      >
      > I acquired 100 complex points (of course it isn't complex data - it is
      > magnitude) so I ran this to get out of difficulties.....
      >
      > #!/bin/csh
      >
      > var2pipe -in ./fid -swap \
      > -xN 2048 -yN 200 \
      > -xT 1024 -yT 200 \
      > -xMODE Complex -yMODE Real \
      > -xSW 5000.000 -ySW 27146.250 \
      > -xOBS 599.769 -yOBS 150.827 \
      > -xCAR 4.773 -yCAR 105.952 \
      > -xLAB H1 -yLAB C13 \
      > -ndim 2 -aq2D Magnitude \
      > -out ./test.fid -verb -ov
      >
      > #!/bin/csh
      >
      > nmrPipe -in test.fid \
      > | nmrPipe -fn SP -off 0 -end 1 -pow 1 -c 0.5 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -auto \
      > | nmrPipe -fn TP \
      > | nmrPipe -fn COADD -cList 1 0 -time \
      > | nmrPipe -fn SP -off 0.0 -end 1 -pow 1 -c 0.5 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -neg \
      > | nmrPipe -fn MC \
      > | nmrPipe -fn TP \
      > -out plane2.dat -ov
      >
      > nmrPipe -in test.fid \
      > | nmrPipe -fn SP -off 0 -end 1 -pow 1 -c 0.5 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -auto \
      > | nmrPipe -fn TP \
      > | nmrPipe -fn COADD -cList 0 1 -time \
      > | nmrPipe -fn SP -off 0.0 -end 1 -pow 1 -c 0.5 \
      > | nmrPipe -fn ZF -auto \
      > | nmrPipe -fn FT -neg \
      > | nmrPipe -fn MC \
      > | nmrPipe -fn TP \
      > -out plane3.dat -ov
      >
      > addNMR -in1 plane2.dat -in2 plane3.dat -out HMBC.dat
      >
      > ---------------------------------------------------------------------------------------------------------------------------------------
      > So if there are any more 'idiots' out there (comme moi) and do I I did
      > not reading manuals and running spectra during beer club on Friday night
      > and being used to 'complex' data with protein style experiments then you
      > can still get your data back. (and save money).
      >
      > hope this helps someone - sometime - somewhere.
      > Cheers
      > Jimbo
      >
      > Dr James Swarbrick
      >
      > Department of Medicinal Chemistry
      > Victorian College of Pharmacy
      > Parkville
      > Melbourne
      > Australia
      > 3052
      >
      >
      >
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >
      >
      >
      >
    • James Swarbrick
      Hi guyz Can also do it similarly like this......as a pseudo 3D take your pick. cheers Jimbo #!/bin/csh var2pipe -in ./fid -swap -xN 2048 -yN
      Message 2 of 4 , Apr 11, 2006
      • 0 Attachment
        Hi guyz

        Can also do it similarly like this......as a pseudo 3D
        take your pick.
        cheers
        Jimbo

        #!/bin/csh

        var2pipe -in ./fid -swap \
        -xN 2048 -yN 100 -zN 2\
        -xT 1024 -yT 100 -zT 1\
        -xMODE Complex -yMODE Real \
        -xSW 5000.000 -ySW 27146.250 \
        -xOBS 599.769 -yOBS 150.827 \
        -xCAR 4.773 -yCAR 105.952 \
        -xLAB H1 -yLAB C13 \
        -ndim 3 -aq2D Magnitude \
        | pipe2xyz -out FID/temp_%03d.fid -x -ov -to 0 -verb

        nmrPipe -in FID/temp_001.fid \
        | nmrPipe -fn SP -off 0 -end 1 -pow 1 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -auto \
        | nmrPipe -fn TP \
        | nmrPipe -fn SP -off 0.0 -end 1 -pow 1 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -neg \
        | nmrPipe -fn MC \
        | nmrPipe -fn TP \
        -out plane2a.dat -ov

        nmrPipe -in FID/temp_002.fid \
        | nmrPipe -fn SP -off 0 -end 1 -pow 1 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -auto \
        | nmrPipe -fn TP \
        | nmrPipe -fn SP -off 0.0 -end 1 -pow 1 -c 0.5 \
        | nmrPipe -fn ZF -auto \
        | nmrPipe -fn FT -neg \
        | nmrPipe -fn MC \
        | nmrPipe -fn TP \
        -out plane3a.dat -ov

        addNMR -in1 plane2a.dat -in2 plane3a.dat -out HMBCa.dat

        Frank Delaglio wrote:
        >
        >
        > oo!
        >
        > Well, perhaps its an idiot's HMBC, but it's surely a brilliant solution.
        >
        > Kids who want to try this at home: note that James has correctly
        > combined the data after the MC ... the phased data in the time-domain
        > would likely cancel through interference if added, but the magnitude
        > data will not.
        >
        > -big fd
        >
        > On Tue, 11 Apr 2006, James Swarbrick wrote:
        >
        > > Hi there
        > >
        > > I stuffed up at my first HMBC spectra on a Varian Spectrometer the
        > other day.
        > > I arrayed using phase = 1,2 and I got some strange looking spectra.
        > >
        > > I acquired 100 complex points (of course it isn't complex data - it is
        > > magnitude) so I ran this to get out of difficulties.....
        > >
        > > #!/bin/csh
        > >
        > > var2pipe -in ./fid -swap \
        > > -xN 2048 -yN 200 \
        > > -xT 1024 -yT 200 \
        > > -xMODE Complex -yMODE Real \
        > > -xSW 5000.000 -ySW 27146.250 \
        > > -xOBS 599.769 -yOBS 150.827 \
        > > -xCAR 4.773 -yCAR 105.952 \
        > > -xLAB H1 -yLAB C13 \
        > > -ndim 2 -aq2D Magnitude \
        > > -out ./test.fid -verb -ov
        > >
        > > #!/bin/csh
        > >
        > > nmrPipe -in test.fid \
        > > | nmrPipe -fn SP -off 0 -end 1 -pow 1 -c 0.5 \
        > > | nmrPipe -fn ZF -auto \
        > > | nmrPipe -fn FT -auto \
        > > | nmrPipe -fn TP \
        > > | nmrPipe -fn COADD -cList 1 0 -time \
        > > | nmrPipe -fn SP -off 0.0 -end 1 -pow 1 -c 0.5 \
        > > | nmrPipe -fn ZF -auto \
        > > | nmrPipe -fn FT -neg \
        > > | nmrPipe -fn MC \
        > > | nmrPipe -fn TP \
        > > -out plane2.dat -ov
        > >
        > > nmrPipe -in test.fid \
        > > | nmrPipe -fn SP -off 0 -end 1 -pow 1 -c 0.5 \
        > > | nmrPipe -fn ZF -auto \
        > > | nmrPipe -fn FT -auto \
        > > | nmrPipe -fn TP \
        > > | nmrPipe -fn COADD -cList 0 1 -time \
        > > | nmrPipe -fn SP -off 0.0 -end 1 -pow 1 -c 0.5 \
        > > | nmrPipe -fn ZF -auto \
        > > | nmrPipe -fn FT -neg \
        > > | nmrPipe -fn MC \
        > > | nmrPipe -fn TP \
        > > -out plane3.dat -ov
        > >
        > > addNMR -in1 plane2.dat -in2 plane3.dat -out HMBC.dat
        > >
        > >
        > ---------------------------------------------------------------------------------------------------------------------------------------
        > > So if there are any more 'idiots' out there (comme moi) and do I I did
        > > not reading manuals and running spectra during beer club on Friday
        > night
        > > and being used to 'complex' data with protein style experiments then
        > you
        > > can still get your data back. (and save money).
        > >
        > > hope this helps someone - sometime - somewhere.
        > > Cheers
        > > Jimbo
        > >
        > > Dr James Swarbrick
        > >
        > > Department of Medicinal Chemistry
        > > Victorian College of Pharmacy
        > > Parkville
        > > Melbourne
        > > Australia
        > > 3052
        > >
        > >
        > >
        > >
        > >
        > >
        > > Yahoo! Groups Links
        > >
        > >
        > >
        > >
        > >
        > >
        > >
        >
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