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Re: 13C-NOESYHSQC and Back-prediction

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  • Patrick van der Wel
    Hello, I just wanted to comment that I have recently seen unusual artefacts being generated when using back prediction in a similar fashion. I have not yet had
    Message 1 of 3 , Apr 1, 2012
      Hello,

      I just wanted to comment that I have recently seen unusual artefacts
      being generated when using back prediction in a similar fashion. I have
      not yet had a chance to trouble shoot in detail, but am tempted to say
      that this is a new thing as I don't recall having ever noticed this
      before. (By the way, this is using the Mac version of nmrpipe, and
      running it on Lion 10.7)

      Patrick
    • delaglio@nmrscience.com
      Hi All, Thanks for bringing this up, and sorry for any problems. As a work-around, I think LP -before will work better with root-fixing turned off using the
      Message 2 of 3 , Apr 2, 2012
        Hi All,

        Thanks for bringing this up, and sorry for any problems.

        As a work-around, I think "LP -before" will work better with root-fixing
        turned off using the "-nofix" option.

        Also, if there is distorted data, it's usually best to replace it
        before doing "special" processing in other dimensions. So, just to
        check things, try a simple FT processing first:

        usual FT of X-axis
        usual FT of Y-axis
        baseline correct X-axis
        "LP -before -pred 2 -nofix" in Z-axis
        usual FT of Z-axis



        Quoting Patrick van der Wel <pvdwel@...>:

        > Hello,
        >
        > I just wanted to comment that I have recently seen unusual artefacts
        > being generated when using back prediction in a similar fashion. I have
        > not yet had a chance to trouble shoot in detail, but am tempted to say
        > that this is a new thing as I don't recall having ever noticed this
        > before. (By the way, this is using the Mac version of nmrpipe, and
        > running it on Lion 10.7)
        >
        > Patrick
        >


        Quoting "sameer.wahid" <sameer.wahid@...>:

        > Hi all,
        >
        > I have a 13C NOESYHSQC dataset acquired with no half-dwell delay
        > (i.e. f1180=n on Varian) and am trying to back-predict the first two
        > points in 13C to correct baseline roll. However, the
        > back-prediction creates considerable 'noise' in all over my spectra
        > - difficult to describe without a picture, but similar to cryo-noise
        > (i.e. many small, sharp peaks, in every f1f3 plane of the 3D).
        >
        > When I look at the time domain vectors along 'z' (skipping the final
        > FT) there is much more noise in the f3 slices corresponding to the
        > first two points in t1.
        >
        > The noise goes away in the 3D and the f1f3 planes if I comment out
        > the "LP -before" line, and is not present in the FIDs or non-LP'd
        > spectra. I've duplicated the problem with a dataset acquired on an
        > RT probe.
        >
        > I'd be grateful if anyone could point me in the right direction!
        >
        > Thanks,
        > Sameer
        > Quebec/Eastern Canada High Field NMR Facility
        >
        >
        >
        >
        > PS: I've tried a few scripts with no success - one example is below
        > (originally from the NANUC script library)
        >
        > xyz2pipe -in data/test%03d.fid -x -verb \
        > | nmrPipe -fn SP -off 0.4 -end 1.0 -pow 2 -c 0.5 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 41.6 -p1 57.8 -di \
        > | nmrPipe -fn EXT -x1 6.0ppm -xn -1.0ppm -sw \
        > | pipe2xyz -out ft/test%03d.ft3 -x
        >
        > xyz2pipe -in ft/test%03d.ft3 -z -verb \
        > | nmrPipe -fn SP -off 0.5 -end 0.95 -pow 1 -c 0.5 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 -3.2 -p1 0.0 -di \
        > | pipe2xyz -out ft/test%03d.ft3 -z -inPlace
        >
        > xyz2pipe -in ft/test%03d.ft3 -y -verb \
        > | nmrPipe -fn LP -fb \
        > | nmrPipe -fn SP -off 0.4 -end 1.0 -pow 2 -c 0.5 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 0 -p1 0.0 -di \
        > #| nmrPipe -fn POLY -auto \
        > | pipe2xyz -out ft/test%03d.ft3 -y -inPlace
        >
        > xyz2pipe -in ft/test%03d.ft3 -z -verb \
        > | nmrPipe -fn HT -auto \
        > | nmrPipe -fn PS -inv -hdr \
        > | nmrPipe -fn FT -inv \
        > | nmrPipe -fn ZF -inv \
        > | nmrPipe -fn SP -inv -hdr \
        > | nmrPipe -fn LP -before -fb -pred 2 \
        > | nmrPipe -fn LP -fb \
        > | nmrPipe -fn SP -off 0.5 -end 1.0 -pow 2 -c 0.5 \
        > | nmrPipe -fn ZF -auto \
        > | nmrPipe -fn FT \
        > | nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
        > | pipe2xyz -out ft/test%03d.ft3 -z -inPlace
        >
        >
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