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inverse cosine tuned to 35 HNCACB

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  • Kelly, Mark
    Dear nmrPipe group, I m trying process the CaCb dimension of an HNCACB and would like to multiplying the t1 time domain with an inverse cosine tuned to 35 Hz
    Message 1 of 2 , Oct 4, 2012
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      Dear nmrPipe group,

      I'm trying process the CaCb dimension of an HNCACB and would like to multiplying the t1 time domain with an inverse cosine tuned to 35 Hz to remove the JCa-Cb coupling (ref below). Can you tell me what this would look like in a pipe script?

      Many thanks, Mark


      Wittekind, M. & Mueller, L. (1993). "HNCACB, a High-Sensitivy 3D NMR Experiment to Correlate Amide-Proton and Nitrogen Resonances with the Alpha- and Beta-Carbon Resonances in Proteins". J. Magn. Reson., Series B. B101: 201-205.
    • delaglio@nmrscience.com
      You could do this with the NMRPipe adjustable sine-bell window SP , but NMRPipe has a related window function called JMOD, with parameters specifically for
      Message 2 of 2 , Oct 8, 2012
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        You could do this with the NMRPipe adjustable sine-bell window "SP",
        but NMRPipe has a related "window" function called JMOD, with parameters
        specifically for coupling. So, multiplying by a 35 Hz cosine modulation
        would be:

        | nmrPipe -fn JMOD -j 35 -cos \

        Add the "-inv" flag to divide by the coupling modulation instead.
        This will only work if the coupling is small enough that its
        modulation does not cross zero. Removing a coupling in this
        way will also likely increase the noise level.

        For general purpose application of j deconvolution, some have
        have proposed using maximum entropy reconstruction. NMRPipe's
        MEM can be used for this, but I've only done so with synthetic
        test cases.

        JMOD: Options for J-Modulation Profile:
        -off off [0.0] Modulation Start*PI. (Q1)
        -j jHz [0.0] J-Modulation, Hz. (Q2)
        -lb lbHz [0.0] Line Broadening, Hz. (Q3)
        -sin Sine Modulation. (Q1 = 0.0)
        -cos Cosine Modulation. (Q1 = 0.5)
        General Options:
        -size aSize [APOD] Apodize Length.
        -start aStart [1] Apodize Start.
        -c fScale [1] Point 1 Scale.
        -one Outside = 1.
        -hdr Use Q Values from Header.
        -inv Invert Window.

        Quoting "Kelly, Mark" <Mark.Kelly@...>:

        >
        > Dear nmrPipe group,
        >
        > I'm trying process the CaCb dimension of an HNCACB and would like to
        > multiplying the t1 time domain with an inverse cosine tuned to 35 Hz
        > to remove the JCa-Cb coupling (ref below). Can you tell me what this
        > would look like in a pipe script?
        >
        > Many thanks, Mark
        >
        >
        > Wittekind, M. & Mueller, L. (1993). "HNCACB, a High-Sensitivy 3D NMR
        > Experiment to Correlate Amide-Proton and Nitrogen Resonances with
        > the Alpha- and Beta-Carbon Resonances in Proteins". J. Magn. Reson.,
        > Series B. B101: 201-205.
        >
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