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Re: [nmrpipe] inverse cosine tuned to 35 HNCACB

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  • 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 1 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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