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Re: [nmrpipe] phasing in nmrview

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  • earle adams
    ... From: Jim Kempf To: nmrpipe@yahoogroups.com Sent: Tuesday, July 30, 2002 10:43 AM Subject: Re: [nmrpipe] phasing in nmrview Jim, thank you...I shall try it
    Message 1 of 3 , Jul 30, 2002
      ----- Original Message -----
      From: Jim Kempf
      Sent: Tuesday, July 30, 2002 10:43 AM
      Subject: Re: [nmrpipe] phasing in nmrview

      thank you...I shall try it out.

      Earle, I also recently ran into this phasing issue.

      nmrDraw enables you to choose a pivot to phase the spectrum according to

                phi = phi0 + phi1*(nu - nuPivot)
                     = (phi0 - phi1*nuPivot) + phi1*nu

      The second line shows how a nonzero pivot is equivalent to phasing without a pivot, but using a distinct zero-order phase.  Thus one can always phase with an arbitrary pivot and use the default (only?) value available in nmrPipe.

      To phase with nmrDraw, set the pivot point to coincide with a well-isolated peak, then set the zero-order phase to give a pure absorptive line there.  Finally, adjust the first order phase to alter the peaks about it.  This final adjustment actually changes both zero and first order phases displayed by nmrDraw, giving the equivalent phase params for a pivot at the highest ppm value in the phased dimension (i.e., pivot = point 1).  Thus the values shown are appropriate to write in to your nmrPipe macro, since (as best I can tell) it uses only the default pivot = 1.

      Cheers, Jim Kempf.

      earle adams wrote:

      Hello nmrpipers,      I would like to ask the group a phasing question. I am trying to rephase a 2D noesy from avarian nmr after processing it in nmrpipe. I bring up the processed noesy in nmrDraw andtry to phase the rows and columns. I can use a pivot in nmrDraw but I haven't found a pivotparameter in nmrpipe. Is there a way I can properly translate my phase values from nmrDrawto reprocess in nmrpipe? I may be going about this the wrong way and there may justbe a better way to rephase a processed nmrpipe 2d noesy. Thank you for any suggestions. Sincerely, Earle Adams

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