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Re: the varian NMR "procpar" file

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  • ethernet3399
    Thanks a lot, you guys! I should think before I leap, I mean I should read the messages posted thoroughly before I present a question:) Thanks!
    Message 1 of 9 , Jun 11, 2005
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      Thanks a lot, you guys!
      I should think before I leap, I mean I should read the messages posted
      thoroughly before I present a question:)

      Thanks!


      --- In nmrpipe@yahoogroups.com, Atom Crystal <crystalatom@y...> wrote:
      > Many thanks Patrik for clearifying.
      >
      > You are right that one does not need -sw in CS.
      >
      > It turns out the "CS -rs 1" compensates sw change
      > caused by REV. So if I use REV -sw, I don't need the
      > CS line. So the following are equivalent:
      >
      > nmrPipe -fn FT -neg
      > nmrPipe -fn SIGN -i | nmrPipe -fn FT
      > nmrPipe -fn FT | nmrPipe -fn REV -sw
      > nmrPipe -fn FT | nmrPipe -fn REV | nmrPipe -fn CS -rs
      > 1
      >
      > but maybe the first one is most efficient?
      >
      > Yufeng
    • Alex Breeze
      To expand on Patrik and Frans comments: Concerning the influence of moving the central 180 in a CT experiment in opposite directions to effect chemical shift
      Message 2 of 9 , Jun 15, 2005
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        To expand on Patrik and Frans' comments:

        Concerning the influence of moving the central 180 in a CT experiment in opposite directions to effect chemical shift evolution of S spin magnetisation, think of it the following way:

                      ¦____A____¦¦____B____¦

        For simplicity, and taking into account only chemical shift evolution, consider -Sy at start of the CT period:

        -Sy -----> -Sy cos wS (A-B) + Sx sin wS (A-B)

        If the 180 moves to the right, A-B is positive, whereas if the 180 moves to the left A-B is negative.

        Since cos(y) = cos(-y), the real part is unaffected, whereas since sin(x) = -sin(-x), the imaginary part of the signal is negated in the latter case and the apparent precession sense is reversed (simply an artefact of quadrature detection). Therefore one needs to negate the imaginaries in processing:

        nmrPipe -fn SIGN -i
        | nmrPipe -fn FT

        or

        nmrPipe -fn FT -neg

        if the data were acquired with a leftwards shift of the 180, but not for a rightwards shift of the 180 (all other things being equal - of course the sense of the States phase shift of the quadrature-shifted 90 -- and which 90 is shifted -- have an effect as well).

        Alex

        Patrik Lundström wrote:

        Yufeng,

        Since I always use and write pulse-sequences that are upside up, I wouldn't know :-) If no one else wants to comment on this, I guess the easy way out is to compare spectra processed w/ "nmrPipe -fn FT -neg" and "nmrPipe -fn FT | nmrPipe -fn REV | nmrPipe -fn CS -rs 1" and check if referencing changes.

        Concerning the question regarding opposite direction of chemical shift evolution, it means that it starts at time zero and moves to negative times for the next increments. Since the cosine-modulated (real) component doesn't care about this but the sine-modulated (imaginary) gets the opposite sign compared to positive evolution, negating the imaginaries correctly fixes this problem.

        / Patrik

        ----- Original Message -----
        From: Atom Crystal <crystalatom@...>
        Date: Friday, June 10, 2005 8:14 pm
        Subject: Re: [nmrpipe] the varian NMR "procpar" file

        >
        > Hi Patrik,
        >
        > I am wondering whether it is neccessary to add the -sw
        > option for CS, i.e.
        >
        > nmrPipe -fn CS -rs 1 -sw
        >
        > to make referencing info consistent.
        >
        > Yufeng

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