> However, should these reonances be in separate PeakContribs?
Analysis does not currently manipulate peakContribs, so unless you're
writing your own code there may be little advantage in setting them.
> now should I have
>
> peak[1].PeakConribs[0] = [<PeakDimContrib for reonance A H >,
> <PeakDimContrib for reonance B H >, <PeakDimContrib for reonance A N >,
> <PeakDimContrib for reonance B N >]
>
> or should I have
>
> peak[1].PeakConribs[0] = [<PeakDimContrib for reonance A H >,
> <PeakDimContrib for reonance A N >](with weight 0.5)
> peak[1].PeakConribs[1] = [<PeakDimContrib for reonance B H >,
> <PeakDimContrib for reonance B N >](with weight 0.5)
The latter. PeakContribs can be thought of as mutually exclusive sets of
assignment possibilities.
> Further to this
>
> 1. if I have a peak which I know is residue 13 but I don't know what the
> chain assignment for the peak is what should my my setup be then, whould
> it be:
>
> peak[1].PeakConribs[0] = [<PeakDimContrib for reonance A H >,
> <PeakDimContrib for reonance A N >](with weight 0.0)
> peak[1].PeakConribs[1] = [<PeakDimContrib for reonance B H >,
> <PeakDimContrib for reonance B N >](with weight 0.0)
Yes. A default weight of 0.0 for both peakContribs is what we'd suggest if
the assignment could be one or the other. Non-zero weights suggest that
both are present and superimposed.
> 2. do all assignments arising from the combinatorial nature of a
> peakContrib have to be reasonable?
You can set whatever you like. As Analysis doesn't use these yet there are
no restrictions.
> Thus for example you can have an overlapped hcch-tocsy peak where the
> 13C and 1H resonances are overlapped but you know for example what some
> of the indirect proton shifts come from one residue and the rest from
> another. What should you do then two separate peakcontribs with the
> subsets in them and weights of 0...
I'd make separate peakContribs each with the same 13C and direct 1H
peakDimContribs but different indirect 1H peakDimContribs. i.e. just to say
that these go together. I would not use zero weights if I know both
possibilities are present.
> 3. (most probably for the ccpn team) This is clearly complicated and I
> am not sure i follow the implications and reasoning in all cases. Can
> you expand on why the peakcontrib is there and what it's practical uses
> are in the round covering the common cases...
The class is present to say either that:
There is superimposition and a peak arises from different resonance
combinations in different proportions.
A peak could be derived from one of several possible distinct resonance
combinations.
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766022 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.pantonia.co.uk
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