Dear Cristoph,
The idea of the Rersonance is that it can be assigned to a given Atom in a
given Molecule - but may not be so assigned yet. Resonances are supposed
to appear in different ShiftLists. The most obvious example is a
temperature series. You would want a different ShiftList for each
temperature, but you would want the same Resonances in all of them - those
are the same atoms, after all.
In your case the most obvious approach would be to consider the free and
the bound form of the protein as different, and use two different sets
of Resonances. After all, you might have mixtures of free and bound
protein in the same tube. In that case the problem you have is that
someone has assigned a peak in the bound form to a proton Resonance (or
atom) that belongs in the free form. That peak assignment is then the
problem.
Alternatively, the data model would allow you to treat free and bound
protein as a single molecule in two different states, which would
correspond to using the same resonances for both, but adding some extra
gymnasitis. I am not sure that Analysis supports this option, though, and
I would not recommend using it.
Yours,
Rasmus
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Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Fri, 2 Feb 2007, Christoph Brockmann wrote:
> Hi all,
>
> it might just be that I don't understand the concepts behind things
> correctly, but I think we got us into a quite murky state of our
> analysis project, that to my understanding of things should be impossible.
>
> We have a project that contains data for a protein in complex with a
> peptide and for comparison some fully assigned HSQC-spectra of the free
> protein that are assigned to a shiftlist different from all other
> spectra. However, we got ourselves into a state, where a couple of
> resonances ended up belonging to both shiftlists, which of course causes
> all sorts of trouble. I do not know how we managed to get into this
> state but it seems fairly difficult to sort this out, since I can't see
> how I could break the relationship of a resonance to one of the
> shiftlists without removing it from both (this is what the delete-button
> does in the browse resonances window).
>
> I might be wrong, but to my mind there should be a strictly hierarchical
> relationship with resonances being children of their respective
> shiftlist. Thus the program shouldn't allow me to assign the same
> resonance to two different shiftlists.
>
> If you got any advice on how to avoid situations like this in the future
> and what might be my problem in understanding the underlying concepts,
> it would be really appreciated.
>
> Christoph
>
> --
> ---------------------------------------------------------
> Dr. Christoph Brockmann
> Division of Structural Studies
> MRC Laboratory of Molecular Biology
> Hills Road
> Cambridge, CB2 2QH
> phone: +44-1223-40-2261 or +44-1223-40-2068
> e-mail: [log in to unmask]
> ---------------------------------------------------------
>
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