Thanks a lot, I see much clearer now. I guess we will try to go for a
second set of resonances for the bound protein (an additional chain for
the free form on setup would have helped, but I guess its to late now).
Still it would be great if the assignment of resonances to shift-lists
was a bit more transparent, because this influences the assignment of
other resonances to atoms even if there are no assignments within the
same shiftlist (although I believe there was a way in the past that
allowed to merge two resonances assigned to the same atom).
Rasmus Fogh wrote:
> 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.
>
I guess this is where we ended up. So we will need to clean this up
along the way that Tim suggested
> 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.
>
Is there a way to do so without actually copying all the peaks into the
new shiftlist? Because if you start from a new peak you have to give it
new resonances before you can assign it to an atom because the other
resonces obviously belong to a different shiftlist and will not appear
as assignment options.
yours,
Christoph
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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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