> I have substantially increased the tolerance levels on spectra which
> contain J and residual dipolar couplings. That way I am still able to
> assign the peaks. However, sometimes this still doesn't seem to work.
> E.g. I have a peak at 119.370 ppm and the resonance I want to assign it
> to is at 120.557ppm, yet even when the tolerance is set to 2ppm in 15N
> for that spectrum the correct resonance does not appear as an option in
> the Assignment box (though there are other options which go up to a
> delta value of 1.75). There are other residues for which I have the same
> problem. Selecting 'Double tolerances' does not appear to change the
> options available when the tolerance is set to 2ppm (but it does at
> lower values). Is there a maximum number of residues which can be
> displayed in the assignment box? Is there a way I can force an
> assignment which I want to make? Is there a reason why it might be
> leaving out the assignment option which I want to make?
There is a fundamental mechanism within Analysis which means that the
options won't appear if the shift difference is too large. The reason is
that the shifts are put into (overlapping) bins, so that when a ppm match
is needed Analysis doesn't have to look through the whole shift list. If
it did Analysis would be impossibly slow for big projects. I don't want to
increase the bin size as this will make things slower for only one
situation that really ought to be handled in a different way.
The best way to deal with very different shifts in general is to split the
experiments between different shift lists. This way the shift average is
separate for the separate situations, the variance is smaller and you
wouldn't need to extend the tolerances as assignment is always appropriate
to the shift list.
Having said that, using shift lists is not the Data Model way of dealing
with couplings. There is a dedicated mechanism just for that, where split
(sub)peak positions are relative to a peak at the 'unsplit' position. This
way you can have underlying resonance assignments at their regular ppm
values and separate resonances allocated to the splitting.
Getting SubPeaks and couplings set up properly is definitely on my to-do
list.
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (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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