> if i get a relevant peak from my peaklist and then use 'Assign', i can only
> re-assign to e.g. He1 or He2. is there an He* resonance? i think have a dim
> memory of linkResonances complaining about these names.
The issue here is that by default Analysis (and possibly FormatConverter)
treats aromatic protons like Phe Hd or He as two separate resonances,
which would mean that (like Hb2,Hb3 prochirals) if you have a peak which
refers to both He1 and He2 you have to make two separate peak dimension
contributions (which would automatically generate the He* annotation).
This default exists simply because it is the most flexible option, i.e. in
the absence of further information you can treat the atoms both singly and
combined (albeit inefficiently).
Given that He1 and He2 are usually equivalent in NMR experiments, of
course you should be able to describe the He* atom set with a single
resonance. However, this option needs to be decided by the user,
potentially on a per residue basis. - The mechanism of handling atomic
information is generic and can be used on arbitrary chemical compounds
where the equivalency decision is not necessarily straight-forward.
In essence, I've not yet put the 'theseProtonsAreEquivalent' function into
Analysis. Although, I'll move it up my list of things to do so that it may
get into the next release.
In anticipation of sorting this out, the function to go from separate to
combined atom sets, but not the other way around, already exists in
MoleculeBasic ( makeResidueAtomSetsEquivalent(residue) ). You could run
this on your aromatics to get the combined atom sets to link a single
resonance to. You'll have to make a new resonance or reassign extant He
resonances to the new atoms sets, which in practice would mean
deleting/merging.
Alternatively, just use two peakDimContribs for now and wait for a later
version of Analysis that will do all the combining/splitting for you.
Tim
-------------------------------------------------------------------------------
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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