Hi Igor,
> Thanks for the explanation. If I understand correctly, I don't need to
> run link resonances at all if the the peak assignments correspond to the
> resonances.
Indeed
> I noticed that on import the stereospecificly assigned protons they were
> mapped on a and b automatically. The same happened when I imported
> Sparky resonance assignment table - stereospecific assignmets were
> automatically converted to non-stereospecific. So my question is, what
> controls the mapping.
This is an option in linkResonances. You can either assume that all
protons are stereospecifically assigned by clicking on by selecting
'Complete stereospecific assignment' in the 'Link resonances setup' popup
(this appears if you don't link with the default settings), or assume that
they are all non-stereospecific by having the 'Complete stereospecific
assignment' option deselected.
There are very few formats out there that clearly distinguish the
stereospecific assigment status of prochirals, hence the 'global' approach
to how stereospecific assignments are handled on import. Where there is a
distincion, as in for example NMR-STAR, I use the ambiguity code when
importing to set the status correctly.
> 2. When the peak assignments are imported, I presume the mappy is done
> through chemical shifts. What happens if restraints are imported? For
> Cyana or CNS restrains the information on the chemical shifts is
> available. Will it be used to map stereospecific assignments to a and b?
It will map the imported resonances to the resonance with the same
original Cyana/CNS name, but shouldn't change the stereospecific
assignment in the data model itself (unless I'm mistaken).
In any case, if things do go wrong, you can use the 'Process -> Check
stereo status prochirals' popup to (re)set the stereospecific assignments
in your particular project. Or use the equivalent option in Analysis, of
course.
Wim
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