> assigned prochirals with non-degenereated shifts. While the assignment
> dialogue treats those as amibiguous (which is fine in the first place,
> since you don't have stereospecific assignments) the "Violation
> Analysis" _does_as_well_. In this case, the stereochemistry is already
> "swapped" by virtue of the structure calculation. Thus in my opinion the
> "Violation Analysis" should default to Hda* -> Hd1* (and so forth) as
> the "Restraint Production" part does.
To clarify and be a pedant, the constraint generation within Analysis does
not make an arbitrary resolution of prochirals. It doesn't have to, as the
information is still in the data model. The resolution only comes with
export into a legacy format.
For violations, is taking an average (or using the closest?) for the two
atomic possibilities for a prochiral any worse than potentially picking
the wrong one half the time? I don't know really and I'm to tired to think
clearly. I'm happy to make changes, but I'd like to see what the community
think. In some sense the situation is a bit annoying because the legacy
program data is incomplete and I was doing my best to represent what is
clear in the data model.
If the structure calculation engines could pass their resolutions back
then the problem would be solved. As Rasmus points, out a consistent
mapping of Hga* to Hg2 etc in creating constraints would allow you to
check where stereochemistries (but not atom names) have been swapped -
i.e. the IUPAC stereochemistry is wrong. However this wouldn't work for
all calculation engines, and is not exactly future-proof.
Is there any other way to treat unresolved prochiral violations? Take the
closest? Something else?
I am happy to go with the community in any event...
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 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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