Hi Eugene
> If I were to deal with your example, I would look into distance
> profile between residues in coordinate section, which then
> gives answer to your question.
OK that's interesting, I hadn't realised that the interatomic distances
played an active role in determining connectivity: I had assumed the
whole point of the various connectivity specifiers was to avoid reliance
on distance calculations. But resolution of the kind of ambiguity I
illustrated would not occur automatically, or would it? - i.e. would the
need for it only become clear when the structure was checked manually?
Of course it makes sense to use distance information for fully-refined
structures such as those that are (hopefully!) deposited with the PDB,
but it would be more of an issue with refinement programs that have to
deal with all kinds of errant input geometry! I suppose the fundamental
problem is that we're trying to use the same format for both purposes
and there are fundamentally conflicting requirements.
Cheers
-- Ian
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