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.
yes where distances are unreliable or where you cannot unambiguously
determine the link point, e.g. when it's apriori unclear which atom
is leaving upon linking, how many hydrogens are involved etc.
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?
I think this depends on the quality of your data. If you have a remote
model and poor resolution then the difficulties arise. You do not LINKR
everything, or do you? If two atoms may be automatically referenced
in a residue, the same can be done for the mainchain, so I would think
that one uses LINKR when things are not self-obvious from structural
positions.
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.
Probably that's why there are LINKs and LINKRs I guess.
Regards,
Eugene.
Cheers
-- Ian
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