Hi Igor,
When you import coordinates you don't have to run linkResonances
(coordinates are directly linked to atoms when importing). The warning
messages you get appear because you're trying to link resonances that were
already there in your project and that were not created by the FC import.
Resonances are linked to all NMR(derived) info like constraints, shifts,
..., but coordinates are not (there is no need for a complex system to
link coordinates to atoms because we assume a 1-1 correspondence between
the two).
In any case, your coordinates are probably read in correctly. Just ignore
any popups asking you to link resonances.
As for documentation, I've tried to document the common tasks, but as some
import options are seldom used, documenting those is low on the priority
list. In any case, for importing coordinates the options are:
Maximum number of models to read: if you've got, say, 20 models you can
read only the first 5 one (or whatever).
Link unrecognized atoms: if there are coordinates with atoms names the FC
doesn't recognize (there's all kinds of names out there), then it will ask
you which atom to link the coordinate to. Untoggle if you want to ignore
these (useful for automation).
Reset chain mapping: the FC will reset the mapping between the chains in
the format file and the chains inside the data model.
Match to internal atom names: the FC will, as a second option, try to
match unrecognized atom names for a coordinate to the actual atom name
inside the data model (basically it will use IUPAC naming as a backup to
link the coordinates to atoms).
Minimal interaction: popups are only shown if absolutely necessary.
Bye,
Wim
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