Hi Wim,

Thanks for the explanations, it makes more sense now. If there is no
need to link resonance, it would be better to remove linkResonances
popup to avoid confusion (unless there are cases when one needs to do
this). It would also be nice to expand the explanations for each option
that you get when clicking the corresponding "i" button. For many option
the current explanation doesn't add much to what is already in the popup.

On a related issue, when importing CYANA shifts/peaks there is an option
 "Match existing resonances" with the explanation that the "the script
will not try to match the newly created resonances to existing ones".
What is the difference between this option and using linkResonances?

Cheers
Igor

Wim Vranken wrote:
> 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


-- 
Dr. Igor Barsukov

Biological NMR Centre,
University of Leicester
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