Hi Patrick,
> There is another non-standard character right after the #, perhaps inserted
> by accident?
Yep I figured that out - it does have something to do with inserting a #
sign on my Mac though, and I can only see the extra sign on a Linux box.
Will look into that a bit more today, and hopefully the annoying but
harmless message will disappear in the next release.
> This seems to figure out the referencing / nuclear frequencies on the basis
> of an assumed centering of the 1H freq on the water signal at 4.773ppm. The
> thing I should mention at this point is that I was importing some solid
> state NMR data, and had created some new experimental prototypes (to the
> best of my abilities) that lack a proton dimension. This then caused a
> problem for the function mentioned above. It looks possible to hack a quick
> work-around in the code, but I was not sure in what context the procedure is
> needed. I did manage to load the experiments themselves (i.e. open the
> sparky files using the newly defined prototypes) and I suspect that the
> function call is mostly used to generate a temporary(?) dummy experiment
> during the importing of the peaks (if you don't select an existing
> experiment). Any ideas/suggestions?
The FC indeed generates dummy experiments for peak lists if the actual
experiment data is not available. This has to be done because you cannot
have a peak list without an experiment, and you need to set up some
vaguely reasonable parameters for the 'DataDims' and 'DataDimRefs' to
handle chemical shift referencing and the likes for the peak list.
Anyway, I can do a couple of things: put in a hack that it always sets the
proton frequency to 500.0 (or something), or give a popup where you can
enter the correct proton reference frequency... since they are dummy
experiments the first option is probably reasonable enough. I could also
get the C or N reference frequency out and use that instead of the proton
one, but then one would have to enter a sensible reference ppm value for C
or N.
As for the solid state part, CCPN is working on extending the data model
(and reference experiments) so that it can be handled more smoothly - this
is in collaboration with Oschkinat's group. The first tryout version will
be available in the next release. Eventually, reference labelling schemes
and direct interaction with ARIA for solid state calculations will also be
provided. The people mostly involved in this are Rasmus (mail him if you
have suggestions for experiments to be included) and Tim (for handling
solid state data in Analysis).
Wim
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Wim Vranken [log in to unmask]
Macromolecular Structure Database (MSD) group
European Bioinformatics Institute (EMBL outstation)
Wellcome Trust Genome Campus
Cambridge CB10 1SD, UK
Tel: +44-1223-494682 Fax: +44-1223-494487
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