> > Is there something that needs changing?
>
> unless I'm out of date on this, the reimported peak lists contribute
> equally to the shift lists with the originals and so shift values can be
> pulled away from their correct values.
Yes indeed this is still the case. I tend to use less weight for the shift
contribution of the more ambiguous NOESY 1H dim which minimises such
issues. Due to the way this has been modelled the weighting will effect
both the original and the exported peak list, which is perhaps a
limitation. Although, in the end my 'original' will end up fairly close to
the ARIA one and I wouldn't want it to be an authoritative source of
shifts either.
> If I'm still right about this then I guess my suggestion would be
> that the reimported peak lists have weight 0 for shiftList calculation.
Agreed, although I would say very small rather than absolutely zero, given
the issue that the original and ARIA peak lists will use the same
weightings. Also, on occasion there is a shift where the only place the
resonance is seen in the NOESY.
This is personal taste, but I sometimes don't change the weightings for
the heteroatom bound (and thus mostly unambiguous) dimension so that I can
see where something odd is happening. Detecting the outliers in the
Resonance Info can show where ARIA is trying to 'explain' a peak that is
bogus or caused by resonances that are missing.
> I guess that apart from user confusion, the strange pairings you mention
> can also cause havoc with e.g. quality reports - maybe the reimported
> peak lists should be flagged to be ignored by them?
Indeed, we do need a check for this in the exports. The only problem is
one of time and manpower (short until after v3). The link to ARIA will be
looked at again at some stage.
> ...but if I remember right you get all the structures calculated in those
> iterations rather than the "best" N whatever N is.
I suspect you're right, but I didn't realise that there was a problem
here.
> > You can select and load multiple PDB files in analysis and [Merge Into
> > Ensemble] rather than use external scripts.
>
> OK that's a good feature I'd so far missed. Any chance of the import being
> able to interpret ARIA .float files to get prochirals the right way round,
> or do you see that as ARIA's responsibility?
Sort of. This is ARIA using FormatConverter so not directly Analysis.
However, we can take another look when the interface is next updated. What
we might have to do is take the ARIA interface into the CCPN repository
(not that we want more to maintain) so we can update in the usual CCPN
way.
> > Also, I would say that subjectively selecting PDB files
>
> Whoaa! who said anything about subjectively? I would absloutely advise
> objective selection - lowest restraint energy, lowest overall energy, or
> some other appropriate objective criterion.
What I mean is that our objective is to explain the data and not to
minimise the energy per se. Hence we select the lowest energy models with
caution, although arguably any heuristic is subjective. Perhaps a debate
for another time. However, I don't think we really disagree and I have no
problem with selecting the same models as ARIA or looking at a
distribution to see the MD failures.
> - it would help to keep users away from focusing their violation
> analysis on a single conformation (and risk biasing it towards that
> structure) if the "show on structure" functionallity worked nore slickly
> as you switch the structure displayed from an ensemble.
Indeed. There are some technical issues in v2 which makes displaying
ensembles tricky. However, we are in the process of updating the ensemble
data model and the Qt+OpenGL structure display in v3 ought to be quicker
and much more flexible. So make sure we are reminded at the appropriate
time...
T.
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.ccpn.ac.uk
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