> -in problem peaks/assign errors what does it mean by 'excessive bonds'
This means that a resonance has more 'onebond' partners, according to the
type of spectra that it is assigned in, than the chemical bonds if its
assigned atom would allow.
> or 'multiple 1H bonds'?
This means there is a 1H resonance with more than one 'onebond' resonance,
again according to experiment types. Note that resonances need not be
assigned to atoms to get this warning.
> The assignments seem completely reasonable to me eg
> 43LeuHg 43LeuHa 43LeuCg says '43Hg excessive bonds'.
So this peak probably isn't the offender, but does carry the offending
resonance. If you take a look at the resonance report you will hopefully
see the problem from the other end, i.e. the Hg resonance will display
multiple bound partners.
> -what's with the red flags for peaks with large volumes? surely they are 99%
> going to be things like Hba-Hbb?
In my tests (across different types of spectra) most of the really intense
peaks were from terminus and other highly flexible residues. The peak
intensity checks aim to be fairly permissive; the analysis is done in log
space and you have to be 3 standard deviations from the mean to get red.
Also, what the expectation is, and hence the threshold, does depend on
spectrum type, e.g. In the future I will make corrections for NOESY peaks
assigned to methyls.
You can ignore these warnings as you see fit. If you can explain the
flagged peaks then fine, the report is mostly designed to draw your
attention to things.
> -in problem resonances what is 'type prob'?
This is how well the assigned chemical shift fits the BMRB distribution.
The absolute value is not especially meaningful at present. The BMRB
distributions are used as a lookup table, and if very few other atoms of a
given type have ever had such a shift it is flagged. This analysis does
not use a mean or a model distribution.
> also the BMRB mean for Arg Ne is reported here as ~93 but the ref
> chemical shift graph has the peak for this spread between 80-90, and all
> mine seem to come around 83-5. Is it just a typo?
No. The mean is skewed because of the presence of improperly unaliased Arg
Ne chemical shifts in the BMRB. Analysis will move over to a cleaner data
set if I ever get the time.
> -in problem resonances I get the idea of the 'bound resonances' column but
> why do I get a flag for 19GlyHab because it is bound to 20GluN and 19GlyCa?
It should be just bound to one thing, the Ca, in the chemical bond sense.
This is distinct from being connected via multiple bonds given a spectrum.
> the peak 'binding' it to 20GluN is in a HNcocH, assignment 20H 19Hab 20N
> with these linked to 5 1 4 in the ref measurement.
I don't understand what is happening here. If 19Hab is on step 1 and the
amide is on steps 4 & 5 then only the amide proton and nitrogen will have
a 'bond' connection. Maybe the resonances are linked elsewhere or possibly
the experiment dims don't match the ref dims (although I'd expect lots of
warnings of this was so).
> Also is it possible to sort these tables to bring all the red flags to
> the top? for most columns this works just because you get a flag for a
> high number in eg SD , but this doesn't work for bound resonances.
I'm not going to mess with the sorting, but I am planning an option to
toggle only the unflagged rows off.
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
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Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.pantonia.co.uk
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