> i'm trying to use analysis to measure rdcs from ipap spectra in which i've
> edited the two doublet components into separate spectra - say, ipap_sum
> and ipap_dif. i'm thinking of starting from an assigned n-hsqc and
> stepping through each peak in turn, copying the assignments to the doublet
> components of the ipap spectra as i go along (need to examine each in turn
> because sometimes peaks overlap, disappear etc.) the problem with this
> approach, if i understand the program correctly, is that each resonance
> would have to be associated with 3 peaks with very different chemical
> shifts from which an average value would be calculated. maybe i could set
> the contributions for the ip+ap and ip-ap to zero, but is this sort of
> approach the best?
>
> also, i've noticed that an 'rdc' class exists already.
> any ideas on how to proceed / how you envisaged people using analysis to
> measure rdcs?
In essence, all of this sort of thing is on our "To Do" list.
The way that RDCs will eventually be handled, and indeed the way that they
are modelled, is that the doublet components will be sub-peaks (whether or
not you actually see the 'original' peak). The difference between a peak
and a sub-peak is that the position of a peak is indicative of chemical
shift, whereas the position of a sub-peak is a combination of chemical
shift and a splitting value. Thus, you can assign peaks and sub-peaks to
the same resonance at the same shift but have the splitting, and hence the
value you are trying to derive, represented by the positional difference
at the sub peak. There will then be a custom interface to convert the
splitting values into the property you are trying to measure.
Before this sort of thing is put into Analysis, the approach you mention,
of setting the shift weighting to zero for your component spectra, seems
fair enough. To get the splitting you would just have to interrogate the
peakDims for the appropriate resonances and pull out the split positions.
Note that you will probably have to set the assignment tolerance to
something fairly large to get the unsplit resonance to come up as a
possibility for the split spectra.
Also, resonances can have several different chemical shifts, for example
when experiments are done under different conditions; the resonance is
caused by the same thing, but the value will vary with pH, temperature
etc. Although different ShiftLists for different experiments is not fully
implemented in Analysis, if you're into writing macros it would be
possible to make new ShiftLists for each of the component experiments,
assign the spit and non-split peaks to the same resonances (but now this
means different shifts in different lists). Pulling out the splitting
would then be a matter of comparing the three shift values for each
resonance.
Tim
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766022 (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.pantonia.co.uk
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