Brian Smith wrote:
> Hi Wim,
>
> On Wed, 13 Feb 2008, Wim Vranken wrote:
>
>>>> 3. Is there anyway to get analysis to assign groups of peaks (akin
>>>> to the ClustID found in nmrDraw). I don't know if analysis has any
>>>> such use for this, but it will be nice to have as nLin uses these
>>>> ID's to simultaneously fit clustered peaks. There is a tcl macro
>>>> in nmrDraw called clustTab.tcl that works okay, but really requires
>>>> close (and often time consuming) inspection by hand after running.
>>>> It would be nice to have these from analysis (if possible).
>>>
>>> In nmrDraw clusters roughly map to analysis/data model spin systems
>>> for assigned peaks, at least for this purpose. The problem is in
>>> storing the mapping between spin sytem and cluster. I can't
>>> remember the constraints on cluster numbering. As far as I remember
>>> formatConverter knows about clustIDs but we need to figure how to
>>> map these to spin systems in the data model. In principle I guess
>>> this could be done at the level of a spin system annotation string
>>> (nmrdraw.clustid=X) that could be parsed by formatConverter? Of
>>> course it would be nice to make this a two way process for peak
>>> checking and and reimport of the linewidths. Any thoughts Wim?
>>
>> I can track the clustId, sure... probably best on a peak level
>> though. Anyway the question is how to generate these for the first
>> time when exporting - the NmrDraw documentation says:
>>
>> CLUSTID
>> identifies the cluster of peaks that a given peak over-
>> laps. Peaks with the same CLUSTID value are considered
>> to be in one overlapped group.
>>
>> So this is quite different from a spin system, no? Or at least it
>> would depend on the type of spectrum (and overlap).
>
> In the sense of this generic definition you're right of course. In
> the context of fitting peaks from a series of (HSQC based)
> experiments, the CLUSTID seems to be used to identify peaks from the
> different spectra that originate from the same spin system. I guess
> this is also how they're used in 3D 15N or triple resonance spectra en
> route to automatic assignment etc. Given the generic definition they
> may also be used to associate sub peaks of multiplets or all sorts of
> other context specific things.
For the nlinLS peak fitting that we have been doing, the peak clusters
are more used to indicate overlapping peaks, which typically are
actually not part of the same residue/spinsystem. It just tells the peak
fitting routines to consider the clustered peaks in a single operation
so that it 'deconvolutes' the overlapping peaks (assuming a certain line
shape of course).
Patrick
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