Brian
As far as I know the CLUSTID does not have to begin at one. I have
manually adjusted these values and they don't have to be sequential
either. At least for nlinLS fitting.
Johnny
---------------------------------------------
Johnny Croy, Ph.D
University of Colorado, Boulder
Post-doctoral Fellow
Wuttke Lab
UCB 215
Boulder, CO 80309-0215
Lab Phone: (303) 492-2369
---------------------------------------------
On Feb 13, 2008, at 5:59 AM, Brian Smith <[log in to unmask]> 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.
>
>> Importing them from an nmrDraw file, then exporting the same
>> numbers is easy enough, but probably not very useful I imagine
>> (also any new peaks picked in Analysis would 'drop out'). To do
>> this thoroughly you would need some interface window in Analysis.
>
> How about just a "treat spin systems as clusters" flag/button on
> export and vice versa on import? The only thing I wondered was
> whether NmrPipe/Draw insisted on numbering them from 1 or something.
>
> Brian
>
> --
> Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk
> Division of Biochemistry & Molecular Biology,
> Institute Biomedical & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459/3089 Fax: 0141 330 8640
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