Just to put my two-cents in...
>> 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.
The CLUSTID is completely different from a spin system. It simply tells nlinLS to fit a given set of peaks together. Under no given circumstance do this peaks have to be in the same spin system... for a 2D 15N HSQC, they absolutely would not be.
In Johnny's analysis of pseudo3D relaxation data, the peak INDEX number identifies the "spin system" or amide which is relaxing in each pseudo3D. A given peak will then be fit simultaneously across the pseudo3D. If two peaks are overlapped and share a CLUSTID, they will be fit together across the pseudo3D.
Finally, CLUSTID has nothing to do with triple resonance data or automatic assignments. It does not seem to me that there is a function in Analysis analogous to CLUSTID. Again, it only exists in NMRPipe for lineshape analysis, so overlapped peaks can be fit simultaneously.
>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.
>
Given what I have written above, this would only work if every peak in the spectrum were well resolved.
Like I said.. just throwing this out there.
Cheers,
Mike
Michael Latham
Graduate Student
Department of Chemistry and Biochemistry
University of Colorado, Boulder
Phone: 303-492-8085
Fax: 303-492-2439
---- Original message ----
>Date: Wed, 13 Feb 2008 12:59:13 +0000
>From: Brian Smith <[log in to unmask]>
>Subject: Re: Linewidth information from exported peak table
>To: [log in to unmask]
>
>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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