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CCPNMR  June 2007

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Subject:

Re: spectrum doubles

From:

"Gary S. Thompson" <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Mon, 18 Jun 2007 09:24:34 +0100

Content-Type:

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Vicky Higman wrote:

> Dear Lieven,
>
> I wonder if this may have arisen because you had both spectra showing 
> when you were picking peaks.
> When you pick peaks, these are picked in all spectra which are showing 
> in that window (i.e. which are 'on' in the toolbar). Thus if you were 
> picking a peak in the HNCO at 165 ppm and the HNCACB was also selected 
> (but not directly visible because it was shown at a different ppm 
> range), this peak may have also been placed in the HNCACB spectrum. 
> Analysis will have noticed this at some stage and then expanded the 
> HNCACB aliased range to go down to 165 ppm. The same thing may have 
> happened the other way round, too, meaning that your HNCO is shown at 
> low ppm values. So it may be worth checking whether you have incorrect 
> peaks in your spectra at these high/low ppm values which should only 
> be on in one and not two spectra. If you remove those and then change 
> your aliased ranges back to what they were, hopefully you will be rid 
> of your doubled spectra. When picking peaks by hand, always make sure 
> that only the spectrum which you want to pick is selected in that 
> window - easily forgotten, though, as I find myself from time to time 
> :) .
>
> Vicky
>
>
Hi Vickey and Lieven

I agree that is the most likley answer and it its a bit of a pain*. I 
did have a request for enhancement That tim and I worked out that should 
squash most of these problems,  which is that the first time you 
manually peak pick a spectrum with an empty peak list analysis should 
ask if you want to start adding peaks to the list...

Also as an aside the quikest wayI have found to clean up this sort of 
thing and return you spectrums display with to  its original sweep  
widths is to go experiment->edit spectra , select a spectrum, click 
referencing and then and then delete the minimum and maximum alias 
frequencies so they  are  _EMPTY_ fields. This will reset the original 
sweep widths (this is a trick wayne gave me;-))

regards
gary

> Lieven Buts wrote:
>
>> Hello all,
>>
>> I am pretty new to macromolecular NMR in general and the
>> CCPNMR programs in particular, so bear with me :-) . I think
>> I am also seeing the spectrum duplication issue.
>>
>> I am working on some triple-resonance spectra of a small
>> protein, and I am looking at (among others) a HNCACB and
>> and a HNCO spectrum in a 3D window with 1H, 13C and 15N
>> axes. The HNCACB spectrum has 13C frequencies in the
>> range from 8 to 88 ppm, while the HNCO spectrum ranges from 165 to 
>> 185 ppm.
>>
>> While picking and assigning peaks, a second copy of the
>> HNCACB spectrum appeared, with the frequency range shifted
>> to 88-165 pm (fitting snugly between the proper limits
>> of the two spectra). Some time later, six equally-spaced
>> "ghost images" of the HNCO spectrum appeared, with the
>> top one reaching up to 50pm on the 13C axis.
>> (Image at http://ultr23.vub.ac.be/~lieven/spectra.png )
>>
>>   
>
>


-- 
-------------------------------------------------------------------
Dr Gary Thompson
Astbury Centre for Structural Molecular Biology,
University of Leeds, Astbury Building,
Leeds, LS2 9JT, West-Yorkshire, UK             Tel. +44-113-3433024
email: [log in to unmask]                   Fax  +44-113-2331407
-------------------------------------------------------------------

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