Hello,
That was my first thought as well. But Marielle sent us the project and Rasmus has just figured out what the problem was, and it was that one of the experiments had N bound to the wrong H, and that confused Analysis sufficiently to get this strange prediction.
You can check for this kind of oddity using the Assignment --> Quality Reports dialog (in this case the Resonances tab, which showed incorrect bonds).
Wayne
On 9 Sep 2013, at 13:55, Dr Andy Herbert wrote:
> Hi,
>
> Just as a matter of interest, have you tried deleting your orphan resonances recently... I've found on occasion that doing this can clear up some seemingly mysterious behaviours of analysis.
>
> Andy
>
> On 09/09/13 11:04, Wälti Marielle wrote:
>> Dear Brian,
>>
>> thank you for the feedback. I did follow what you suggested but the outcome from ccpnmr does not make sense.
>> I have for sure an Ala residue and the corresponding shifts are perfectly matching the BMRB statistics.
>> Please see the picture below.
>> Nonetheless, the program ccpnmr still provides wrong guess or missing possibility.
>> As you can see only the Ca, HN and N resonance types are set. The two other resonances are not and based on his algorithm he should propose me the Ala residue.
>> But it does not and that is the problem.
>> Hope you see my point.
>>
>> Many thanks
>>
>>
>> [cid:7F707AD3-51EA-4B61-BB2E-5D88725E1B0B@ethz.ch]
>>
>> Marielle Wälti
>> ETH Zurich
>> [log in to unmask]<mailto:[log in to unmask]>
>>
>>
>>
>> On Sep 9, 2013, at 10:33 AM, Brian Smith wrote:
>>
>>
>> I think Melanie's suggestion is probably the root of your problem. So the residue type prediction will work with resonances that have been added to a spin system that do not yet have an atom type assigned. Once you assign an atom type, analysis then pays attention to your assignment and so does not consider assignment of a spin system containing a prochiral HB resonance to an alanine as very likely. There isn't currently a "this is an HB but I really don't know what sort" atom type. So your strategy should be to add resonances to a spin system, but not atom type them (beyond the certain ones) until you know the residue type.
>>
>> An other thing that can cause analysis not to predict the residue type unexpectedly that I have noticed previously is if you have carbonyl carbon resonances, but they are not assigned to the carbonyl carbon type. I think this is a weakness in the prediction algorithm.
>>
>> On Mon, 9 Sep 2013, Wälti Marielle wrote:
>>
>> Dear Melanie,
>> Thanks a lot for your quick answer, but it did not help. And also I don't think it should be like that because I would need this prediction if I don't know which amino acid it is and then I also don't know how to call it properly.
>> Cheers,
>> marielle
>>
>> From: Melanie Schwarten <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>>
>> Subject: Re: Predict spin system type
>> Date: September 9, 2013 10:03:28 AM GMT+02:00
>> To: <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>>
>> Reply-To: CcpNmr software mailing list <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>>
>>
>> Hi,
>>
>> maybe it is a problem of the nomenclature? For Ala the HB ist called
>> 'HB*', if it is now called 'HB' that might cause the problem. Similar
>> with the Leu where you have 'HB2' and 'HB3'?
>>
>> Cheers,
>> Melanie
>>
>>
>> On 09/09/2013 09:53 AM, Wälti Marielle wrote:
>> Dear all,
>>
>> I am using ccpNMR analysis 2.3.1 and have a problem with the prediction of a spin system type. I have some of my spin systems, where ccp does not give me any suggestions and others where I really dont understand why it proposes a certain amino acid type. I attached two screenshots with one of each example.
>> The first one: In my opinion it should be an Alanine but ccp proposes only (to 100%) a Threonine. If I look it up on the bmrb table for the statistics of the shifts I really dont see why this should be rather a Thr instead of an Ala? Especially the CA and HB dont fit to a Thr at all but quite well to an Ala. Does anyone see why this is? I found this feature of ccpnmr very useful and it would be a pity if I could not trust on it.
>> Then the second one: In my eyes the Amino acid should be a Leucine but why is ccpNMR not proposing me anything? I dont see any violations if I look up the chemical shifts in the bmrb table. What is there the problem?
>> (As a remark: I did add the whole sequence in the Mol System 1, Chain A, which has Alanines and Leucines. So this can not be the problem).
>>
>> Thanks,
>> Marielle
>>
>> [cid:F3983971-9670-4A0D-BB87-46C536B2A6D2@SitecomWL366][cid:E4B671F3-AF46-4437-999F-DD193C85B50A@SitecomWL366]
>>
>>
>>
>> --
>> Dr. Melanie Schwarten
>>
>> ICS-6 / Structural Biochemistry
>> Forschungszentrum Jülich
>> D-52425 Jülich, Germany
>> phone: +49-2461-61-5874 fax: -61-2023
>> http://www.fz-juelich.de/ics/ics-6/
>> --
>> Heinrich-Heine-Universität Düsseldorf
>> Institut für Physikalische Biologie
>> 40225 Düsseldorf
>> http://www.hhu.de/MathNat/ipb/
>>
>>
>>
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>> --
>> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
>> Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
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>
> --
> Dr Andy Herbert
> Department of Chemistry
> University of Edinburgh
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