Hi Rasmus,
Firstly, the CO experiment problem is fixed, Tim contacted me and recommended that I check and change the full experiment type, so it was just that I had set something up wrongly.
As for the "... any i -> i-1 specific experiments" error, it is still occuring unfortunately. The full experiment types are
HNCACB: H[N[{CA|ca[Cali]}]]
HNCOCACB: H[N[{co[{CA|ca[C]}]]
It seems the error occurs if only the HNCACB and HNCOCACB experiments are selected for querying and matching. It happens both ways around, ie no matter which of these two is set as query (and thus the other as match). It does not happen if only the HNCO and HNCACO are used, or if the carbonyl and alpha/beta data sets are used in parallel, only when the alpha/betas are used alone. Not sure if I have set something up wrongly in the alpha/beta experiments?
Thanks so much for all your help!
Ruht
Neither query nor matches spectra represent any i->i-1 specific experiments
________________________________________
From: CcpNmr software mailing list [[log in to unmask]] on behalf of Rasmus Fogh [[log in to unmask]]
Sent: Monday, 2 November 2009 9:29 PM
To: [log in to unmask]
Subject: Re: protein seq assign problem
Dear Ruth,
The "... any i -> i-1 specific experiments" error should not appear when
you have both HNCACB and HNCOCACB, provided the experiment types are set
correctl;y and everything is working. If it is not too difficult, could
you 1) check that you still have the problem, and 2) tell me the
Experiment Type ('Full Type') setting for both, (From Experiment:Edit
Experiments:{Experimetn Types}?
As for not finding the CO experiments, there is one thing to check. The
program lets you select one carbon window adn one proton window. The
spectra it lets you select are those that are dislpayed (and visible, I
think) in the window. Do you have a carbon window where both HNCACB,
HNCACACB, HNCACOm HNCO are displayed? If not, try making one and see if it
helps.
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Fri, 30 Oct 2009, Ms Ruth Mirams wrote:
> Hi everyone,
>
> I was also trying to use the "Protein Sequence Assignment" function, and
> I have come across the same problem as Vicky, and another problem as
> well. I was using a HNCACB as the query and a HNCOCACB as the match, and
> got the same error message. I did find however, that if I query or match
> more than one experiment at the same time, the error does not appear.
>
> Also, I am trying to match the accompanying carbonyl data as well (HNCACO and HNCO), but for some reason the HNCACO experiment is not given as an option to either query or match in the settings tab of the Protein Sequence Assignment function (but the others all appear there). As far as I can tell all the parameters for this spectrum are the same as for the others, but is there something stupid I have overlooked? Or is there something else going on?
>
> Any help you can give me is greatly appreciated,
> Thanks,
> Ruth
> ________________________________________
> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Vicky Higman [[log in to unmask]]
> Sent: Friday, 2 October 2009 7:45 PM
> To: [log in to unmask]
> Subject: protein seq assign problem
>
> Hi,
>
> I'am trying to use the "Protein Sequence Assignment" function in the
> same way as I previously used the "Link Seq Spin System" one, but am
> getting a pop-up box error saying "Neither query nor matches spectra
> represent any i -> i-1 specific experiments" and it doesn't look
> for/find any matches. No message in the terminal window.
> Unfortunately, I really can't work out what the problem is - I am using
> a CBCANH as my query and CBCACONH as the match spectrum and I am
> reasonably confident that I have the correct experiment prototypes
> attached to these (see attached figure) - I certainly couldn't find any
> that fitted these expts any better.
> Am I missing something really obvious? Is there a bug here?
> Any help gratefully received.
> Thanks,
>
> Vicky
>
>
> --
> *********************************************************
> Dr. Victoria A. Higman
>
> Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
> NMR-Supported Structural Biology
> Robert-Roessle-Str. 10
> 13125 Berlin
> Germany
> and
> School of Chemistry
> University of Bristol
> Bristol BS8 1TS
> United Kingdom
>
> Phone: +44-117-95-46325
> E-mail: [log in to unmask] (or [log in to unmask])
>
> http://www.protein-nmr.org.uk
> *********************************************************
>
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