> Yes, I was thinking about this and created a new CCPNMR project with a part
> of my data, just 3dNnoesy data. I ran Aria on this project and I have got
> two isotope errors only after openning the CCPNMR project. Interestingly,
> when I replaced importFromCcpn.py and Protocol.py with your files and did
> another run, this time I have got only one error. So I decided to create a
> CCPNMR project with different data - 3daroCnoesy spectrum only. These data
> were giving me the most error messages in my old CCPNMR projects, but now
> they gave me no error. Thus I have concluded that the isotope-mismatch
> problem has been fixed with those three python scripts but the newly created
> project with 3dNnoesy data contains some problem which still causes the
> isotope-mismatch error in some cases. So I digged deeply in the 3dNnoesy
> containing CCPNMR project and I have found that some cells of the column
> 'Bound' are empty and some resonances are repeated in the 'Problem
> resonances' table. I imported these data from my Cyana calculation and I
> guess that the import was not quite correct. I was trying to figure out how
> to fix it but I could not. Could you please advise me on this as well.
I think we are getting nearer the mark.
There is an issue with ARIA in that it doesn't (yet) explicitly record
which proton dim is which with regard to the type of experiment that has
been run. This makes the mapping from CCPN to ARIA and/or ARIA to CCPN
tricky, especially considering that the ordering of dims varies
from user to user (HnHxN, HxHnN, HnNHx, HxNHn... ). The way to know, at
least for a 3D, which H dim is which is to find the one that is bound to
the N; it is then known that this must go with the ARIA proton dim that is
also bound.
The problem may be that the reference experiment type in CCPN has the
dimensions in the wrong order, and so some reimported ARIA dims are getting
swapped. However, this can be set Experiment::Experiment Types:|Ref Exp
Dim| - There is no a priori way of the software necessarily knowing which
dim is which. But if you look though the Ref Measurements you can see
which dim is which with regards to the magnetisation transfer, so for
example with an H[N]_H.NOESY the transfer goes 1) Hn - 2) N - 3) Hn - 4)
Hx so the Hn is the dim measured at steps 1) & 3) and Hx at step 4).
If you swap these reference dims or set the experiment type you can use
the resonance quality report to see if the bound resonances make sense.
Another solution (although ref experiments should always be set right)
would be to use CCPN constraints and forget about spectra. You can combine
shift matched and regular distance constraints and put them into ARIA for
violation analysis. (Although keep restraints from different original
spectra separate so they can be calibrated separately).
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.pantonia.co.uk
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