> I have encountered some problems with "Copy Peak Assignments" tool. I have
> done ARIA calculation on CCPNGrid Portal which created a new peak list for a
> spectrum, that is, there are two peaks lists (one was in the project before
> ARIA run and the second was created by ARIA) and a chemshift list linked to
> the same spectrum. Because the second peak list contained only peaks for
> which ARIA was able to make an assignment and all unassigned peaks were
> missing in the peak list (is it supposed to be like this?),
You'll have to ask the ARIA people that one...
> I've ended up
> copying ARIA assignments to the original full peak list. After I've done
> this the chemshifts assignment got screwed up for some resonances. Please
> find attached screenshots which (I hope) contain the relevant information.
> There I've shown the data for a selected resonance 27TyrH.
It is possible that this is due to a dimension order issue that was
present in ARIA, which has now been fixed, but which _might_ not have made
its way to CCPNGrid. I will press for this to be fixed if so (but I don't
have direct control). One other slight possibility is that your 'onebond'
dimensions for the NOESY spectrum are set incorrectly, such that the 1H
dims are swapped with regard to what is bound to the 15N. Look in
Experiment::Experiment Types to set the reference dimension mapping. -
This information has to be used in the ARIA:CCPN interface as ARIA does
not (yet) label the direct dimension.
Hopefully if you delete the aberrant assignments all the shifts will sort
themselves. You can find the aberrant shifts at Assignment::Quality
Reports.
A lazy approach, if the grid ARIA needs updating, would be to wait for the
upgrade, and then re-import and copy assignments over to a blanked peak
list.
> Please also note a warning in the shell.
Alan who works on the grid system is aware of this issue, although I don't
know what the status is, but it may be related to the dimension orders.
> I am not sure if other problems are related to the above. In the Peak
> Selection popup you may notice that for the resonance 27TyrH in the direct
> dimension F1 there are multiple assignments (89Val/27Tyr)N in nitrogen
> dimension. And opposite: in F1 (27Tyr/29Arg)H are attached to F2 27TyrN.
> Besides, in this popup particularly (and in others) it gives choices to
> select in 3Dnoesy these views: "(F1)1H(F2)1H 15N in window1" or
> "(F2)1H(F1)1H 15N in window1", while F2 is nitrogen dimension in the "Edit
> spectrum referencing" popup.
Looks like you are using an out-of-date version of Analysis. The labels
like "(F1)1H(F2)1H 15N in window1" don't exist any more, they have now
been changed to "1H 15N - in window1" and similar (indicating the x-y
plane mapping).
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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