> I ran the initialiseHSQC macro and I notice this assigns each peak to a
> single spin system, with a resonance for the N15 dimension and one for the
> 1H dimension i.e. not specifically assigning the peak to backbone N15 and 1H
> atoms. So is it the case that once I determine which spin system the peak
> belongs to, I then have to specifically assign the N15 dimension to the
> backbone nitrogen and the H1 dimension to the amide proton?
Hi Kate,
You can do the atom type assignment in a few easy steps via the resonance
browser's [Set Atom Type Button]. Sort by shift, isotope and assignment
to cluster the amides.
Or you can set resonance.assignNames if you wanted to change the macro...
> I understand that this may be because not all peaks in the HSQC will belong
> to backbone amides, but the vast majority do so wouldn't it be easier to
> assign everything as backbone amides initially and then go in and change the
> side-chain peaks afterwards?
It is mostly only because the initialiseHSQC macro is very old and could
probably do with an overhaul. Also, in a way it is easier to miss a step,
not store the intermediate type information at all and only assign the
peak when the exact atom is known.
However, I agree that to do things formally and set the atom type
knowledge is best. To make this a smooth process though, a new popup is
required which will also work with HNCO etc and which will also predict
NH2 groups. This is on the Analysis to-do list.
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
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