I have a spectrum that has uncertainty in the peak assignment (a peak could be either A32 or A42). When exporting my chemical shift list data as a NEF file for BMRB deposition, is there a way to include an ambiguity code column?
Hi,
As far as I am aware it is not possible to deposit shifts in such case and there is no option to annotate such ambiguity in NEF file that we use for export.
Ambiguity code in BMRB (NMR Star files) are not designed for such purpose, they are mainly to indicate prochiral / stereospecific assignment of methylenes / Leu, Val methyls / aromatic rings assignment.
I am not sure if i would include such shift in deposition at all. It depends on whether this is a case for overlap, in which case your A32 and A42 shifts would have the same value, or is it that you cannot confidently say what it is. If this is the second case, this is essentially unknown shift which should not really be annotated as belonging to specific residue.
BW,
Eliza
I second Eliza’s opinion here. So:
If you know that A32 and A42 are overlapped under the same crosspeak it’s fine to assign the crosspeak to both and this will populate your shiftList appropriately. NEF & BMRB can handle peaks that have multiple assignments and the two sets of shifts will be in your shiftList.
If you don’t know whether the peak should be assigned to A32 or A42 and this peak is the only source for the shifts of those particular NmrAtoms (e.g. A.32.N, A.32.H, etc.) then you don’t know the shifts and should not be depositing them as if you do. Leave the peak unassigned and purge the orphaned shifts from your shiftList.
Best wishes,
Brian