repost of Ken Cameron`s post on CCPNs JISC mail and Geerten`s reply for the record
Can anybody help with the values that v3 shows for the 1H-15N CSP. The values look like they are just the Dd(H) and Dd(N) added together. I cannot find any documentation although I would have assumed the same equation as v2 would have been transferred. There is a relative contribution which is defaulted to a weighting of 7 for 1H and 1 for 15N. The CSP values are much too high for the usual RMS values used which make sit tricky to set cut-offs and to compare to previous data.
Senior NMR Scientist
Drug Discovery Unit
CRUK Beatson Institute
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I forward your question to Luca, as he ultimately is the author of the Module.
My reading is that it should be the same algorithm
There seem to be two implimentations: a macro which is for HN only
In ChemicalShiftMapping.py in v3 the code is
delta = (((d[`Hpos`]- start_H)*7)**2 + (d[`Npos`] - start_N)**2)**0.5
Which uses the same factor of 7. It would however be good to have the factor modifiable (maybe with a warning?) as some papers use a factor of 5 and it is a pain to have to modify the source coded every time you want match someone else`s method.
secondly there is the ChemicalShiftMappingModule
this uses getNmrResidueDeltas in peakUtils.py which has a weights in the same file by atom type
DefaultAtomWeights = OrderedDict(((H, 7.00), (N, 1.00), (C, 4.00), (OTHER, 1.00)))
So in both cases the weighting is correct in the sense that the algorithm is the same
So if Ken`s data is coming out wrong this suggests an unintentional bug or some other problem... in the later case maybe its that spectrum isn`t being recognised as a 15N spectrum*?
Over to Luca!
* I haven`t quite dug to the point where I can see where this is set, does the spectrum type need to be set for this to work or is it set somewhere in the UI? Actually I have now: the values of the default weights can be set in the configuration dialog for the module (the gear at the top right) see this screen shot from the tutorial (Help->Tutorials->CSP Tutorial)
If you used the module did you change this Ken?, if so what do the fields there say...