repost of Ken Camerons post on CCPNs JISC mail and Geertens reply for the record
Hi all,
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.
Thanks,
Ken
Senior NMR Scientist
Drug Discovery Unit
CRUK Beatson Institute
Garscube Estate
Switchback Road
Bearsden
Scotland G61 1BD
k.cameron@beatson.gla.ac.uk
Tel: 0141 330 6410
Dear Ken:
I forward your question to Luca, as he ultimately is the author of the Module.
…
Best
Geerten Vuister
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
def calculateChemicalShift(data):
…
delta = (((d[
Hpos]- start_H)*7)**2 + (d[Npos] - start_N)**2)**0.5Which 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. <br /> <br /> <br /> secondly there is the ChemicalShiftMappingModule<br /> <br /> this uses getNmrResidueDeltas in peakUtils.py which has a weights in the same file by atom type<br /> <br /> DefaultAtomWeights = OrderedDict(((H, 7.00), (N, 1.00), (C, 4.00), (OTHER, 1.00)))<br /> <br /> <br /> So in both cases the weighting is correct in the sense that the algorithm is the same<br /> <br /> <span style="font-size: small;" class="mycode_size">So if Kens data is coming out wrong this suggests an unintentional bug or some other problem… in the later case maybe its that spectrum isnt being recognised as a 15N spectrum*?</span><br /> <br /> Over to Luca!<br /> <br /> regards<br /> Gary<br /> <br /> *<span style="text-decoration: line-through;" class="mycode_s"> I havent 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…
