repost of Ken Cameron's post on CCPNs JISC mail and Geerten's 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)**0.5
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!
regards
Gary
* 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)
[img]blob:https://www.ccpn.ac.uk/f1ee7d7a-221e-4c8f-9a73-b6550a84ce23[/img]
If you used the module did you change this Ken?, if so what do the fields there say...
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)**0.5
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!
regards
Gary
* 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)
[img]blob:https://www.ccpn.ac.uk/f1ee7d7a-221e-4c8f-9a73-b6550a84ce23[/img]
If you used the module did you change this Ken?, if so what do the fields there say...
