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Thank you for you answer. 2014/1/7 Brian Smith <[log in to unmask]> > On Tue, 7 Jan 2014, Jan Zalesak wrote: > > I did not find a reliable way to follow the distance calculations from >> intensities/volumes of the peaks. >> >> I have tried 3 steps (lets say I have overlap of 3Adenine H6-H2' peak >> with 2Ura H6-H2' >> peak) >> 1) I have put 3Adenine H6-H2' peak >> 2) I have manually added the second (2Ura H6-H2' peak) - "crosses" - on >> one peak >> (manually). >> 3) I have deleted (2Ura H6-H2' peak) and filled the assignment of it to >> the assignment >> of the first peak (so i have ambiguous restraint) >> >> After every step I check the peak intensities, peak volumes) and I >> calculate the >> distances. >> But surprisingly the values (all of them - intensities, peak volumes, >> calculated >> distances) do not change for any of the two resonances. >> > > If your peak created in step 2 is close to the first peak then it will > pick up the same intensity value & volume because it's looking at the same > bit of the spectrum. > > When you create a distance restraint from a peak in analysis, you simply > map the intensity or volume to a distance by the algorithm you choose > (1/r6, bins, etc.), so that won't change from situation to situation you > describe. What that then means to the structure calculation program depends > on the structure calculation program - for ambiguous restraints you want to > use one that treats the distance to intensity mapping as "sum" in ARIA/CNS > terminology. > > You should use the third case you have (ambiguous) - you might want to > reduce the weighting of the contribution of the NOE spectrum in the > chemical shift list if you're going to manually assign multiple > possibilities to an ambiguous peak that might be a little off the exact > shift of each possible contributor. You could leave ambiguous peaks > (partially) unassigned and use "make shift match restraints" to avoid this > issue. > > Is there a way to handle this? >> Or is there a way to do it properly, but in a way program will understand >> that there are >> two peaks and the distance I want him to calculate should be smaller than >> if there was a >> single peak? >> > > I think you misunderstood the intensity->distance mapping process. > > > Can I for example change the peak boxes manually (or at least visualize >> them?) >> > > It would be nice to have peak "footprints" that would allow the use of > overlapped NOE peaks more completely in the creation of ambiguous distance > restraints - currently, really overlapped peaks just have to be discarded. > > -- > Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk > Institute of Molecular, Cell and Systems Biology & School of Life Sciences, > College of Medical, Veterinary & Life Sciences, > Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK. > Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600 > ---------------------------------------------------------------------- > The University of Glasgow, charity number SC004401 >