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On Monday 08 September 2008 13:29:24 Jon Wright wrote: > Borhani, David wrote: > > ... > > but I think pretty much everyone has converged on using it for the > > past many years. > > Many small molecule crystallographers seem to refine on intensity and so > avoid need this procedure. I would rather say: ... small molecule crystallographers retain the original value of Iobs and therefor can continually refine the model that maps Icalc onto Iobs. > In short - if your observations are supposed to be noisy in the > "plus_or_minus sigma" sense then the peaks which are much less than the > sigma should come out negative almost half of the time. Truncate would > appear to be for the case where you want an estimate of the true > magnitude of the structure factor, "F", and not your experimental data. You lost me there. Truncate is for the case when you want the value (Xobs - Xcalc)/sig(Xobs) to actually mean something. If "X" is "I" then you don't need to do anything special. If "X" is "F" then some extra step or bookkeeping is needed in order to handle negative Iobs. In either case the idea is to match your predicted value (Icalc or Fcalc) to the experimental data. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742