I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%, Allowed 5,14% and Prefered 93.62%.I am wondering if there is a simply explain for the difference which I don't know? Or I just made some silly mistakes?
It's not you - I believe that Coot and Molprobity/Phenix both use the Richardson lab's data, but this isn't the first complaint I've heard about discrepancies in the statistics, so I suspect that the cutoffs are slightly stricter in Coot. Will check this later today.
-Nat
