Hi Xiaopeng, If you are feeding both programs exactly the same file then you are not doing anything wrong. Notice that, if you calculate the Ramachandran plot on Molprobity and then you go on coot, do a round of manual refinement, and only then calculate the Ramachandran, then that can be the source of the difference. But I would bet that it is because different programs have their own definition of what is allowed and what is an outlier.
I personally use the Ramachandran plot on coot just to guide my refinement, but use another program (Molprobity is pretty good) to do a thorough validation. Good luck, Mario Sanches 2011/9/30 Xiaopeng Hu <[email protected]> > Dear all, > > 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? > > Best wishes, > > xiaopeng > -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches
