Hi Fengyun,
On Wed, Sep 1, 2010 at 11:12 AM,
I am now checking the model manually. With the "rotamer analysis" in coot, the plot shows that most of the rotamer outliers are Leu. Is this the common case that Leu appears as the rotamer outlier most often?
Yes, Leu sidechains are often misfit. It's very easy at medium resolution to fit a Leu sidechain ~180 degrees backward, which is almost always an unfavorable conformation. Flipping them back around should arrive at a highly populated, favorable conformation. This problem also effects Thr and Val sidechains, and Ile at times, too. You can read more about this here: http://www.ncbi.nlm.nih.gov/pubmed/19002604 Coot is very good at fixing these errors with the 'autofit best rotamer' tool, and most should also be fixed with the PHENIX 'fix rotamers' tool. Jeff