On Tue, Jul 30, 2013 at 10:28 AM, Pavel Afonine
This is because Coot and Phenix use slightly different Ramachandran plot libraries. I guess Paul Emsley or/and Jeff can offer more comments on this.
Both are actually derived from MolProbity, but there are two differences: 1) The phi/psi distributions in Phenix 1.8.1 or newer come from an expanded set of high-resolution structures ("Top8000" instead of "Top500"), and also have separate distributions for Ile/Val and cis versus trans-Proline. (This should be consistent with the MolProbity server.) 2) The distributions in Coot are stored in 10-degree increments, versus 2-degree increments in Phenix. Interpolation is used to estimate the actual frequency for exact phi/psi values, but this is less accurate with a coarser distribution. So I would trust the numbers in Phenix over the ones in Coot. (I have no idea what the PDB is using at this point, but I suspect you'll get a completely different set of numbers, as usual.) -Nat