Pavel, 1.8.1-1168 also has this problem.
I found this problem existed with some dataset, but not all dataset. 1.8.1 give better map, so I built model with 1.8.1 map and go back to 1.7.3 before I deposit the structure to PDB. When I compared the B factor from 1.8.x and 1.7.3, I found B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem. 2012/11/3, Pavel Afonine <pafon...@gmail.com>: > Joao, > > I am using the latest version of phenix 1.8.1-1168 > > > 1.8.1-1168 should not have that "problem". > > If you suspect there is still a problem, you can send me the data and model > files off list, explain what exactly the problem is, and I will have a look > right away. > > FYI: there is Phenix mailing list for Phenix-specific questions, where I > can also explain in great details the behavior with the B-factors you > observe. > > All the best, > Pavel >