[phenixbb] weaker density in maps

We sometimes build model into density at ~0.8 sigma, refine, and the Rfree becomes lower. So we believe that we put model where it should be. Running the same data and same model in phenix under default conditions at the command line, we obtain maps that do not show the weaker features in which we believe in CNS. We are wondering if we can believe the weaker density or is it that we are not toggling something on in phenix. We routinely view the phenix-generated maps after transforming them to dsn6 files in mapman. thanks, Dave --