First off sorry for the cross post across bbs I have a molecular replacement solution for a single site mutant for data that goes out to 2.8 A. After molecular replacement in phaser I run the following and examine the maps for bias from the model. Option1: simluated annealing refinement in phenix using the phaser mtz Option2: take the phaser mtz and then just run prime and switch in resolve and look at the map Option3: First part: take the phaser mtz and then run simulated annealing and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s model phases and modified Fs I am observing that Option 1 and Option 2 the maps are indistinguishable from each other and show very little bias from the model. In Option 3 just cns simulated annealing does not go as far at removing bias as cns simulated annealing plus prime-and-switch. Although my estimate of model bias is just a "look and see" feeling. Since I lack a thorough understanding of the relative merits of these algorithms I have the following questions 1)Does simulated annealing refinement as implemented in phenix use a prime-and-switch style approach to modify phases at any point to guide the refinement 2) Am I wrong in assuming that just simulated annealing and sigma-aa weighted maps for cns (Option 3 part 1) are not as good as cns simulated annealing + sigmaa+ prime_and_switch ( option3 part 2) Hoping to get a better idea on how well these approaches fair at removing model bias Hari Jayaram Postdoc , Brandeis University