Hi Pascal,
1-As Phenix started it generated a fobs_experimental_phases_free_Rflag.mtz file. I have been using this file and no longer my data.hkl file for further refinement. I would like to know why the best_solution after the automatic building run does not contain any of the Bromide ions. It has water molecules but no Bromide ions? What is the reason for that?
Since Tom Terwilliger is off-line through Jan 21 I dare to offer a guess: transferring the heavy atoms to the refined model is simply not implemented.
2-I have been refining against the mtz file I mentioned but without any of these Bromide ions and although the refinement is converging , I suspect I have been doing something bad and wrong. Should I start my refinement again from the first best pdb after automatic building and include right away the bromide ions with simultaneous f_prime, f_double_prime and occupancy refinement for the anomalous scatterers?
I think I'd keep the current protein model, but I'd discard all waters and add the Br before continuing with the refinement. I think once the Br are in the PDB file they will survive when you run the wizards. Ralf