[phenixbb] strategy of refinement for a structure phased by bromide soaking

[Ralf W. Grosse-Kunstleve]

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