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

[Pavel Afonine]

Hi,

> 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.
>
> (...)
>   
> 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.
>   

I'm agree with Ralf. Just to add: once you have added back all Br ions 
don't forget to run phenix.refine again with ordered_solvent=true option 
(to restore removed waters), possibly with more than default number of 
macro-cycles (like 10; default is 3).
Also, I would refine individual occupancies for all Br ions and remove 
those with zero occupancy values after refinement (of huge B-factors). 
You can do all this in one refinement run.

Pavel.