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

Pavel Afonine PAfonine at lbl.gov
Thu Jan 10 17:01:19 PST 2008


> 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.


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