Hi Jose,
In order to reset ADPs to an average value, shall I use: set_b_iso=30 ?
phenix.pdbtools model.pdb set_b_iso=30 will do it. If you have atoms with ANISOU then convert them to isotropic first: phenix.pdbtools model.pdb convert_to_isotropic.
Could you suggest a good starting point for wxc_scale and wxu_scale for my resolution (3.2 A). Or maybe I should estimate these values empirically?
No need to do this. Either you run with the default values that are determined automatically, or let the program optimize them in which case it will try an array of values and pick the good one. See relevant (and most recent) paper discussing this here: http://www.phenix-online.org/newsletter/CCN_2011_07.pdf
I would also like to include the heavy metals in my structure, in this case I guess it is important to have DANO and SIGDANO as you also suggested.
I am not sure if "reconstructed" Fobs(+) and Fobs(-) from FP and DANO is exactly the same thing as genuine original Fobs(+) and Fobs(-). In any case, all refinement does it refines against the values you give it. In case you have Fobs(+) and Fobs(-) (or FP and DANO) phenix.refine will compute anomalous difference map for you. Whether refining against Fobs(+) and Fobs(-) or F=(Fobs(+) + Fobs(-))/2 has benefits is not clear, unless you refine f' and f'' for anomalous scatterers. Pavel