[phenixbb] Problem with R-free assignment

Pavel Afonine pafonine at lbl.gov
Fri Sep 2 06:29:05 PDT 2011

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 

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:

> 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.


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