[phenixbb] R free set in twinned dataset

Pavel Afonine PAfonine at lbl.gov
Mon Oct 8 14:10:28 PDT 2007

> Any suggestions to remove the old R-free memories? I normally use a 
> simulated annealing at 5000 K.  Don't know if there is any faster way 
> to do it.

I saw cases where even simulated annealing didn't help; but this is 
relatively rare. You can do shake coordinates and B-factors and do 
refinement as many macro-cycles as necessary (eg., until the gap 
Rfree-Rwork does not grow anymore):

phenix.refine model.pdb data.mtz modify_start_model.sites.shake=1.0 

Instead of modify_start_model.adp.randomize=true you can use 

The values in modify_start_model.sites.shake=1.0 is something to play 
with, but something like 1.0 ... 1.5 is ok in most of cases.

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