[phenixbb] R free set in twinned dataset

Jianghai Zhu jzhu at cbr.med.harvard.edu
Mon Oct 8 14:18:48 PDT 2007

> 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
> modify_start_model.adp.randomize=true
> Instead of modify_start_model.adp.randomize=true you can use
> modify_start_model.adp.set_b_iso=25.0
> 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.

Is this coordiantes and B-factors shaking as effective as SA?  I  
believe it should be much faster.

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