[phenixbb] questions on refinement

Pavel Afonine pafonine at lbl.gov
Wed Feb 23 10:56:41 PST 2011

  Hi Ram,

> How many cycles are required to remove the Rfree bias for different 
> R-free data set. I usually do annealing at CNS.

- slightly shake coordinates and ADPs;
- remove water (if present);
- run phenix.refine with or without SA, refine coordinates, B-factors, 
use automated water update option, as many macro-cycles as necessary to 
achieve convergence (for example, R-factors stop changing).

Alternatively, you may consider running your model through 
phenix.autobuild (which will be more thorough but time consuming option).

The above strategy may (significantly) vary depending on the data 


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