[phenixbb] Refinement with new mtz.file

Pavel Afonine pafonine at lbl.gov
Tue Jul 22 13:53:49 PDT 2014

Hi Aleksandar,

okay, from amount of emails it starts seeming to me that the problem is 
really exaggerated, while I don't see any problem at all.

Here is the simplest solution that can't fail:

- given new data, forget about old data, remove PDB file header;
- modify model: shake coordinates by 0.5A, shake B-factors, remove all 
- run phenix.refine first with all defaults and ask it to generate new 
free-r set;
- run phenix.refine again using the outcome of previous run. This time:
   -- run say 10 macro-cycles;
   -- enable automated water update;
   -- enable weights optimization;
   -- enable whatever else is appropriate given your data resolution.

This is it.


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