[phenixbb] lastest phenix.refine reproducible problem

Pavel Afonine pafonine at lbl.gov
Wed May 9 12:57:25 PDT 2012


> I had two steps refinement:
> 1->phenix.refine data.mtz model.pdb xray_data.high_resolution=3 
> fix_rotamers=true strategy=individual+adp+individual_sites+tls
> 2->phenix.refine data.mtz model-refined.pdb 
> xray_data.high_resolution=3  fix_rotamers=false strategy=none 
> main.number_of_macro_cycles=1

may I ask why is the step #2 ?

> model-refined.pdb is actually from the 1st step, so in principle the 
> R/R-free values should be the same for 1 and 2. However in my case, I 
> had 0.2506/0.2996 for the 1st step but 0.2503/0.2998 for the second.

Well, 0.2506/0.2996 vs 0.2503/0.2998 I would say the same. Ralf made a 
great comment about this sometime ago - if interested search in phenixbb 
archives. Something like a tiny rounding while reading out/in makes the 
scaling to take a route to a slightly different minimum and voila - a 
slightly different R. Or that same rounding makes density sampling a 
tiny bit different and here is tiny bit difference. I guess one can 
imagine a long list of such things.

> I use the latest version of phenix, phenix-dev-1009.

As of today the latest is 1054, so you are 45+ days behind -:)


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