[phenixbb] lastest phenix.refine reproducible problem
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
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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