[phenixbb] R/Rfree discrepancy Phenix vs Refmac

Pavel Afonine pafonine at lbl.gov
Fri Aug 12 08:34:46 PDT 2011

Hi Sabine,

> For instance after MR I did a bit of shaking the coordinates with 
> pdbset (noise 0.1), 

there are many ways of doing it using PHENIX:

- using the tool that is specifically designed to do this and many more 
of similar manipulations with your model:
phenix.pdbtools model.pdb sites.shake=0.1

- using phenix.refine: it can modify you model before refinement starts 
(so you don't have to run phenix.pdbtools):

phenix.refine model.pdb data.mtz modify_start_model.sites.shake=0.1

- by the way, 0.1 is ridiculously small. 2A or even larger is within 
convergence radius of phenix.refine most of the time. It depends on 
resolution, of course.

> followed by simulated annealing in Phenix.

Cartesian or torsion?

> Phenix states after SA:
> Start R-work = 0.2671, R-free = 0.2992
> Final R-work = 0.2312, R-free = 0.2666
> When I use the output pdb of phenix directly in Refmac (with same mtz 
> as input for Phenix)
> Refmac tells me:
> Initial R factor    0.2392   R free    0.2887
> So I am quite puzzled about the discrepancy. Or can someone tell me if 
> I made an error in reasoning somewhere?

There may be 10+ reasons for this, I'm sure I listed them before (about 
a year ago or more), so you can find it in phenixbb archives. Also, see 
Nat's reply. Some them:

- Fobs outliers removal in phenix.refine;
- efficient bulk-solvent and anisotropic scaling (P.V. Afonine, R.W. 
Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005). D61, 850-855. "A 
robust bulk-solvent correction and anisotropic scaling procedure") and 
mask parameters optimization;
- If your input data file contains Iobs (not Fobs) then different 
algorithms of conversion Iobs to Fobs (phenix.refine uses French&Wilson 
... and many many many more....

In practice, I was only able obtain IDENTICAL R-factors between 
phenix.refine and SHELXL in a very artificial test (where bulk-solvent 
was turned off, I was using identical scattering factors, etc..).


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