[phenixbb] R/Rfree discrepancy Phenix vs Refmac

Sabine Schneider sabine.schneider at mytum.de
Fri Aug 12 05:57:45 PDT 2011

Hello Partha,

At the moment I was more looking, if it makes a difference what comes 
out from Refmac, when I feed it different start models; straight from 
Phaser, reset B-values, after shaking coordinates, after shaking 
coordinates and SA, and so on....

I assumed, if I put the output from Phenix (with R/Rfree X/X  reported 
by phenix) to be identical to the R/Rfree Refmac reports as START value 
when it gets directly the output pdb from phenix?
I thought the reported R/Rfree values are just something like 'model vs 
data'? That's what I am confused about...

No twinning, no automated water building, just 1mol/asu, no twinning


On 08/12/2011 02:36 PM, Partha Chakrabarti wrote:
> Hi Sabine,
> I believe the comparison should be with same input, not output of one 
> piped into another.
> How different are the geometry? Different programs use different 
> algorithm and different xray:geometry term by default. Hence, it might 
> only make sense if the RMSD are almost exactly the same. Furthermore, 
> is one program detecting NCS  or twining or building waters 
> automatically? Then everything is blown up anyway.
> In any case, refinemt program A vs. B is an interesting topic! I would 
> not start one.. ;)
> MFG,
> Partha
> On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider 
> <sabine.schneider at mytum.de <mailto:sabine.schneider at mytum.de>> wrote:
>     Hello,
>     I am refining a structure at 2.1A solved by MR. For curiosity I'm
>     testing things like 'shaking' coordinates, simulated annealing,
>     refinement Refmac vs Phenix and so on, to see what influence that
>     has on stats, maps etc.
>     For instance after MR I did a bit of shaking the coordinates with
>     pdbset (noise 0.1), followed by simulated annealing in Phenix.
>     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?
>     Thanks a lot for the help!
>     Sabine
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