[phenixbb] R/Rfree discrepancy Phenix vs Refmac

Partha Chakrabarti ppchak at gmail.com
Fri Aug 12 05:36:07 PDT 2011

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.. ;)

On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider <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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