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.

On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider <sabine.schneider@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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