[phenixbb] R/Rfree discrepancy Phenix vs Refmac
sabine.schneider at mytum.de
Fri Aug 12 05:57:45 PDT 2011
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.. ;)
> On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider
> <sabine.schneider at mytum.de <mailto:sabine.schneider at mytum.de>> wrote:
> 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!
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
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