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
Sabine
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
<[email protected]>
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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