about 2 or sqrt(3)?
P
Jianghai Zhu wrote:I checked a few structures I refined with both phenix.refine and refmac5.� The estimated coordinate error from phenix.refine is about 2 times of that from refmac5 in every case.� I have an impression that the coordinate error is about one tenth of the data resolution.� So which value is more accurate?
Jianghai
+++++++++++++++++++++++++++++++Jianghai Zhu, Ph.DCBR Institute for Biomedical ResearchDepartment of PathologyHarvard Medical School200 Longwood Ave.,�Boston, MA 02115Ph: 617-278-3211Fx: 618-278-3232+++++++++++++++++++++++++++++++
On Aug 1, 2007, at 3:05 PM, Pavel Afonine wrote:
Hi Jianghai,
I do not know what Refmac uses to get this estimations (I have some ideas but I prefer to refrain from such delicate guessing) and we never did systematic comparisons. phenix.refine estimates a coordinate error as described in:
1) V.Yu., Lunin & T.P., Skovoroda. Acta Cryst. (1995). A51, 880-887. "R-free likelihood-based estimates of errors for phases calculated from atomic models"
2) V.Y., Lunin, P.V. Afonine & A.G., Urzhumtsev. Acta Cryst. (2002). A58, 270-282. "Likelihood-based refinement. I. Irremovable model errors"
The formula is actually in the second paper, but to get a general overview look at both papers.
This error estimation is more or less ok for "relatively high" resolution structures towards� the "end" of refinement. Bulk solvent correction must be turned on as well.
Pavel.
Jianghai Zhu wrote:Hi,
I am refining a 2.6 A structure using both phenix.refine and refmac5.� Both programs give me similar R and Rfree values.� But the estimated coordinate errors are quite different.
From phenix.refine:maximum likelihood estimate for coordinate error: 0.42 A
From refmac5:estimated overall coordinate error:ESU based on R value: 0.427 AESU based on Free R value: 0.293 AESU based on maximum likelihood: 0.239 A
I am wondering why they are different.
Jianghai
+++++++++++++++++++++++++++++++Jianghai Zhu, Ph.DCBR Institute for Biomedical ResearchDepartment of PathologyHarvard Medical School200 Longwood Ave.,�Boston, MA 02115Ph: 617-278-3211Fx: 618-278-3232+++++++++++++++++++++++++++++++
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