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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