[phenixbb] estimated coordinate error
jzhu at cbr.med.harvard.edu
Wed Aug 1 14:47:58 PDT 2007
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 Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
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.
> Jianghai Zhu wrote:
>> 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 A
>> ESU based on Free R value: 0.293 A
>> ESU based on maximum likelihood: 0.239 A
>> I am wondering why they are different.
>> Jianghai Zhu, Ph.D
>> CBR Institute for Biomedical Research
>> Department of Pathology
>> Harvard Medical School
>> 200 Longwood Ave., Boston, MA 02115
>> Ph: 617-278-3211
>> Fx: 618-278-3232
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
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