[phenixbb] estimated coordinate error

[Jianghai Zhu]

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.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
+++++++++++++++++++++++++++++++



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 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
>>
>> +++++++++++++++++++++++++++++++
>> 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
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
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