[phenixbb] estimated coordinate error

[Peter Zwart]

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.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
>>> +++++++++++++++++++++++++++++++
>>>
>>>
>>>
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