[phenixbb] estimated coordinate error

[Jianghai Zhu]

It varies from 1.7 to 1.9.

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 5:55 PM, Peter Zwart wrote:

> 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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