[phenixbb] estimated coordinate error
Jianghai Zhu
jzhu at cbr.med.harvard.edu
Wed Aug 1 15:01:12 PDT 2007
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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>>
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