[phenixbb] Gap between R and Rfree

[Simon Kolstoe]

oh yes please Pavel (command line polygon/statistics overview) - could  
the output be a pdf or ps rather than just starting up the GUI?

Simon



On 25 Feb 2010, at 19:39, Pavel Afonine wrote:

> Hi Francis,
>
> in PHENIX GUI: "Validation" -> "PDB Statistics Overview"
>
> or:
>
> in PHENIX GUI: "Validation" -> "POLYGON"
>
> The underlying idea is published here:
>
> Crystallographic model quality at a glance. L. Urzhumtseva, P. V.  
> Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009)
>
> I can add a command line version if anyone is interested.
>
> Pavel.
>
>
>
> On 2/25/10 9:45 AM, Francis E Reyes wrote:
>> Pavel
>>
>> What phenix utility produces such information?
>> Thx
>>
>> FR
>>
>> On Feb 25, 2010, at 10:43 AM, Pavel Afonine <PAfonine at lbl.gov> wrote:
>>
>>> Hi Young-Jin,
>>>
>>> the distribution of R-factors for all structures in PDB refined at  
>>> resolutions between 2.4 and 2.6 A is following:
>>>
>>> Histogram of Rwork for all model in PDB at resolution 2.40-2.60:
>>>   0.115 - 0.141      : 5
>>>   0.141 - 0.168      : 69
>>>   0.168 - 0.194      : 414
>>>   0.194 - 0.220      : 955  <<<<< your structure
>>>   0.220 - 0.246      : 695
>>>   0.246 - 0.273      : 153
>>>   0.273 - 0.299      : 25
>>>   0.299 - 0.325      : 5
>>>   0.325 - 0.352      : 0
>>>   0.352 - 0.378      : 1
>>> Histogram of Rfree for all model in PDB at resolution 2.40-2.60:
>>>   0.146 - 0.178      : 3
>>>   0.178 - 0.210      : 41
>>>   0.210 - 0.242      : 404
>>>   0.242 - 0.274      : 1104
>>>   0.274 - 0.305      : 653   <<<<< your structure
>>>   0.305 - 0.337      : 108
>>>   0.337 - 0.369      : 8
>>>   0.369 - 0.401      : 0
>>>   0.401 - 0.433      : 0
>>>   0.433 - 0.465      : 1
>>> Histogram of Rfree-Rwork for all model in PDB at resolution  
>>> 2.40-2.60:
>>>   0.002 - 0.012      : 28
>>>   0.012 - 0.022      : 83
>>>   0.022 - 0.031      : 232
>>>   0.031 - 0.041      : 430
>>>   0.041 - 0.051      : 458
>>>   0.051 - 0.061      : 493
>>>   0.061 - 0.071      : 298
>>>   0.071 - 0.080      : 186
>>>   0.080 - 0.090      : 85   <<<<< your structure
>>>   0.090 - 0.100      : 29
>>>
>>> which I interpret as your Rwork is most likely good as well as  
>>> Rfree, but the gap Rfree-Rwork is too large meaning possible  
>>> overfitting.
>>>
>>> A few tips:
>>> - if you have NCS - use it in refinement;
>>> - optimize refinement target weights: a) automatically:  
>>> "optimize_wxc=true optimize_wxu=true", or b) manually using  
>>> wxc_scale and wxu_scale parameters;
>>> - make sure you use the latest PHENIX version.
>>>
>>> Let me now if you have any questions.
>>>
>>> Pavel.
>>>
>>>
>>> On 2/25/10 9:17 AM, Young-Jin Cho wrote:
>>>> Hi everyone,
>>>> I recently got a diffraction data and am trying to refine it. The  
>>>> question is whatever I did the gap between R and Rfree stay far  
>>>> away: .2140/.2982 around 2.5 A resolution. (water added and  
>>>> isotropic(individual_adp) and so on).
>>>> Although I am redoing with many different approaches, if anyone  
>>>> can give me any comments or suggestions, it would be helpful.
>>>>
>>>> Thanks in advance,
>>>>
>>>> Young-Jin
>>>>
>>>>
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