[phenixbb] R-free problem with phenix.refine

[sbiswas2 at ncsu.edu]

Hi Pavel,
I got the answer from your paper:
 J. Appl. Cryst. 2010, 43, 669-676. I was just confused why it is
recomputing the values.
thanks,
Shya




>   Hi Vinson,
>
> so, this means that your data and model are ok, and the statistics is
> consistent. Meaning that what you have reported in your PDB file header
> (R-factors, and so on) are correct and correspond to the data. Great!
> Then you should go back to PDB and explain this.
>
> Reference to phenix.model_vs_data is:
>
> Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW,
> Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD:
> phenix.model_vs_data: a high-level tool for the calculation of
> crystallographic model and data statistics
> J. Appl. Cryst. 2010, 43, 669-676.
>
> Good luck and let us know if you have any other problems or questions!
> Pavel.
>
>
> On 10/21/10 11:21 PM, Vinson LIANG wrote:
>> Dear Pavel,
>> Thank you very much for your suggestion.
>> I run phenix.model_vs_data model.pdb data.mtz, and the output
>> statistics matches the one I deposited to PDB. The data should be OK.
>> I very appreciate your help.
>> Best wishes,
>> Vinson
>>
>>
>> ------------------------------------------------------------------------
>> *发件人：* Pavel Afonine <pafonine at lbl.gov>
>> *收件人：* PHENIX user mailing list <phenixbb at phenix-online.org>
>> *抄 送：* Vinson LIANG <lwg_conrad_1983 at yahoo.com.cn>
>> *发送日期：* 2010/10/22 (周五) 12:44:58 上午
>> *主 题：* Re: [phenixbb] R-free problem with phenix.refine
>>
>> Hi,
>>
>>> Recently I deposited a structure to PDB. However, I was told
>>> >>  The R value of SF check are different from your reported value.
>>> >>
>>> >>      R work in SF check = 0.2859
>>> >>      your reported R work = 0.1474
>>> >>  Also there are no R free flags in your sending files, but you
>>> reported R
>>> >>  free value in your all deposition.
>>
>> well, SF check is not the best tool to check things - it's not just my
>> only vision, see lots of conversations on this topic on bb.
>>
>> Just run
>>
>> phenix.model_vs_data model.pdb data.hkl
>>
>> and if output statistics matches the one you deposited to PDB, then
>> you are 100% good. If it doesn't match then there is something to
>> worry about.
>>
>>> So, I rerun my deposited file with phenix.refine, and it gave a
>>> R-work=0.1475, R-free=0.1742.
>>
>> Sounds good.
>>
>>> However, when I tried to run the same file with refmac5, error came
>>> with "Free R label has not been set". I guess phenix.refine gives
>>> Rree-R label that other program could not recognize.
>>
>> No surprises. Jumping between programs is tricky. You have to account
>> for a lot of things to match things that different programs expect
>> differently.
>>
>>> Could anyone please help me to solve this problem?
>>
>> Step-by-step:
>>
>> 1) Run
>> phenix.model_vs_data model.pdb data.hkl
>>
>> 2) if output statistics matches the one you deposited to PDB, then you
>> are 100% good. Come back to PDB and say this.
>>
>> 3) If it doesn't match then there is something that you need to fix.
>> If you can't fix or have no idea what's wrong, you can send me the
>> data and model and I will have a look.
>>
>> Pavel.
>>
>>
>>
>>
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