[phenixbb] R-free problem with phenix.refine

Pavel Afonine pafonine at lbl.gov
Thu Oct 21 23:30:12 PDT 2010

  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!

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.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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