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 收件人： PHENIX user mailing list 抄 送： Vinson LIANG 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.

Hi Pavel, I have a related question, when you run phenix.model_vs_data you get recomputed R and R free values, what does this mean? I ran my data and got the following: Model_vs_Data: r_work(re-computed) : 0.1823 r_free(re-computed) : 0.2076 bulk_solvent_(k_sol,b_sol) : 0.36 44.79 overall_anisotropic_scale_(b_cart) : 21.60 -11.34 -9.52 -0.00 -0.00 -0.00 solvent_content_estimated_via_mask : 41.5 % 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 *收件人：* PHENIX user mailing list *抄 送：* Vinson LIANG *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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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 *收件人：* PHENIX user mailing list *抄 送：* Vinson LIANG *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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb