[phenixbb] Discrepancy between phenix.refine and phenix.model_vs_data R-factors

Pavel Afonine pafonine at lbl.gov
Mon Jun 10 11:51:51 PDT 2013


Hi Abhinav,

I have your email and files from last week. I did not have chance to 
address it yet, sorry. Hopefully will do it in a day or two.

Pavel

On 6/10/13 11:42 AM, Abhinav Kumar wrote:
> I am getting a significant difference between the R-factors written by 
> phenix.refine and phenix.model_vs_data.
>
> 1. Phenix.refine
> phenix.refine "in.pdb" "Fobs.mtz" 
> "refinement.input.xray_data.labels=FP SIGFP" 
> "refinement.input.xray_data.high_resolution=2.50" "fix_rotamers=True" 
> "ordered_solvent=True" "strategy=tls+individual_sites+individual_adp"
>
>    Final R-work = 0.1829, R-free = 0.2141
>
>
> 2. Phenix.model_vs_data
> phenix.model_vs_data out.pdb Fobs.mtz f_obs_label="FP" 
> r_free_flags_label="FreeR_flag" high_resolution=2.50 comprehensive=true
>
>     r_work(re-computed)               : 0.1808
>     r_free(re-computed)                : 0.2099
>
> How can I reproduce the phenix.refine R-factors in phenix.model_vs_data?
>
> -- 
> Thanks,
> Abhinav
>
> JCSG at SSRL, SLAC
> (650) 926-2992
>
>
>
>
>
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> phenixbb at phenix-online.org
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