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

[Pavel Afonine]

Hi Abhinav,

thanks again for sending me the files off list. This let me to identify 
the problem and fix it. The difference between R-factors in 
phenix.refine and phenix.model_vs_data was due to a slightly different 
accounting for scattering contribution from H atoms. In both cases it 
was correct though. If I check in my changes today then next available 
nightly build will have it fixed.

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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130611/8825dde8/attachment.htm>