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

Abhinav Kumar abhinavk at slac.stanford.edu
Tue Jun 11 15:32:53 PDT 2013


Thanks Pavel.
Will await the next build.

Thanks,
Abhinav

JCSG at SSRL, SLAC
(650) 926-2992

On 06/11/2013 11:40 AM, Pavel Afonine wrote:
> 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
>>

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