Discrepancy between phenix.refine and phenix.model_vs_data R-factors
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@SSRL, SLAC (650) 926-2992
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@SSRL, SLAC (650) 926-2992
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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@SSRL, SLAC (650) 926-2992
Thanks Pavel. Will await the next build. Thanks, Abhinav JCSG@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@SSRL, SLAC (650) 926-2992
participants (2)
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Abhinav Kumar -
Pavel Afonine