Re: [ccp4bb] why I can't reproduce R based on the same program?
Hi Hailiang, I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given by the header. I therefore generated the PDB with the total anisotropic B, based on which I tried REFMAC. However, the initial R_free was higher than provide by PDB (0.226 vs 0.216). Not sure why I can't reproduce R based on the same program. Thanks for any advice. 1. Unless something isn't right (with the data, model or your scripts or all of them), (normally) you don't have to do the refinement to reproduce the R-factor reported in PDB file header of a deposited structure. 2. For particular structure you mentioned in this thread (1ss8) the R-factor is easily reproducible with phenix.model_vs_data (*): phenix.model_vs_data pdb1ss8.ent 1ss8.mtz gives me: (...) Model_vs_Data: r_work(re-computed): 0.214 r_free(re-computed): 0.243 (...) Information extracted from PDB file header: program_name: REFMAC year: 4 r_work : 0.215 r_free : 0.249 (...) which is close given the diffeernces in how the bulk-solvent and anisotropic scaling is done and loss of accuracy due to back-and-forth conversions of ADPs (from total to partial+TLS matrices and from partial+TLS matrices to total). Pavel. (*) 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, 43:677-685.
Re: [ccp4bb] why I can't reproduce R based on the same program?
Thanks for all the advices. The REFMAC PDB didn't provide ksol and bsol in the author's refinement, otherwise I would fix them in my refinement. Best Regards, Hailiang Hi Hailiang, I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given by the header. I therefore generated the PDB with the total anisotropic B, based on which I tried REFMAC. However, the initial R_free was higher than provide by PDB (0.226 vs 0.216). Not sure why I can't reproduce R based on the same program. Thanks for any advice. 1. Unless something isn't right (with the data, model or your scripts or all of them), (normally) you don't have to do the refinement to reproduce the R-factor reported in PDB file header of a deposited structure. 2. For particular structure you mentioned in this thread (1ss8) the R-factor is easily reproducible with phenix.model_vs_data (*): phenix.model_vs_data pdb1ss8.ent 1ss8.mtz gives me: (...) Model_vs_Data: r_work(re-computed): 0.214 r_free(re-computed): 0.243 (...) Information extracted from PDB file header: program_name: REFMAC year: 4 r_work : 0.215 r_free : 0.249 (...) which is close given the diffeernces in how the bulk-solvent and anisotropic scaling is done and loss of accuracy due to back-and-forth conversions of ADPs (from total to partial+TLS matrices and from partial+TLS matrices to total). Pavel. (*) 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, 43:677-685.
[ccp4bb] why I can't reproduce R based on the same program?
Hi there: I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given by the header. I therefore generated the PDB with the total anisotropic B, based on which I tried REFMAC. However, the initial R_free was higher than provide by PDB (0.226 vs 0.216). Not sure why I can't reproduce R based on the same program. Thanks for any advice. Best Regards, Hailiang
Re: [ccp4bb] why I can't reproduce R based on the same program?
I see in your script you used Weight Auto - play a bit with that value and you will find a better fit. Have you used the same TLS groups ? I don't see that you are using TLS refinement in your script. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Sep 10, 2010, at 1:33 AM, Hailiang Zhang wrote: Hi there: I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS given by the header. I therefore generated the PDB with the total anisotropic B, based on which I tried REFMAC. However, the initial R_free was higher than provide by PDB (0.226 vs 0.216). Not sure why I can't reproduce R based on the same program. Thanks for any advice. Best Regards, Hailiang
