Hi All, I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong. Any insight/advice would be appreciated. Thanks, Mike Thompson -- Michael C. Thompson Graduate Student Yeates Lab Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles [email protected]
On Tue, Sep 14, 2010 at 12:02 PM,
I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong.
The structure was probably refined with "implicit" hydrogens in Refmac, which aren't included in the PDB file. model_vs_data won't assume anything about atoms it can't see, and the absence of hydrogens could easily lead to a 2% difference in R-factor at higher resolutions. (An excellent reason to always include hydrogens in your PDB depositions!) -Nat
Hi Mike, if you send me the input files (model and data) then I might be able to find out why you observe this difference. Some possible sources of difference are discussed in the paper that Jeff mentioned in previous email: 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, 669-67. Pavel. On 9/14/10 12:02 PM, [email protected] wrote:
Hi All,
I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong.
Any insight/advice would be appreciated.
Thanks,
Mike Thompson
participants (3)
-
miket＠chem.ucla.edu -
Nathaniel Echols -
Pavel Afonine