On Tuesday 13 July 2010 12:32:48 pm Ariel Talavera wrote: > Hi CCP4ers, > > Is there any differences in the way of calculating the Rfactor between > PHENIX.refine and other programs implemented in CCP4i, like Refmac5 or > sfcheck, or the EDS server? > > I asking this because I have a structure solved at 1.4 Å resolution. > Phenix,refine was used for its refinement and for the final model > Rfactor was 14.5%. But during the validation with sfcheck (CCP4i), I got > an Rfactor of 20.8%.
Should be in an FAQ somewhere: Q: Why does sfcheck not reproduce my original R factors? A: Because instead of using the Fc in your file, sfcheck tries to re-calculate Fc using only your atom names, coordinates and isotropic B factors. This is bad, because it ignores any contributions to your original Fc from things like F_partial, Anisotropic corrections, TLS models, scattering factor corrections, riding hydrogens, etc. My advice is to use sfcheck only to evaluate the Fobs file resulting from your data collection. It is not a suitable tool for validating a refined model. > The same happened when I used this final model as starting model for a > refinement with Refmac5. Again I got an Rfactor of 20.8%. Probably you failed to describe the full model to refmac. Refmac and phenix.refine can both handle all the contributing factors listed above, but it may take some work to pick a the correct corresponding set of options. Ethan > As far as I know, Phenix uses different algorithms for the refinement > than other programs, which in some cases can make Phenix gets better > Rfactors. Could these differences be the reason for this large > difference in the calculated Rfactors? Or I have to recheck my procedure > for mistakes? > > Thanks a lot in advanced. > Looking forward to hearing form you. > > Cheers, > Ariel > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742