Hi, There are differences in the algorithm used by Phenix and (for example) Refmac for the solvent treatment. These can account for a 3 to 4 percent difference in Rfactor. I do not understand why there is such a large discrepancy in your case, unless you have for example a solvent model in Phenix and no solvent model in Refmac. Also if you carry out TLS refinement in Phenix but drop the TLS part during analysis this will result in an increase in the R-factor.
There is a tool in Phenix (I think it's called model_vs_data but it's difficult for me to tell you if it's exactly that, I am at home and cannot access my workstation where this information is stored... And did not manage to find it in the Phenix manual right now). This tool should provide you with nearly the same statistics than those used during Phenix refinement. Also, at such a high resolution you might want to do individual atomic anisotropic temperature factor refinement. And unless it has changed recently, there is no such temperature factor refinement in Phenix. Fred. > Message du 13/07/10 21:30 > De : "Ariel Talavera" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] differences Rfactor calculations > > > 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%. 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%. > > 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 > >
