Thanks a lot for all the quick replays to my post. It seems to be a controversial topic. Bellow are to replays which more or less summarize the answers to my post.
Cheers, Ariel On Wed, 2010-07-14 at 07:44 -0500, Eleanor Dodson wrote: > Everything said is true, but one of the most important factors in > calculating structure factors and hence Rvalues is the scaling and > solvent model. All of these are pretty inadequate - probably all protein > "crystals" have large volumes of multiply ordered atoms - water > networks, alternate conformations etc - and our calculations try to take > these into account in different ways. Hence there can be quite big > differences between R factors although the Fcalcs are very similar. > > Eleanor > > > . Dirk Kostrewa wrote: > > ... yes, and this is the reason why sfcheck should be replaced by a > > more modern program at the Protein Data Bank! > > > > Best regards, > > > > Dirk. > > > > Am 13.07.10 22:15, schrieb Ethan Merritt: > >> 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 > >>> > >
