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
