Hi Ariel,
here is how the R-factor is defined and computed in phenix.refine and
related tools (such as phenix.model_vs_data):
http://cci.lbl.gov/~afonine/FandR/Fmodel_and_Rfactor.pdf
and here is the link to almost exactly the same questions asked a few
days ago on ccp4bb:
[log in to unmask]" target="_blank">http:[log in to unmask]
Pavel.
On 7/13/10 12:32 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%. 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
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