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:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg16463.html
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
