... 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
>>
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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D-81377 Munich
Germany
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