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
>>>
>
|