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SFCHECK and R-factor??
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Well, this question may sound silly to most of the people
here, but I want someone to enlighten me (and may be others) with
The topic is "R-factor and SFCHECK"..
While depositing the coordinates and SF in the PDB (at
RCSB), the validation tools (in ADIT) commonly used are SFCHECK (for
Model quality against SF data) and PROCHECK (for stereochemical
quality checks). In case of SFCHECK, the coordinates needed to be
in PDB or mmCIF format and the SF data (preferably) in mmCIF format.
Coming to the topic, the values of the R-factor calculated
in SFCHECK is (in most cases) won't tally with the one reported by
the author in the HEADER. This, if I am not wrong, may be due to
some 'scaling' procedure involved here?
Say for example, in the present scenario, I have completed
the model refinement using REFMAC. The calculation of R-factor (I
presume) *not* only involves Fobs and Fcalc, but a scaling factor too?
In case of bulk solvent correction, the information is stored as
FPART and PHIPART. So, the R-value from the program (REFMAC) has
solvent contribution involved, whereas in SFCHECK, this information
is not present (as the reflectionfile has H,K,L,FObs and SigFObs.).
So, is this the reason for the difference in R-values between
the one reported by the author at PDB and the one SFCHECK prints out??
If I am *grossly* wrong on my views, I am sorry and hope
someone can enlighten me (and others too.).
PS:- I hope some *experts* will be around in the CCP4BB, as the dates
for the Glasgow 'eclipse' are approaching!
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