Hi Mahesh,
They will be close but not the same. RMSDs should be very close normally,
but different treatment of hetero compounds (ligands and such), outliers and
LINKs added during annotation may cause small deviations. The deviations in
R-factors can be much larger for all sorts of reasons. The data that is used
now can be (slightly) different from what was used before due to different
scaling, merging of I+ and I-, conversion from F to I, outlier rejection,
R-free set annotation, deposition errors (i.e. missing data), or deposition
of all measured data, not just the data used in the final refinement (this
is actually a good thing). Different programs have different treatment of
bulk solvent. There can be rounding errors is the conversion from TLS to
anisotropic B-factors. The use of riding hydrogens can also make a big
difference.
There are several papers that discuss the sources of these R-factor
deviations, e.g. papers about EDS, PDB_REDO and phenix.model_vs_data.
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Mahesh Lingaraju
> Sent: Friday, October 11, 2013 21:59
> To: [log in to unmask]
> Subject: [ccp4bb] R and R free from CIF file deposited in PDB
>
> Hello Experts,
>
> I was wondering if the R, Rfree, RMSD for bonds and angles calculated by
> polygon plug in in PHENIX GUI using the cif file & pdb file deposited in
protein
> structure database would be the same as reported in database/publication ?
>
> I apologize in advance if this is a PHENIX specific question.
>
> Many thanks
>
> Mahesh
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