[phenixbb] Reflection file woes phenix/ccp4/PDB

Ed Pozharski epozh001 at umaryland.edu
Thu Dec 15 10:39:05 PST 2011

On Thu, 2011-12-15 at 10:21 -0800, Nathaniel Echols wrote:

> I thought the PDB finally fixed this?  Their R-factor validation is
> nearly useless anyway, but this seems like such an obvious and easy
> mistake to avoid.

The refmac based validation that PDB runs is not without problems.  For
instance, I recently had about 7% jump in R values upon deposition,
which turned out to be due to fixed TLS from the header being applied to
a file which (per PDB requirements) had the full B-factors listed
already.  However, I disagree that it is useless.  It surely does guard
against accidentally depositing the wrong dataset.  It also warns you if
you have poor electron density match for heteroatoms, which does help to
keep the "creative" electron density interpretation in check.

> Does freerflag take into account the possibility of twinning?  

Not to my knowledge.

Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                                Julian, King of Lemurs

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