[phenixbb] completeness using Intensities vs. structure factor

Nathaniel Echols nechols at lbl.gov
Tue Dec 4 15:12:04 PST 2012

On Tue, Dec 4, 2012 at 2:47 PM, Yarrow Madrona <amadrona at uci.edu> wrote:
> I recently refined a structure using experimental Intensities and compared
> it to the same structure refined with calculated structure factors.
> I know if you provide intensities Phenix.refine will convert to structure
> factors. I am not sure if it runs truncate or what.

It runs the French & Wilson treatment that Jeff implemented in CCTBX -
this should effectively be the same as what Truncate does.

> When I run using structure factors (Truncate run in Scala) I get the
> following:
> Completeness in resolution range: 0.901282
> Completeness with d_max=infinity: 0.901259
> Perhaps Scala did not merge anomolous and non-anomolous data?
> This does not may a whole lot of sense to me. Is some data thrown out? Can
> someone explain?

I don't know the explanation, but phenix.refine does perform outlier
rejection, and it's possible that it behaves differently depending on
what input you give it.  That's an awfully big drop in completeness,
though.  Can you please send us the logfiles for the two refinement
runs off-list?  (help at phenix-online.org will cover most of us.)


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