[phenixbb] completeness using Intensities vs. structure factor

Yarrow Madrona amadrona at uci.edu
Tue Dec 4 14:47:41 PST 2012

(Phenix v.1.8.1-1168)

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. Anyway, I get this in
the log file which matches my completeness in the scala log file:

Completeness in resolution range: 0.992202
Completeness with d_max=infinity: 0.992164

When I run using structure factors (Truncate run in Scala) I get the

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?

Thank you.

Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

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