Re: [phenixbb] completeness using Intensities vs. structure factor

O.k, I will send you the log files. Thanks. -Yarow. -Yarrow

On Tue, Dec 4, 2012 at 2:47 PM, Yarrow Madrona 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? ([email protected] will cover most of us.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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