[phenixbb] completeness using Intensities vs. structure factor

Yarrow Madrona amadrona at uci.edu
Tue Dec 4 16:53:30 PST 2012

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


> 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.)
> -Nat
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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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