[phenixbb] completeness using Intensities vs. structure factor

Phil Jeffrey pjeffrey at princeton.edu
Tue Dec 4 15:04:42 PST 2012

What column labels does phenix.refine tell you it is using ?  It's 
likely that phenix.refine is grabbing your anomalous data I(+)/I(-) or 
F(+)/F(-) and using that for refinement if you have these types of 
columns in your MTZ file.  This may or may not explain your issue.

Completeness of each column label is shown in CCP4's MTZDUMP output for 
the MTZ file.  Use:
mtzdump hklin mydata.mtz
and then type "go".

It's a lot easier to give phenix.refine less latitude to do something 
unexpected by giving it only the columns you want to use for refinement. 
  Use CCP4's CAD program for that (the LABOUT command to output only the 
required subset of the data).  Obviously this can also provide you with 
the answer to your question relating completeness in refinement and data 
column usage.

Phil Jeffrey

On 12/4/12 5:47 PM, Yarrow Madrona wrote:
> Hi,
> (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
> 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?
> Thank you.

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