[phenixbb] WAS: changing TLS groups mid refinement

Phil Jeffrey pjeffrey at princeton.edu
Tue May 18 07:49:28 PDT 2010

I recently went through this - I had a .sca file that had gone through 
the Scalepack2mtz -> Truncate route, then used it in phenix, and since 
Imean and SigImean are still present in the MTZ file phenix.refine uses 
those.  As per Pavel it simply converts them to F's by square root, 
discards Imean less than/equal to zero.  This is the DEFAULT behavior, 
and so quite pernicious and easy to miss.

I caught this while checking R-free in shells and noticed lower 
completeness than Scalepack indicated, as per my example.


> Phil,
> I have always used denzo/scalepack, and then scalepack2mtz to
> convert .sca file to .mtz file.  So my data is always processed
> according to French&Wilson.
> Now from what you are saying I understand that there is some possibility
> to get into using non-truncated data with phenix?  And not only that, it
> seems to be the default?
> I suspect that French&Wilson statistics is actually applied by phenix
> internally if the supplied mtz-file only has intensities.  If that is
> not the case, the problem is more serious than I thought.  Otherwise it
> would take deliberate user effort to get into trouble, since
> TRUNCATE=YES is the default of the corresponding CCP4 program.
> Ed.

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