[phenixbb] Completeness issue by phenix

[Rupert Russell]

Dear Ralf,

I too have experienced this issue many times before.  My .mtz files were 
generated through the ccp4i "import merged data" tab (default 
parameters), after the data were processed with scalepack.  Letting 
phenix use the .sca file instead overcomes this but this is not an ideal 
situation for cross-compatibility between different programs.

Cheers

Rupert Russell


Ralf W. Grosse-Kunstleve wrote:
> Hi YoungJin,
>
> I suspect phenix.refine decided your mtz file contains anomalous data
> when you actually have non-anomalous data. Could you look in the
> phenix.refine output for something like this:
>
> ================================== X-ray data =================================
>
> F-obs:
>   1yjp.mtz:FOBS_X,SIGFOBS_X
>
> R-free flags:
>   1yjp.mtz:R-free-flags
>
> Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X
> Observation type: xray.amplitude
> Type of data: double, size=495
> Type of sigmas: double, size=495
> Number of Miller indices: 495
> Anomalous flag: False
>                 ^^^^^
>                 in particular here
>
> If you see "Anomalous flag: True" try adding this to the phenix.refine
> command line:
>
>   xray_data.force_anomalous_flag_to_be_equal_to=False
>
> Let me know if this doesn't help.
> If it does help, I'd be interested to know how the .mtz file was
> generated.
>
> Ralf
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>
>