[phenixbb] Completeness issue by phenix

Engin Ozkan eozkan at stanford.edu
Mon Dec 15 10:52:56 PST 2008

I believe the default in scalepack2mtz in ccp4i is Anomalous on.  That clearly explains your observations.
You should consider Ralf's point that the data might have been converted to mtz with separate Friedel pairs, even though it was scaled initially as not.


----- Original Message -----
From: "Rupert Russell" <rjmr at st-andrews.ac.uk>
To: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>, "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Monday, December 15, 2008 10:44:03 AM GMT -08:00 US/Canada Pacific
Subject: Re: [phenixbb] Completeness issue by phenix

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.


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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