[phenixbb] Completeness issue by phenix

Young-Jin Cho yjcho at brandeis.edu
Tue Dec 16 08:43:23 PST 2008

Thanks Ralf,
You were right. I found that my .log file has Anomalous flag:True.  As it was pointed out, my mtz file was came from ccp4 where it uses anomalous data by default.  

Another small wondering is about differently automatic(?) resolution pick up: my refmac assigned resolution range between 1.48 and 54.23 whereas my phenix.refine set it between 1.363 and 31.041 by default. Also while the refmac provides both entire and high resolution bin completeness, the phenix only gives a whole completeness. Is there any way I can investigate high resolution bin completeness? and why I have different resolution ranges by default without specifically assigning them?

Thanks again.


----- Original Message -----
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
To: phenixbb at phenix-online.org
Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Completeness issue by phenix

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 =================================


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:


Let me know if this doesn't help.
If it does help, I'd be interested to know how the .mtz file was

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