[phenixbb] Completeness issue by phenix - revisited

J. Fleming moloch525 at gmail.com
Wed Feb 3 19:42:40 PST 2010


  I'm having a problem using phenix.refine with my x-ray data.  My
completeness is always 89% when it should be 99%.  My data was originally
processed with CCP4i.  I found an old post (see below) with a potential fix
that doesn't work for me.  I've tried changing the 'Anomalous flag: True' to
'Anomalous flag: False'  but my completeness is still 89%.  I've clicked
through a variety of other setting in the GUI that I thought would help but
no luck. Does anyone have any ideas?

Thanks in advance,

----- 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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