Hi,
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,
Jon
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve" http://www.phenix-online.org/mailman/listinfo/phenixbb>
To: phenixbb at phenix-online.org
http://www.phenix-online.org/mailman/listinfo/phenixbb
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 =================================
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
