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" <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 =================================


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