Hi,<br> <br> 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? <br>
<br>Thanks in advance,<br>Jon<br><br><br><pre>----- Original Message -----<br>From: "Ralf W. Grosse-Kunstleve" <<a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">rwgk at cci.lbl.gov</a>><br>
To: <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">phenixbb at phenix-online.org</a><br>Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern<br>Subject: Re: [phenixbb] Completeness issue by phenix<br>
<br>Hi YoungJin,<br><br>I suspect phenix.refine decided your mtz file contains anomalous data<br>when you actually have non-anomalous data. Could you look in the<br>phenix.refine output for something like this:<br><br>================================== X-ray data =================================<br>
<br>F-obs:<br> 1yjp.mtz:FOBS_X,SIGFOBS_X<br><br>R-free flags:<br> 1yjp.mtz:R-free-flags<br><br>Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X<br>Observation type: xray.amplitude<br>Type of data: double, size=495<br>Type of sigmas: double, size=495<br>
Number of Miller indices: 495<br>Anomalous flag: False<br> ^^^^^<br> in particular here<br><br>If you see "Anomalous flag: True" try adding this to the phenix.refine<br>command line:<br>
<br> xray_data.force_anomalous_flag_to_be_equal_to=False<br><br>Let me know if this doesn't help.<br>If it does help, I'd be interested to know how the .mtz file was<br>generated.<br><br>Ralf<br></pre><br>