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Hi Jon,<br>
<br>
please run<br>
<br>
phenix.model_vs_data mode.pdb data.mtz <br>
<br>
and that will give the the numbers for data completeness. Please send
me the output of the above command if it doesn't clarify this issue.
Let me know if you have any questions.<br>
<br>
Pavel.<br>
<br>
<br>
On 2/3/10 7:48 PM, Mischa Machius wrote:
<blockquote cite="mid:345C9D84-F946-41C1-99D9-F3CBFAF806A9@med.unc.edu"
type="cite">Could it be that you reserved 10% of your data for Rfree
and are looking at the completeness for the work set? Do you have an
I/sigma(I) cutoff that is high? If not, it might help to post the some
of the Phenix output, e.g., the table with the completeness data along
with the resolution limits, etc. Best - MM
<div><br>
<div>
<div>On Feb 3, 2010, at 10:42 PM, J. Fleming wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">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 -----
From: "Ralf W. Grosse-Kunstleve" <<a moz-do-not-send="true"
href="http://www.phenix-online.org/mailman/listinfo/phenixbb">rwgk at cci.lbl.gov</a>>
To: <a moz-do-not-send="true"
href="http://www.phenix-online.org/mailman/listinfo/phenixbb">phenixbb at phenix-online.org</a>
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
</pre>
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