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<div>Hi Pavel and Phenix users.</div><div><br></div><div>Thank you for your reply.</div><div><br></div><div>I see in 2y78.mtz (example I used below) has both in the MTZ:</div><div><br></div><div> F(+),SIGF(+),F(-),SIGF(-) </div><div><span style="line-height: 1.33;"> I(+),SIGI(+),I(-),SIGI(-) </span></div><br>I am confused, why? One is sufficient isn't it?<div><br></div><div>Thank you,</div><div><div><br></div><div><br></div><div><br><blockquote style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px"><div class="msgHeaders">-----Original Message-----<br><b>From:</b> pafonine@lbl.gov<br><b>Sent:</b> Sat, 30 Aug 2014 09:45:58 -0700<br><b>To:</b> patrick.cossins@inbox.com, phenixbb@phenix-online.org<br><b>Subject:</b> Re: [phenixbb] phenix.refine and R free values<br><br></div><div class="oldBody"><div>
Hello,<br>
<br>
<blockquote cite="mid:24468A45E8C.000004CFpatrick.cossins@inbox.com" type="cite">
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<div>Hi Phenix users,</div>
<div><br>
</div>
<div>I was trying to experiment with phenix.refine using default
parameters (2Y78.pdb) and I got the following message.</div>
<div><span _style="line-height: 1.33;"><br>
</span></div>
<div><span _style="line-height: 1.33;">Multiple equally suitable
arrays of observed </span>X-ray<span _style="line-height:
1.33;"> data found.</span></div>
<div><br>
</div>
<div>Possible choices:</div>
<div> 2Y78.mtz:IOBS,SIGIOBS</div>
<div> 2Y78.mtz:I(+),SIGI(+),I(-),SIGI(-)</div>
<div><br>
</div>
<div>Please use refinement.input.xray_data.labels</div>
<div>to specify an unambiguous substring of the target label.</div>
<div><br>
</div>
<div>Anyway, two questions related to this:</div>
<div><br>
</div>
<div>1) How does one pick of the two options above? <br>
</div>
</blockquote>
<br>
If your question is about the syntax:<br>
<br>
phenix.refine model.pdb data.mtz xray_data.labels="IOBS,SIGIOBS"<br>
or<br>
phenix.refine model.pdb data.mtz xray_data.labels="I(+),SIGI(+" <br>
(sub-string should work).<br>
<br>
If your question is about choice anomalous vs non-anomalous data to
be used: I would use anomalous because it is a richer source of
information, you will get anomalous difference map, you can refine
anomalous f'&f'', etc.<br>
<br>
<blockquote cite="mid:24468A45E8C.000004CFpatrick.cossins@inbox.com" type="cite">
<div>2) If R work/R free went from 0.1044/0.1142 to 0.1096/0.1200
is that bad or is it acceptable?</div>
</blockquote>
<br>
R-factors look similar to me. Systematic slight increase may mean
you need to adjust target weights or choose refinement strategy more
tailored to the quality of input data and model.<br>
<br>
Pavel<br>
<br>
</div></div></blockquote>
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