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<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Pavel,</div><div><br></div><div>I use same data set for refinement, so Rfree is also marked for same reflection. The only difference is that I chose “Data labels” from Phenix IMEAN or I(+) I(-). By the way, I use version 1.8.2 for refinement. Newer versions gives higher R/Rfree. </div><div><br></div><div>Guangyu</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>><br><span style="font-weight:bold">Date: </span> Friday, February 6, 2015 at 1:46 PM<br><span style="font-weight:bold">To: </span> Guangyu Zhu <<a href="mailto:gzhu@hwi.buffalo.edu">gzhu@hwi.buffalo.edu</a>>, "<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>" <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [phenixbb] refinement with anomalous data<br></div><div><br></div><div><div bgcolor="#FFFFFF" text="#000000">
Hello,<br><br><blockquote cite="mid:D0FA7440.1214%25gzhu@hwi.buffalo.edu" type="cite"><div>I have a data set for refinement at 3.8A (outshell I/sigma ~1.0). When I processed the data, I kept anomalous data I+/I-. Because at that time I think I might have anomalous signal. But later I found that the protein coordinated with wrong metal, so I
don’t really have anomalous scatters. I have good model from high resolution data. </div><div><br></div><div>When I refined the structure, I found that refined against I+/I- give lower R/Rfree (23.0%/27.0%) than against Imean (25.1%/28.3%). When I used I+/I-, I knew I doubled reflections/parameters ratio. I also let Phenix both X-ray stereochemistry/ADP weight.
The refined models have similar geometry. So should I use I+/I- for refinement since it gives lower R factor?<br></div></blockquote><br>
you cannot compare R-factors calculated using different sets of reflections, they are simply not comparable. So 23.0%/27.0% versus 25.1%/28.3% doesn't really mean anything in this case.<br><br>
If data set is not anomalous then you can use "force_anomalous_flag_to_be_equal_to=False" so that phenix.refine uses Fobs_mean = (Fobs(+) - Fobs(-))/2 in refinement.<br><br>
Pavel<br><br></div></div></span></body></html>