<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
F(+),SIGF(+),F(-),SIGF(-) are derived from <span
style="line-height: 1.33;">I(+),SIGI(+),I(-),SIGI(-) using various
approximations that depend on underlying model</span>. In this
sense <span style="line-height: 1.33;">I(+),SIGI(+),I(-),SIGI(-) is
more original and richer data than </span>F(+),SIGF(+),F(-),SIGF(-).<br>
<br>
If F(+),SIGF(+),F(-),SIGF(-) were used in refinement to obtain
deposited structure then this would be a good reason to have both, F
and I.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/3/14 8:33 AM, PC wrote:<br>
</div>
<blockquote cite="mid:560826A4005.000013FApatrick.cossins@inbox.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<meta content="INBOX.COM" name="GENERATOR">
<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> <a class="moz-txt-link-abbreviated" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a><br>
<b>Sent:</b> Sat, 30 Aug 2014 09:45:58 -0700<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:patrick.cossins@inbox.com">patrick.cossins@inbox.com</a>,
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><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">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<meta content="INBOX.COM" name="GENERATOR">
<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>
</div>
</div>
<hr style="clear:both;margin-top:10px;height:1px;"
noshade="noshade" size="1px">
<div style="font:12px
Verdana,sans-serif;color:Black;background:white;padding:3px;line-height:1.3em"><span
style="font-weight:bold;">Free Online Photosharing</span> -
Share your photos online with your friends and family!<br>
Visit <a moz-do-not-send="true"
href="http://www.inbox.com/photosharing">http://www.inbox.com/photosharing</a>
to find out more!</div>
</blockquote>
<br>
</body>
</html>