<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Exchange Server">
<!-- converted from text --><style><!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left: #800000 2px solid; } --></style>
</head>
<body>
<meta content="text/html; charset=UTF-8">
<style type="text/css" style="">
<!--
p
{margin-top:0;
margin-bottom:0}
-->
</style>
<div dir="ltr">
<div id="x_divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi Pat,</p>
<p><br>
</p>
<p>I believe they suggest using target weight optimization in this case. It can be specified on the command line as below:</p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">optimize_xyz_weight=true optimize_adp_weight=true</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">I've found for a couple structures I had to use this or else the geometry was much worse. They also
</span>recommend<span style="font-size:12pt"> to use this in the last round of refinement.</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Cheers,</span></p>
<p><span style="font-size:12pt">Nick</span></p>
<p></p>
<pre class="x_literal-block" style="margin-left:2em; margin-right:2em"><br></pre>
<p></p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Patrick Loll <pat.loll@drexel.edu><br>
<b>Sent:</b> Thursday, May 4, 2017 1:25:21 PM<br>
<b>To:</b> Pavel Afonine; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Different stats with different number of macrocycles</font>
<div> </div>
</div>
</div>
<font size="2"><span style="font-size:10pt;">
<div class="PlainText">Hi Pavel,<br>
<br>
I agree that the differences in the R values are not large, but I found the geometry differences compelling (RMS bonds/angles can be either 0.005 �/0.9 deg or 0.008 �/1.4 deg).<br>
<br>
I�m glad to hear the strategies may change based on macrocycle number (otherwise I�d question my understanding of refinement). Is there any way a user can change influence this choice of strategy? Given two models with essentially equivalent R values, I�d prefer
the one with nicer geometry.<br>
<br>
Thanks,<br>
<br>
Pat<br>
<br>
> On 4 May 2017, at 12:20 PM, Pavel Afonine <PAfonine@LBL.GOV> wrote:<br>
> <br>
> Hi Patrick,<br>
> <br>
>> I am finishing a refinement at 2.5 �, using the Phenix GUI. I performed a three-macrocycle refinement, and saw that the geometry (RMS bonds/angles) and R/Rfree all got better in the first macrocycle, and then worsened in the subsequent two macrocycles.<br>
> <br>
> it's hard to comment on this one because I don't know how you define "worse". For example, I'd call the same "R/Rfree = 0.208/0.236" and "R/Rfree = 0.209/0.240" but some may think they are different.<br>
> <br>
>> OK, fine. So I repeated the refinement, except I performed only a single macrocycle (starting from the exact same input coordinates). However, the statistics after this one-macrocycle job did not match the stats seen after 1 macrocycle in the 3-macrocycle
job (?!). This doesn�t make sense to me; if you�re starting from the exact same coordinates, shouldn�t the first macrocycle always wind up at the same place, regardless of whether or not the program goes on to do additional macrocycles of refinement?<br>
> <br>
> phenix.refine may change internal strategies based on specified number of macro-cycles. So your observation is not too unexpected to me.<br>
> <br>
> Pavel<br>
> <br>
<br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
phenixbb@phenix-online.org<br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: phenixbb-leave@phenix-online.org</div>
</span></font>
</body>
</html>