<div dir="ltr"><div>Hi George,</div><div><br></div><div>Just in case you haven&#39;t seen it already - CCN from 2013 contains a case study regarding optimal use of ER (p51).</div><div><br></div><div><a href="https://www.phenix-online.org/newsletter/CCN_2013_07.pdf">https://www.phenix-online.org/newsletter/CCN_2013_07.pdf</a><br></div><div><br></div><div>Best wishes,</div><div><br></div><div>Tom</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 14 February 2016 at 20:25, George Kontopidis <span dir="ltr">&lt;<a href="mailto:gkontopidis@vet.uth.gr" target="_blank">gkontopidis@vet.uth.gr</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EL" link="blue" vlink="purple"><div><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Done it. <u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Now I can see </span><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">ensemble refinement option.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">I would let you know how the results look like.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Many thanks,<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">George</span><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u> <u></u></span></p><div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;"> R. D. Oeffner [mailto:<a href="mailto:rdo20@cam.ac.uk" target="_blank">rdo20@cam.ac.uk</a>] <br><b>Sent:</b> Sunday, February 14, 2016 2:23 PM<br><b>To:</b> George Kontopidis<span class=""><br><b>Cc:</b> &#39;PHENIX user mailing list&#39;<br></span><b>Subject:</b> Re: [phenixbb] ensemble refinement<u></u><u></u></span></p></div></div><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><div><div><div><p class="MsoNormal"><span style="font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:black">You need to enable the “alpha test programs” options. Open the Phenix Preferences dialog, click the “General” button and scroll down to find it. Then close and restart Phenix.<u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:black"> <u></u><u></u></span></p></div><div><div><div><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black">From:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black"> <a href="mailto:gkontopidis@vet.uth.gr" title="gkontopidis@vet.uth.gr" target="_blank">George Kontopidis</a> <u></u><u></u></span></p></div><div><div><p class="MsoNormal" style="background:whitesmoke"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black">Sent:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black"> Sunday, February 14, 2016 11:45<u></u><u></u></span></p></div><div><p class="MsoNormal" style="background:whitesmoke"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black">To:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black"> <a href="mailto:bkpoon@lbl.gov" title="bkpoon@lbl.gov" target="_blank">&#39;Billy Poon&#39;</a> ; <a href="mailto:rdo20@cam.ac.uk" title="rdo20@cam.ac.uk" target="_blank">&#39;R. D. Oeffner&#39;</a> <u></u><u></u></span></p></div><div><p class="MsoNormal" style="background:whitesmoke"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black">Cc:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black"> <a href="mailto:phenixbb@phenix-online.org" title="phenixbb@phenix-online.org" target="_blank">&#39;PHENIX user mailing list&#39;</a> <u></u><u></u></span></p></div><div><p class="MsoNormal" style="background:whitesmoke"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black">Subject:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black"> RE: [phenixbb] ensemble refinement<u></u><u></u></span></p></div></div></div><div><p class="MsoNormal"><span style="font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:black"> <u></u><u></u></span></p></div></div><div><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Hi Bill,<u></u><u></u></span></p><p class="MsoNormal"><span style="color:black"> </span><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Phenix version  dev-2313-000 (nightly builds) have been downloaded and installed.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">GUI (phenix.refine) refinement settings does not seem to have an ensemble refinement option.<u></u><u></u></span></p><p class="MsoNormal"><span style="color:black"> </span><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">Regards, <u></u><u></u></span></p><p class="MsoNormal"><span style="color:black"> </span><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d">George<u></u><u></u></span></p><p class="MsoNormal"><span style="color:black"> </span><span lang="EN-US" style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1f497d"><u></u><u></u></span></p><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black">From:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:black"> Billy Poon [<a href="mailto:bkpoon@lbl.gov" target="_blank">mailto:bkpoon@lbl.gov</a>] <br><b>Sent:</b> Saturday, February 13, 2016 10:46 PM<br><b>To:</b> R. D. Oeffner<br><b>Cc:</b> George Kontopidis; PHENIX user mailing list<br><b>Subject:</b> Re: [phenixbb] ensemble refinement<u></u><u></u></span></p><p class="MsoNormal"><span style="color:black"> <u></u><u></u></span></p><div><p class="MsoNormal"><span style="color:black">Hi George,<u></u><u></u></span></p><div><p class="MsoNormal"><span style="color:black"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">You should use one of the newer nightly builds if you want to use the GUI since there have been updates to the GUI. <u></u><u></u></span></p></div></div><div><p class="MsoNormal"><span style="color:black"><br clear="all"><u></u><u></u></span></p><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><p class="MsoNormal"><span style="color:black">--<u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:9.5pt;color:black">Billy K. Poon</span><span style="color:black"><u></u><u></u></span></p></div></div><div><p class="MsoNormal"><span style="color:black">Research Scientist, Molecular Biophysics and Integrated Bioimaging<u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">Lawrence Berkeley National Laboratory<u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">1 Cyclotron Road, M/S 33R0345<u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">Berkeley, CA 94720<u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">Tel: <a href="tel:%28510%29%20486-5709" value="+15104865709" target="_blank">(510) 486-5709</a><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">Fax: <a href="tel:%28510%29%20486-5909" value="+15104865909" target="_blank">(510) 486-5909</a><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="color:black">Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a><u></u><u></u></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div></div><p class="MsoNormal"><span style="color:black"> <u></u><u></u></span></p><div><p class="MsoNormal"><span style="color:black">On Sat, Feb 13, 2016 at 10:51 AM, R. D. Oeffner &lt;<a href="mailto:rdo20@cam.ac.uk" target="_blank">rdo20@cam.ac.uk</a>&gt; wrote:<u></u><u></u></span></p><p class="MsoNormal"><span style="color:black">It’s included as an alpha version in version 1.10.1-2155 so you’ll have to switch on that setting to make it available from the GUI. It also runs from the command line when you call phenix.ensemble_refinement.bat from the phenix command prompt.<br><br>Do let us know about any issues as I don&#39;t think many people have used it in anger on Windows yet.<br><br>Regards,<br><br>Robert<br><br>-- <br>Robert Oeffner, Ph.D.<br>Research Associate, The Read Group<br>Department of Haematology,<br>Cambridge Institute for Medical Research<br>University of Cambridge<br>Cambridge Biomedical Campus<br>Wellcome Trust/MRC Building<br>Hills Road<br>Cambridge CB2 0XY<br><br><a href="http://www.cimr.cam.ac.uk/investigators/read/index.html" target="_blank">www.cimr.cam.ac.uk/investigators/read/index.html</a><br>tel: <a href="tel:%2B44%280%291223%20763234" target="_blank">+44(0)1223 763234</a><br><br><br>From: George Kontopidis<br>Sent: Saturday, February 13, 2016 18:29<br>To: <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>Subject: [phenixbb] ensemble refinement<u></u><u></u></span></p><div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black"><br><br><br>Does ensemble refinement run on Phenix version 1.10.1-2155 (for windows)<br><br>If yes<br><br>can it run from GUI or only using command line?<br><br><br><br>George<br><br><br><br><br><br><br><br><u></u><u></u></span></p></div></div><p class="MsoNormal"><span style="color:black">_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a> <br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><u></u><u></u></span></p></div><p class="MsoNormal"><span style="color:black"> <u></u><u></u></span></p></div></div></div></div></div></div></div></div><br>_______________________________________________<br>
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