<html><head><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; "><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">Dr Felix Frolow <br>Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology<br>Tel Aviv University 69978, Israel<br><br>Acta Crystallographica F, co-editor<br><br>e-mail: <a href="mailto:mbfrolow@post.tau.ac.il">mbfrolow@post.tau.ac.il</a><br>Tel: ++972-3640-8723<br>Fax: ++972-3640-9407<br>Cellular: 0547 459 608</span>
</div>
<br><div><div>On Oct 9, 2013, at 03:30 , Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Okay, everyone experience problems like this in 1.8.4, could you please answer the following survey:<div><br></div></div></blockquote><div><br></div><div>My problems started earlier as the only version I can use without significant diversion R factors (several %) is 1.8.2.1309 (of those still visible on nightly builds).</div><div><br></div><br><blockquote type="cite"><div dir="ltr"><div style="">1) Are you using secondary structure restraints?</div></div></blockquote><div><br></div><div>NO</div><br><blockquote type="cite"><div dir="ltr"><div style="">2) If you turn off secondary structure restraints, does that fix the problem?</div></div></blockquote><div><br></div><div><br></div><div>Irrelevant</div><br><blockquote type="cite"><div dir="ltr">
<div style="">3) If you leave secondary structure restraints on, but set the parameter refinement.secondary_structure.h_bond_restraints.remove_outliers to True, does that also yield a reasonably correct result? (GUI users, you should be able to just do a parameter search for "remove_outliers".)</div></div></blockquote><div><br></div><div>Irrelevant</div><br><blockquote type="cite"><div dir="ltr">
<div style=""><br></div><div style="">Jan: using the files you sent me, the fix in (3) does appear to solve the problem.</div><div style=""><br></div><div style="">Ryan: if you have 1.3� data and you answered yes to (1), you really shouldn't use secondary structure restraints at high resolution. (I'm not sure there's any fixed cutoff at which they become irrelevant or dangerous, but my guess would be anything below 2.0� doesn't need them.)</div>
<div style=""><br></div><div style="">Anyone else: I'm hoping you all downloaded 1.8.4 before this past weekend (or if you're using 64-bit Linux, before this morning). The installers currently online have been patched to fix the problem (I think) - note however that using parameters from restored runs will *not* work properly.</div>
<div style=""><br></div><div style="">thanks,</div><div style="">Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Oct 8, 2013 at 9:31 AM, Ryan Spencer <span dir="ltr"><<a href="mailto:rspencer@uci.edu" target="_blank">rspencer@uci.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-US" link="blue" vlink="purple"><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Nat,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> I�m having a similar issue only in reverse. I�m working with a 1.3A data set and halfway during refinement the RMS angles and bonds shoot up (0.02/2.3) and the Rfree/Rwork drops by two points (17/15). When I don�t use the X-ray/stereochemistry and X-ray/ADP weight optimization the Rfree/Rwork values shoot up 10 points on the second run and the RMS angles/bonds drop significantly. Any help would be appreciated. I�m running the refinement on 1.8.4-1496.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Ryan Spencer<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">University of California, Irvine<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Nowick Research Group <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [mailto:<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] <b>On Behalf Of </b>Nathaniel Echols<br>
<b>Sent:</b> Tuesday, October 08, 2013 4:24 AM<br><b>To:</b> PHENIX user mailing list<br><b>Subject:</b> Re: [phenixbb] Worse R factor with newer version of phenix<u></u><u></u></span></p><div><div class="h5"><p class="MsoNormal">
<u></u> <u></u></p><div><p class="MsoNormal">Whenever you see the bond and angle RMSDs blow up like this, it means that the weight between the X-ray and geometry restraint terms was not calculated correctly. Probably the quickest solution is to set wxc_scale much lower - the default is 0.5 but at this resolution I think 0.1 would be more appropriate, and you could try setting it even lower. (Note that if you have weight optimization turned on this will have no effect.) However, the fact that you didn't see this before suggests that there may be a bug somewhere that is specific to your data. Could you please send us input files and log file at <a href="mailto:bugs@phenix-online.org" target="_blank">bugs@phenix-online.org</a> so one of us can take a look? (These will be kept private, obviously.)<u></u><u></u></p>
<div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">thanks,<u></u><u></u></p></div><div><p class="MsoNormal">Nat<u></u><u></u></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt">
<u></u> <u></u></p><div><p class="MsoNormal">On Mon, Oct 7, 2013 at 12:46 PM, Jan van Agthoven <<a href="mailto:janccp4@gmail.com" target="_blank">janccp4@gmail.com</a>> wrote:<u></u><u></u></p><p class="MsoNormal">
Hi everyone,<br>I've been working on a low resolution structure (3.6A) which was<br>previously refined with phenix 1.8_1069 (with a reference model,<br>strategy=individual_sites,individual_adp ). I used the same input<br>
files and parameters and ended up with significantly different R<br>factors.<br><br>Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059<br><br>Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997<br>
<br>For the old version<br><br>and<br><br>Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141<br>Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737<br><br>with the new version 1.8.4<br><br>
Remarkably it also came with an increased number of C-beta deviation<br>(0 against 16!).<br><br>Adding tls refinement or ramachandran restrains did not help.<br><br>Now because I was using the .eff file of an old version of phenix, it<br>
came with a long list of unused parameters. These parameters however<br>were all used by default.<br><br>What should I do? Should I go back to this old phenix, or is there a<br>way to improve the result?<br><br>Thanks,<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><u></u><u></u></p>
</div><p class="MsoNormal"><u></u> <u></u></p></div></div></div></div><br>_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">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>
<br></blockquote></div><br></div>
_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br></body></html>