<div dir="ltr">Whoops, Pavel beat me to it - I guess GMail is also a little buggy this morning.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Oct 4, 2013 at 7:40 AM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">This is not at all expected; it sounds like there is something specific in your structure that the current code isn't handling properly, but it's impossible to guess based on your description alone. �Can you please send all input files plus the log file for a representative run to <a href="mailto:bugs@phenix-online.org" target="_blank">bugs@phenix-online.org</a> so we can try to reproduce the problem? �(They will of course be kept confidential within our group.)<div>
<br></div><div>thanks,</div><div>Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On Fri, Oct 4, 2013 at 1:14 AM, Hugues Nury <span dir="ltr"><<a href="mailto:hugues.nury@ibs.fr" target="_blank">hugues.nury@ibs.fr</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div style="word-wrap:break-word">Hello everyone,<div><br></div><div>I am experiencing differences with phenix.refine versions 1.8.3 or 1.8.4 compared to 1.8.2. Performing comparable runs, Rs are rising several percents with the latest versions, while marginally decreasing using version 1.8.2.�I am a very recent convert to Phenix, so maybe I'm missing something obvious, but here are the details:</div>
<div><br></div><div>Refinement strategy is xyz+real space+tls+individual Bs at 3.5 A, using NCS and secondary structure restraints, and weight optimization.</div><div>Starting R/Rfree are around 24.5/28.5</div><div><br></div>
<div>Part of the problem seems to come from secondary structure restraints, with (many) messages in the log file of the refinement going wild looking like</div><div><div><font face="Courier">WARNING: could not process nonbonded pair</font></div>
<div><font face="Courier">� � Original error:</font></div><div><font face="Courier">� � � cctbx Internal Error: /net/clover/scratch1/phenix/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/pair_tables.h(663): CCTBX_ASSERT(j_sym >= 0) failure.</font></div>
<div><font face="Courier">� � pdb=" N � GLN B 130 " segid="B � " �pdb=" O � VAL B 115 " segid="B � "</font></div></div><div>In log files of refinement with version 1.8.2, there are no such messages, and in either case the definition of beta strands were done automatically by Phenix</div>
<div><br></div><div>But even secondary structure restraints are switched off, it starts ok but goes wrong at the beginning of cycle 2, during local real space refinement</div><div><div><font face="Courier">start: r_work=0.2271 r_free=0.2785</font></div>
<div><font face="Courier">final: r_work=0.2418 r_free=0.2937</font></div></div><div><font face="Courier">And then continue�to worsen.</font></div><div><font face="Courier"><br></font></div><div>Any help appreciated!</div>
<div><br></div><div>Cheers,</div><div>Hugues</div><div><br></div><div><br></div><br><div><div>--<br>Hugues Nury<br><br>Institut de Biologie Structurale<br>41 rue Jules Horowitz, F-38027 Grenoble�Cedex 1, France<br><a href="tel:%2B33%206%2052%2045%2017%2079" value="+33652451779" target="_blank">+33 6 52 45 17 79</a></div>
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