<div dir="ltr">Hi Andreas,<div><br></div><div>We have seen in the past some cases that cause Reduce to go into an infinite loop, which I thought had been corrected, but perhaps your model has found a corner-case that I have not considered. NCS vs. no NCS is not the direct problem, it likely has to do with a particular set of coordinate positions that you are reaching during refinement which causes the hydrogen position determination to end up in either an infinite loop, or just an optimization that isn't tractable in a reasonable amount of time. Hydrogens are added for both NQH flips and for clashscore calculation if your input model does not have them.</div>
<div><br></div><div>Would you be willing to send me your files (off list) for debugging purposes? If I can recreate the behavior here, I'll be able to figure out exactly where Reduce is getting hung up.</div><div><br>
</div><div>Thanks,<br>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Dec 3, 2013 at 8:11 AM, Andreas F�rster <span dir="ltr"><<a href="mailto:docandreas@gmail.com" target="_blank">docandreas@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
I'm refining a structure with 11 molecules in the asymmetric unit.<br>
<br>
Recently I took out NCS (data are to 2.2A and differences between molecules of interest). �Refinement now stalls halfway through with two reduce jobs running at 100% CPU. �The current job has been sitting like this for four days. �The last entry in the log file are a few XYZ individual lines.<br>
<br>
Refinement includes XYZ, TLS, individual B, weight optimization. �I launched 8 cycles. �Phenix hangs after 4_bss. �I've observed this twice in a row.<br>
<br>
Any suggestions to overcome this, short of going back to using NCS?<br>
<br>
This is with Phenix dev-1538 on RHEL 6.3.<br>
<br>
<br>
Thanks.<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
Andreas<br>
<br>
<br>
-- <br>
� � � � � � � � � Andreas F�rster<br>
� � �Crystallization and Xray Facility Manager<br>
� � � � � �Centre for Structural Biology<br>
� � � � � � � Imperial College London<br>
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