<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks, Nat this is helpful. Would you know the last version that did not have this requirement?<div>Are old versions still available? I suppose I could with a little help, I could lobotomize a version of phenix not</div><div>to do this during refinement but check the structures later one by one.</div><div><br></div><div>Its not clear to me why it would work fine for three copies but not four or more, so it might be 'fixable'?</div><div>I hate to think I am stuck with CNS, as the TLS (and other features of Phenix are much more powerful).</div><div><br></div><div>Geroge</div><div><br><div><br><div><div>On Jul 11, 2013, at 7:33 AM, Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">On Wed, Jul 10, 2013 at 11:15 AM, George Phillips <<a href="mailto:georgep@rice.edu">georgep@rice.edu</a>> wrote:<br><blockquote type="cite">I am trying to adapt my old CNS scripts to to multiple conformer refinements<br>in Phenix, i.e. up to 20 copies of each entire chain.<br>I seem to be OK with up to three copies of the whole chain, but when I try<br>four or more I seem to be in an infinite loop in the 'reduce' phase of a<br>refinement.<br>3 copies runs in less than hour, even with torsion simulated annealing, with<br>four even overnight the program just runs 'reduce for hours and hours'.<br></blockquote><br>This is not surprising, as alternate conformations aren't necessarily<br>considered truly independent copies the way an ensemble of models is.<br>(The reason being that usually the model will be a mix of single and<br>multiple conformations, especially where waters are concerned.)<br>You're handing Reduce a problem that it was never designed to deal<br>with.<br><br><blockquote type="cite">This<br>happens on the standard release and development version 1422.<br>Is there some way to turn off hydrogens as a work around? Test files<br>available on request. : )<br></blockquote><br>Unfortunately the problem is that phenix.refine always (for the last<br>couple of years) calculates the clashscore as part of coordinate<br>refinement, instead of simply using the nonbonded restraints as a<br>target, and the clashscore by definition takes hydrogens into account.<br> So there is no way to entirely avoid adding hydrogens if you are<br>using the individual_sites strategy.<br><br>-Nat<br>_______________________________________________<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><br></blockquote></div><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; ">George N. Phillips, Jr.<br>Ralph and Dorothy Looney Professor<br>Department of Biochemistry and Cell Biology<br>Rice University, MS140<br>6100 Main Street<br>Houston, Texas 77005-1892<br>Office: +1 713.348.6951<br><a href="http://www.bioc.rice.edu/">http://www.bioc.rice.edu/</a><br><br><br></span>
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