<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; ">That would be a great short term fix. If the clash score sucks too badly in subsequent analyses of individual structures, I presume I can manually tweak the weights.<div><br></div><div>G</div><div><br><div><div>On Jul 11, 2013, at 10:17 AM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><blockquote type="cite"><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>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></blockquote><br>I can add a flag to disable reporting Molprobity statistics within phenix.refine: it's a trivial change. Currently it is always calculated, and in case of weight optimization it is actually used to select optimal weights.<br>Proper fix though is to make Probe or Reduce faster.<br><br>Pavel<br><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">
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