<div dir="ltr">Hi Mark,<div><br></div><div>While waiting for Pavel to return, you could do the following:</div><div>Check if the rmsd goes up because all bond rmsds increase or because there are a few outrageous outliers. The validation tab after refinement lists the worst offenders for geometry restraints. </div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 10, 2020 at 3:12 PM Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Mark<div><br></div><div>Pavel is best to answer this but he will return on Thursday. Someone else may offer guidance until then.</div><div><br clear="all"><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 10, 2020 at 1:10 PM White, Mark <<a href="mailto:mawhite@utmb.edu" target="_blank">mawhite@utmb.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hello,</div>
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I am refining a 3.5 Å structure using the latest stable version of Phenix.Refine. After switching to the latest version the Bond RMSDs exploded to ~ 0.035 Å, when using optimize wxc. Turning off Optimize and using the "Fix WXC" parameters in the GUI with increasingly
smaller values had almost no effect on the final bond rmsds, which seems to explode from reasonable values in the "3_xyz" step of refinement. Am I missing something?
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Best regards,</div>
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Mark</div>
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<div>Mark Andrew White, Ph.D.<br>
Associate Professor of Biochemistry & Molecular Biology,<br>
Manager, SCSB Macromolecular X-ray Laboratory<br>
UTMB, Galveston, TX<br>
<a href="http://xray.utmb.edu" target="_blank">http://xray.utmb.edu</a></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Project Scientist, Molecular Biophysics and Integrated Bioimaging<br></div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">https://phenix-online.org</a></div></div></div>