<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Clemens,<div class=""><br class=""></div><div class="">since the 20210716 snapshot update of BUSTER, the <span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">-M HydrogenHybridModel </span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">option becomes available, so I would like to update some of my previous questions </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">as well.</span></div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On 18. Mar 2021, at 11:04, Clemens Vonrhein <<a href="mailto:vonrhein@GLOBALPHASING.COM" class="">vonrhein@GLOBALPHASING.COM</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Wei-Chun,<br class=""></div></div></blockquote><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div class="">One thing to remember after a BUSTER refinement including hydrogens:<br class="">during model validation you might need to tell programs to keep the<br class="">hydrogens as they are and to use the correct (ideal) hydrogen<br class="">position. E.g.<br class=""><br class=""> molprobity.molprobity keep_hydrogens=True nuclear=False refine.pdb<br class=""><br class="">if you used the full occupancy, e-cloud model.<br class=""></div></div></blockquote><div><br class=""></div><div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">In case I have high resolution X-ray data, </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">I use </span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">aB_hydrogenate -full </span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">to place hydrogen atoms and </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">refine the coordinates </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">with </span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">-M HydrogenHybridModel </span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class=""><br class=""></span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">Because the hydrogen atoms are refined with full occupancy </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">and are at </span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">nuclear position, </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">I think there is no need to use </span></div><div class=""><br class=""></div><div class="">nuclear=False</div><div class=""><br class=""></div><div class="">but keep_hydrogens=True</div><div class=""><br class=""></div><div class="">right? <span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">T</span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">he validation </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">results from buster-report,</span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class=""> molprobity.molprobity</span></div><div class=""><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">and the </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">wwPDB validation server should be consistent I suppose?</span></div></div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><blockquote type="cite" class="">Will the<br class="">zero-occupancy hydrogens still improve the geometry of the model at<br class="">this resolution?<br class=""></blockquote><br class="">Yes: they are fully visible to the geometry term and therefore also to<br class="">the contact term - resulting in better placement of e.g. side-chain<br class="">rotamers etc.<br class=""></div></div></blockquote><div><br class=""></div><div><div>For moderate-resolution data, I first use aB_hydrogenate to add H-atoms </div><div>at zero occupancy and refine the coordinates with BUSTER. If I understood correctly, </div><div>buster-report will first run <span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">aB_fix_h_occ to synchronize the occupancy of </span></div><div><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">H-atoms from zero to that of the parent atom. If zero-occupancy H-atoms are invisible to</span></div><div><span style="background-color: rgb(255, 255, 255);" class=""><span style="white-space: pre-wrap;" class="">MolProbity (or some of the molprobity executables), how should I use the BUSTER-refined</span></span></div><div><span style="background-color: rgb(255, 255, 255);" class=""><span style="white-space: pre-wrap;" class="">coordinates </span></span><span style="background-color: rgb(255, 255, 255);" class=""><span style="white-space: pre-wrap;" class="">for </span></span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">wwPDB validation since similar issues </span><span style="white-space: pre-wrap; background-color: rgb(255, 255, 255);" class="">will likely be encountered?</span></div></div><div><br class=""></div><div>Best,</div><div><br class=""></div><div>Wei-Chun</div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><blockquote type="cite" class="">The BUSTER version is snapshot_20210224, the operating system is CentOS 7.<br class=""></blockquote><br class="">Good.<br class=""><br class="">If there are further questions regarding BUSTER and hydrogens, please<br class="">let us know!<br class=""><br class="">Cheers<br class=""><br class="">Clemens<br class=""><br class="">[1] <a href="https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.3330" class="">https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.3330</a><br class="">[2] <a href="https://journals.iucr.org/d/issues/2018/08/00/mn5114/mn5114fig8.html" class="">https://journals.iucr.org/d/issues/2018/08/00/mn5114/mn5114fig8.html</a><br class="">[3] <a href="https://www.globalphasing.com/buster/wiki/index.cgi?BusterRvalues" class="">https://www.globalphasing.com/buster/wiki/index.cgi?BusterRvalues</a><br class=""><br class="">-- <br class=""><br class="">*--------------------------------------------------------------<br class="">* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com<br class="">* Global Phasing Ltd., Sheraton House, Castle Park <br class="">* Cambridge CB3 0AX, UK <a href="http://www.globalphasing.com" class="">www.globalphasing.com</a><br class="">*———————————————————————————————</div></div></blockquote><br class=""></div><div><br class=""></div><br class=""></body></html>