<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear BUSTER developers,<div class=""><br class=""></div><div class="">I am refining a few similar structures ranging from 1.0 to 2.5 Å resolution. I added hydrogen atoms to the models and after refinement, the occupancies of all hydrogen atoms were set to zero. It is clear from refine.log that “All hydrogens are given with zero occupancy, i.e. invisible to X-Ray term”.</div><div class=""><br class=""></div><div class="">I also repeated the 3a4r example in a BUSTER tutorial</div><div class=""><br class=""></div><div class=""><div class=""><a href="https://www.globalphasing.com/buster/wiki/index.cgi?AutobusterHydrogens" class="">https://www.globalphasing.com/buster/wiki/index.cgi?AutobusterHydrogens</a></div></div><div class=""><br class=""></div><div class="">with exactly the same commands, except that I needed to use the -full option of “hydrogenate" which is not stated (or was not available then) to keep the occupancies of the existing hydrogen atoms in 3a4r.pdb. After refinement, the occupancies of hydrogen atoms were set to zero, which is perhaps not supposed to be the case in the tutorial?</div><div class=""><br class=""></div><div class="">I got “best refinement in BUSTER reached for FP,SIGFP with R/Rfree 0.2178/0.2291, which are higher than the results shown in the tutorial 0.1982/0.2120. I guess it’s (partly) the effect of excluding hydrogen atoms for refinement?</div><div class=""><br class=""></div><div class="">I have two sets of questions:</div><div class=""><br class=""></div><div class="">1. Is there a way to keep the occupancies of hydrogen atoms to 1.0 for my 1.0-Å resolution dataset? Interestingly the occupancies of all hydrogen atoms in 3a4r.pdb are all 0.88. Is it even sensible to refine the occupancies of hydrogen atoms?</div><div class=""><br class=""></div><div class="">2. For the 2.0-ish Ā resolution datasets, perhaps it is a better idea to set the occupancies of hydrogen atoms to zero? Is this the way BUSTER treats hydrogen atoms as riding model? Will the zero-occupancy hydrogens still improve the geometry of the model at this resolution? </div><div class=""><br class=""></div><div class="">The BUSTER version is snapshot_20210224, the operating system is CentOS 7.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Wei-Chun</div><div class=""><br class=""></div><div class="">—</div><div class=""><br class=""></div><div class=""><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Dr. rer. nat. Wei-Chun Kao</div><div class="" style="background-color: rgb(255, 255, 255); margin: 0px;"><div class="" style="margin: 0px;"><font color="#888888" face="Proxima Nova Soft" size="2" class=""><a href="mailto:wei-chun.kao@biochemie.uni-freiburg.de" class="">wei-chun.kao@biochemie.uni-freiburg.de</a></font></div></div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(18, 85, 204); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;"><span class="" style="color: rgb(136, 136, 136);">TEL: <span class="" style="color: rgb(18, 85, 204);"><a href="tel:%2B49-761-203-5277" class="">+49-761-203-5277</a></span></span></div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(18, 85, 204); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;"><div class="" style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;"><div class="" style="color: rgb(18, 85, 204); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;"><span class="" style="color: rgb(145, 145, 145); font-size: small;"><a href="http://orcid.org/0000-0001-8687-6334" class="">orcid.org/0000-0001-8687-6334</a><span class="Apple-tab-span" style="white-space: pre;"> </span></span></div></div></div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px; min-height: 15px;"><br class=""></div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Institute for Biochemistry and Molecular Biology</div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">AG Carola Hunte</div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Albert-Ludwigs-Universitaet Freiburg</div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Stefan-Meier-Str. 17</div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">D-79104 Freiburg im Breisgau</div><div class="" style="background-color: rgb(255, 255, 255); color: rgb(136, 136, 136); font-family: "Proxima Nova Soft"; font-size: 13px; margin: 0px;">Germany</div></div><div class=""><br class=""></div><div class=""><br class=""></div></body></html>