<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">I am a relative newcomer to Phenix. I have a large multimeric protein structure docked into an electron density map, and I would like to further refine it by rigid-body refinement using Phenix. Is this a realistic strategy?</div><div class=""><br class=""></div><div class="">I have made some attempts, first by converting the .mrc map file to .mtz as outlined here:</div><div class=""><a href="https://www.phenix-online.org/documentation/reference/map_to_structure_factors.html" class="">https://www.phenix-online.org/documentation/reference/map_to_structure_factors.html</a></div><div class=""><br class=""></div><div class="">Then I tried to refine using rigid body refinement in Phenix. However, the program quits but doesn’t really tell me why. Here’s the last part of the log file:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; font-family: Courier;" class="">Number of unique models: 24</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Time building chain proxies: 36.85, per 1000 atoms: 0.26</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Number of scatterers: 142296</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> At special positions: 0</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Unit cell: (342, 342, 342, 90, 90, 90)</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Space group: P 1 (No. 1)</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Number of sites at special positions: 0</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Number of scattering types: 4</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> Type Number sf(0)</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> S 264 16.00</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> O 27720 8.00</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> N 25872 7.00</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> C 88440 6.00</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> sf(0) = scattering factor at diffraction angle 0.</div><div style="margin: 0px; font-size: 11px; font-family: Courier; min-height: 13px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class="">Writing MTZ file:</div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class=""> /Users/xxx/Documents/Phenix/TEST/Refine_1/Test_refine_data.mtz</div><div style="margin: 0px; font-size: 11px; font-family: Courier; min-height: 13px;" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; font-family: Courier;" class="">Sorry</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Can anyone give me any ideas as to what went wrong? Also, is there a better way to do this?</div><div class=""><br class=""></div><div class="">Thanks very much in advance!!</div><div class=""><br class=""></div><div class="">A.M.</div></body></html>