<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="">Hi Sara,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>There are a couple of problems here. One is that the heme coordinates / bond lengths aren’t very good, so Chimera’s estimates for the atom types is wrong for some of the atoms. The other problem is that because the iron is displaced out of the porphyrin ring, addh is adding hydrogens to the inside of the ring that would normally be prevented by the presence of the iron. Those hydrogens repel the iron of course.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>So, to correct things, you need to:</div><div class=""><br class=""></div><div class="">1) Delete all hydrogens</div><div class="">2) Correct the atom types</div><div class="">3) Add the hydrogens back</div><div class="">4) Delete inward-facing porphyrin-ring hydrogens</div><div class="">5) Add charges</div><div class="">6) Minimize</div><div class=""><br class=""></div><div class="">The commands (Favorites→Command Line) corresponding to those steps are:</div><div class=""><br class=""></div><div class="">1) “del H”</div><div class="">2) “defattr /path/to/heme.defattr raise false” (I have attached the heme.defattr file) </div><div class="">3) “addh”</div><div class="">4) “del :hem@hd”</div><div class="">5) “addch” (this will take awhile with AM1-BCC charges)</div><div class="">6) Minimize however you were doing it before.</div><div class=""><br class=""></div><div class="">I have also attached a session with all the above steps performed. The iron is not yet planar with the ring, but additional minimization will undoubtedly get it there.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><div class=""></div></body></html>