<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 Jacob,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I can’t answer your first question (Greg Couch, our “mmCIF guy”, is the expert there), but I can help with the second. In the PDB standard there are 3 columns allocated to the residue name, followed by a blank column and then one column for the chain ID. Some programs steal that blank column for a 4-character residue name (Amber) and some steal it for a 2-character chain ID. ChimeraX’s PDB code is based on code from Chimera, and Chimera interfaced extensively with Amber programs and therefore interprets that column as as the 4th character of the residue name. So, when that file is read in you get single-character chain IDs (which is fine in your case since you only had ~10 chains that only differed in the second character) and residue names like SERL and ALAL. Obviously, those names are non-standard and therefore ChimeraX writes them out in HETATM records.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The good news is that your problem is pretty easy to fix, at least in this particular case: just throw away the fourth character of the residue name. I have attached a simple Python script that does just that, which you just use the ‘open’ command to run (<i class="">i.e.</i> “open res-fix.py”).</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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 class=""></div></div></body></html>