<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="">Well, since the code is simple, I’ve included it below. You should put it in a file whose name in “.py” to indicate it’s Python code, then you can run it in Chimera simply by opening it. It will create a file named “output” in your home folder. It assumes you’re doing CA-CA distances, not CA-any. Probably still <i class="">very</i> slow.<div class=""><br class=""></div><div class="">from chimera import openModels, Molecule</div><div class="">mol = openModels.list(modelTypes=[Molecule])[0]</div><div class="">cas = [ a for a in mol.atoms if a.name == “CA” and a.element.name == “C”]</div><div class="">import os.path</div><div class="">f = open(os.path.expanduser(“~/output”), “w”)</div><div class="">for i, ca1 in enumerate(cas):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for ca2 in cas[i+1:]:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>print>>f, ca1, ca2, ca1.coord().distance(ca2.coord())</div><div class="">f.close()</div><div class=""><br class=""></div><div class="">Since my mail client does wonky things to quotation marks, I’ve also attached the above as a file.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""></div></body></html>