<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi James,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Yes, undoubtedly in nogui mode there is no Reply Log dialog for you to access. If you are using Python, there are far more direct ways to get an atom's coordinates than using getcrd and trying to parse the reply log anyway. Such as:</div><div><br></div><div>from chimera.selection import OSLSelection</div><div>sel = OSLSelection("#0:%s.%s@CA" % (snpPos, chain))</div><div>a = sel.atoms()[0]</div><div>crd = a.coord() # or a.xformCoord() for transformed coordinates</div><div><br></div><div>I've attached a PDF of a handout from a Chimera development class we just taught here at UCSF. It covers a bunch of handy resources and tips. The first resource it lists, the Programmer's Examples, is something you should look over. They cover how Chimera's molecular data is laid out, how to deal with selections, and so forth.</div><div><br></div><div>--Eric</div><div><br></div><div></div></body></html>