<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Actually, just accidentally noticed a similar reported problem in our bug database. It can happen if you assign non-unique names to atoms in a residue (e.g. multiple hydrogens in a residue just named 'H'). If this sounds like it could be your problem, download the daily build and use that.<div><br></div><div>If you had used Help->Report A Bug to report the problem, I would have noticed this sooner. ;-)</div><div><br></div><div>--Eric</div><div><br><div><div>On Jun 22, 2015, at 12:44 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.EDU">pett@cgl.ucsf.EDU</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Karl,<div><span class="Apple-tab-span" style="white-space:pre"> </span>We have not encountered this behavior. Do you have a session or PDB file where this happens reliably for you? If so, could you use Chimera's Help->Report A Bug and attach the file? I can keep the data private if that's an issue.</div><div><br></div><div>--Eric</div><div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a><br><br></div><div><div>On Jun 19, 2015, at 3:32 PM, Karl Sebby <<a href="mailto:karl.sebby@leftsideresearch.com">karl.sebby@leftsideresearch.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=utf-8"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi<div class="">I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks,</div><div class="">All the best,</div><div class="">Karl<br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">--</div><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">Dr Karl Sebby<br class=""><br class="">Left Side Research LLC<br class="">1661 K M Ranch Road<br class="">Whitefish Montana 59937<br class="">Office: 406 623 4773<br class=""><br class=""></div>
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