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<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Hello,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Could you provide advise on how to remedy the issue below?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">You are now running Chimera version 1.16 (build 42360).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Your previous version was 1.15 (build 42258).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Check the release notes for new features and other info.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">(To access the release notes, use the Help menu to bring up the User's Guide.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Then click the 'Documentation index' link and you will then see a link<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">for the release notes.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">#0, chain X: fatty acid-binding protein, liver<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Model 1 (m1_Fruit_fly+3stm+X.pdb) appears to be a protein without secondary structure assignments.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Automatically computing assignments using 'ksdssp' and parameter values:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> energy cutoff -0.5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> minimum helix length 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> minimum strand length 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Use command 'help ksdssp' for more information.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Traceback from web service request (connection setup):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> self._setup(serviceName, opalURL, sessionData)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> self.sudsClient = Client(self.serviceURL + "?wsdl", **kw)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> self.wsdl = reader.open(url)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> d = self.fn(url, self.options)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> d = reader.open(url)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> d = self.download(url)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> fp = self.options.transport.open(Request(url))<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> return HttpTransport.open(self, request)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 67, in open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> return self.u2open(u2request)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> return url.open(u2request, timeout=tm)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 435, in open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> response = meth(req, response)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 548, in http_response<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> 'http', request, response, code, msg, hdrs)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 467, in error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> result = self._call_chain(*args)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> result = func(*args)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 654, in http_error_302<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> return self.parent.open(new, timeout=req.timeout)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 429, in open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> response = self._open(req, data)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 447, in _open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> '_open', req)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> result = func(*args)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1241, in https_open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> context=self._context)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1198, in do_open<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> raise URLError(err)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Typically, if you get a TypeError, it's a problem on the remote server<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">and it should be fixed shortly. If you get a different error or<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">get TypeError consistently for more than a day, please report the<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">problem using the Report a Bug... entry in the Help menu. Please<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">include the traceback printed above as part of the problem description.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Traceback from web application request:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\share\WebServices\appWebService.py", line 48, in _initApp<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> self.backend = Backend(service, url)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"> raise NonChimeraError("Web service appears "<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">NonChimeraError: Web service appears to be down. See Reply Log for more details.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Service 'opal:ClustalOmegaService' is unavailable. See Reply Log for more details.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Thank you,<br>
Carlie<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Carlie A. LaLone, Ph.D.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Research Bioinformatician<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Great Lakes Toxicology and Ecology Division<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Office of Research and Development<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">U.S. Environmental Protection Agency<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">6201 Congdon Blvd.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Duluth, MN, 55804<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Work: (218)529-5038<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:red">BIG NEWS$B!D(BSeqAPASSv6.0 is now available!!!!!<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Try the
<a href="https://seqapass.epa.gov/seqapass/"><span style="color:#0563C1">Sequence Alignment to Predict Across Species Susceptibility</span></a> (SeqAPASS) tool and predict chemical susceptibility to hundreds to thousands of species<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Publications<o:p></o:p></span></b></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.5214"><span style="color:#0563C1">International Consortium to Advance
Cross$B!>(BSpecies Extrapolation of the Effects of Chemicals in Regulatory Toxicology</span></a><o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://academic.oup.com/toxsci/article-abstract/180/2/212/6112015"><span style="color:#0563C1">Integrative Computational Approaches
to Inform Relative Bioaccumulation Potential of Per-and Polyfluoroalkyl Substances Across Species</span></a><o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://pubs.acs.org/doi/abs/10.1021/acs.est.8b04587"><span style="color:#0563C1">Evidence for Cross Species Extrapolation of Mammalian-Based
High-Throughput Screening Assay Results</span></a><o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://academic.oup.com/toxsci/article/166/1/131/5060571"><span style="color:#0563C1">In Silico Site-Directed Mutagenesis Informs
Species-Specific Predictions of Chemical Susceptibility</span></a><o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.3456"><span style="color:#0563C1">Evaluation of the scientific underpinnings
for identifying estrogenic chemicals in nonmammalian taxa </span></a><o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://academic.oup.com/toxsci/article/153/2/228/2578709"><span style="color:#0563C1">SeqAPASS: A Web-Based Tool for Addressing
the Challenges of Cross-Species Extrapolation </span></a><o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:10.0pt;font-family:"Times New Roman",serif"><a href="https://www.sciencedirect.com/science/article/pii/S0166445X13002312"><span style="color:#0563C1">Molecular target sequence similarity
as a basis for species extrapolation to assess the ecological risk</span></a><o:p></o:p></span></li></ol>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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