[Chimera-users] Web service issue?

Eric Pettersen pett at cgl.ucsf.edu
Tue May 3 09:29:32 PDT 2022

Hi Carlie,
	I am having no trouble reaching/using the Clustal Omega service with Chimera 1.16.  Maybe it was temporary -- does it continue to happen for you?  Does your machine use an HTTP proxy?


	Eric Pettersen
	UCSF Computer Graphics Lab

> On May 3, 2022, at 8:38 AM, LaLone, Carlie via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> Could you provide advise on how to remedy the issue below?
> You are now running Chimera version 1.16 (build 42360).
> Your previous version was 1.15 (build 42258).
> Check the release notes for new features and other info.
> (To access the release notes, use the Help menu to bring up the User's Guide.
> Then click the 'Documentation index' link and you will then see a link
> for the release notes.)
> #0, chain X: fatty acid-binding protein, liver
> Model 1 (m1_Fruit_fly+3stm+X.pdb) appears to be a protein without secondary structure assignments.
> Automatically computing assignments using 'ksdssp' and parameter values:
>   energy cutoff -0.5
>   minimum helix length 3
>   minimum strand length 3
> Use command 'help ksdssp' for more information.
> Traceback from web service request (connection setup):
> Traceback (most recent call last):
>   File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 11, in __init__
>     self._setup(serviceName, opalURL, sessionData)
>   File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 50, in _setup
>     self.sudsClient = Client(self.serviceURL + "?wsdl", **kw)
>   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__
>     self.wsdl = reader.open(url)
>   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
>     d = self.fn(url, self.options)
>   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__
>     d = reader.open(url)
>   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
>     d = self.download(url)
>   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
>     fp = self.options.transport.open(Request(url))
>   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
>     return HttpTransport.open(self, request)
>   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
>     return self.u2open(u2request)
>   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
>     return url.open(u2request, timeout=tm)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 435, in open
>     response = meth(req, response)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 548, in http_response
>     'http', request, response, code, msg, hdrs)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 467, in error
>     result = self._call_chain(*args)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain
>     result = func(*args)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 654, in http_error_302
>     return self.parent.open(new, timeout=req.timeout)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 429, in open
>     response = self._open(req, data)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 447, in _open
>     '_open', req)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 407, in _call_chain
>     result = func(*args)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1241, in https_open
>     context=self._context)
>   File "C:\Program Files\Chimera 1.16\bin\lib\urllib2.py", line 1198, in do_open
>     raise URLError(err)
> URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)>
> Typically, if you get a TypeError, it's a problem on the remote server
> and it should be fixed shortly.  If you get a different error or
> get TypeError consistently for more than a day, please report the
> problem using the Report a Bug... entry in the Help menu.  Please
> include the traceback printed above as part of the problem description.
> Traceback from web application request:
> Traceback (most recent call last):
>   File "C:\Program Files\Chimera 1.16\share\WebServices\appWebService.py", line 48, in _initApp
>     self.backend = Backend(service, url)
>   File "C:\Program Files\Chimera 1.16\share\WebServices\opal_client.py", line 21, in __init__
>     raise NonChimeraError("Web service appears "
> NonChimeraError: Web service appears to be down.  See Reply Log for more details.
> Service 'opal:ClustalOmegaService' is unavailable.  See Reply Log for more details.
> Thank you,
> Carlie
> Carlie A. LaLone, Ph.D.
> Research Bioinformatician
> Great Lakes Toxicology and Ecology Division
> Office of Research and Development
> U.S. Environmental Protection Agency
> 6201 Congdon Blvd.
> Duluth, MN, 55804
> Work: (218)529-5038
> BIG NEWS…SeqAPASSv6.0 is now available!!!!!
> Try the Sequence Alignment to Predict Across Species Susceptibility <https://seqapass.epa.gov/seqapass/> (SeqAPASS) tool and predict chemical susceptibility to hundreds to thousands of species
> Publications
> International Consortium to Advance Cross‐Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology <https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.5214>
> Integrative Computational Approaches to Inform Relative Bioaccumulation Potential of Per-and Polyfluoroalkyl Substances Across Species <https://academic.oup.com/toxsci/article-abstract/180/2/212/6112015>
> Evidence for Cross Species Extrapolation of Mammalian-Based High-Throughput Screening Assay Results <https://pubs.acs.org/doi/abs/10.1021/acs.est.8b04587>
> In Silico Site-Directed Mutagenesis Informs Species-Specific Predictions of Chemical Susceptibility <https://academic.oup.com/toxsci/article/166/1/131/5060571>
> Evaluation of the scientific underpinnings for identifying estrogenic chemicals in nonmammalian taxa  <https://setac.onlinelibrary.wiley.com/doi/full/10.1002/etc.3456>
> SeqAPASS: A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation  <https://academic.oup.com/toxsci/article/153/2/228/2578709>
> Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk <https://www.sciencedirect.com/science/article/pii/S0166445X13002312>
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