[Chimera-users] Web service issue?

LaLone, Carlie lalone.carlie at epa.gov
Tue May 3 08:38:07 PDT 2022

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
  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 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

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