Hi Chara,
 The version of Chimera you are using is quite old and it can no longer reach HTTPS web services (like the "align chain sequences" web service) because its SSL implementation is out of date.  Please upgrade to the current version of Chimera and things will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Apr 29, 2022, at 8:16 AM, Chara Spanou via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear all,

After performing the structure comparison of 2 structures using the "MatchMaker" tool of the chimera software,
I need to run an alignment of the structure sequences using the "align chain sequences" tool of the chimera.

Unfortunately, I am getting the following error message in the reply log that persists for weeks:

Traceback from web service request (connection setup):
Traceback (most recent call last):
  File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 11, in __init__
    self._setup(serviceName, opalURL, sessionData)
  File "C:\Program Files\Chimera 1.12\share\WebServices\opal_client.py", line 50, in _setup
    self.sudsClient = Client(self.serviceURL + "?wsdl", **kw)
  File "C:\Program Files\Chimera 1.12\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 1.12\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 1.12\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 1.12\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 1.12\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 1.12\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 1.12\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 1.12\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 1.12\bin\lib\urllib2.py", line 437, in open
    response = meth(req, response)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 550, in http_response
    'http', request, response, code, msg, hdrs)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 469, in error
    result = self._call_chain(*args)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain
    result = func(*args)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 656, in http_error_302
    return self.parent.open(new, timeout=req.timeout)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 431, in open
    response = self._open(req, data)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 449, in _open
    '_open', req)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 409, in _call_chain
    result = func(*args)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1240, in https_open
    context=self._context)
  File "C:\Program Files\Chimera 1.12\bin\lib\urllib2.py", line 1197, in do_open
    raise URLError(err)
URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)>

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 1.12\share\WebServices\appWebService.py", line 48, in _initApp
    self.backend = Backend(service, url)
  File "C:\Program Files\Chimera 1.12\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.

Can you please help?


Thanks a lot for your time,
Chara
_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users