[Chimera-users] Error in using the "align chain sequences" tool in chimera

[Eric Pettersen]

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can no longer reach HTTPS web services (like the "align chain sequences" web service) because its SSL implementation is out of date.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 at 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 at cgl.ucsf.edu
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220502/52d161b6/attachment.html>