Dear support,

I am actually using Chimera as a GUI for modeller and I came across this nice video tutorial (http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/) but I keep getting some bugs at different stages as follow:

1- When I am trying to fetch ID via UniProt, I get the following bug:

<class 'urllib2.HTTPError'> Exception in Tk callback

  Function: <function command at 0x10a113848> (type: <type 'function'>)

  Args: ()

Traceback (innermost last):

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__

    return apply(self.func, args)

  File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command

    getattr(s, buttonFuncName(txt))()

  File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK

    self.Apply()

  File "/Applications/Chimera.app/Contents/Resources/share/chimera/fetch.py", line 210, in Apply

    func(code, **kw)

  File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/ChimeraExtension.py", line 27, in showUniprotSeq

    self.module().showUniprotSeq(ident)

  File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 291, in showUniprotSeq

    acc = mapUniprotNameID(ident)

  File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 61, in mapUniprotNameID

    response = urllib2.urlopen(request)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 126, in urlopen

    return _opener.open(url, data, timeout)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 400, in open

    response = meth(req, response)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 513, in http_response

    'http', request, response, code, msg, hdrs)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 438, in error

    return self._call_chain(*args)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 372, in _call_chain

    result = func(*args)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default

    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)

<class 'urllib2.HTTPError'>: HTTP Error 407: Proxy Authentication Required

HTTPError: HTTP Error 407: Proxy Authentication Required

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default

    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)

See reply log for Python traceback.

2- I tried to avoid the former step by downloading the sequence file (FASTA) and read it in chimera. But even when I tried Tools -->sequence --> PDB/Uniprot --> tools--> Blast Protein it took ages and it gives me this message:

Blast web server appear to be down and that is the reply log:

Traceback from web service request:

Traceback (most recent call last):

  File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 31, in __init__

    self._setup(serviceName, opalURL, sessionData)

  File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 84, in _setup

    resp = self.appServicePort.getAppMetadata(req)

  File "/Applications/Chimera.app/Contents/Resources/share/WebServices/AppService_client.py", line 40, in getAppMetadata

    response = self.binding.Receive(getAppMetadataResponse.typecode)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 531, in Receive

    self.ReceiveSOAP(**kw)

  File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 416, in ReceiveSOAP

    'Response is "%s", not "text/xml"' % self.reply_headers.type)

TypeError: Response is "text/html", not "text/xml"

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 Blast request:

Traceback (most recent call last):

  File "/Applications/Chimera.app/Contents/Resources/share/blastpdb/Parser.py", line 519, in _initBlast

    self.opal = OpalService(service)

  File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 43, in __init__

    raise NonChimeraError("Web service appears "

NonChimeraError: Web service appears to be down.  See Reply Log for more details.

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.

Blast web service appears to be down.  See Reply Log for more details.

Any help on this matter would be appreciated

Best wishes

Mahmoud

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