This was also submitted to chimera-bugs (which was the appropriate place for it).  For the benefit of anyone searching the mailing-list archive in the future, here is my response on the bug report...

The error indicates that you access the web via a proxy server and that you haven't configured Chimera to use the proxy server. Go to Favorites->Preferences and in the resulting dialog change the settings so that Chimera is using your proxy server. Remember to click 'Save' afterward so that the settings will be used in future Chimera sessions.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 13, 2012, at 5:59 AM, Mahmoud Soliman wrote:

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