Dear Eric, Thanks so much for your prompt response. Your suggestion, in deed, sorted the problem out. Best Wishes Mahmoud ************************************ Mahmoud E. Soliman B.Pharm, M.Pharm, MPhil/PhD (Bath, UK) Senior Lecturer - Pharmaceutical Chemistry School of Pharmacy and Pharmacology Faculty of Health Science University of KwaZulu Natal Westville Campus Private Bag X54001 Durban 4000 South Africa Tel. 0312607413 *********************************** Mahmoud E. Soliman (PhD) Computational Chemistry & Modeling Department of Chemistry University of Bath Bath BA2 7AY United Kingdom http://people.bath.ac.uk/mess20/ http://www.bath.ac.uk/person/812559 **********************************

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Eric Pettersen 01/13/12 9:30 PM >>> 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:

Exception in Tk callback Function: (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) : 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 --

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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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