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<font face="Monaco" size="3">Dear support,</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">I am actually using Chimera as a GUI for modeller and I came across this nice video tutorial (</font><font size="3" face="Monaco" color="#0000ff"><i><u><a href="http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/)">http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/)</a></u></i></font><font face="Monaco" size="3"> but I keep getting some bugs at different stages as follow:</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">1- When I am trying to fetch ID via UniProt, I get the following bug:</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"><class 'urllib2.HTTPError'> Exception in Tk callback</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> Function: <function command at 0x10a113848> (type: <type 'function'>)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> Args: ()</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Traceback (innermost last):</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> return apply(self.func, args)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> getattr(s, buttonFuncName(txt))()</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> self.Apply()</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/chimera/fetch.py", line 210, in Apply</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> func(code, **kw)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/ChimeraExtension.py", line 27, in showUniprotSeq</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> self.module().showUniprotSeq(ident)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 291, in showUniprotSeq</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> acc = mapUniprotNameID(ident)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 61, in mapUniprotNameID</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> response = urllib2.urlopen(request)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 126, in urlopen</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> return _opener.open(url, data, timeout)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 400, in open</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> response = meth(req, response)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 513, in http_response</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> 'http', request, response, code, msg, hdrs)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 438, in error</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> return self._call_chain(*args)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 372, in _call_chain</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> result = func(*args)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"><class 'urllib2.HTTPError'>: HTTP Error 407: Proxy Authentication Required</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">HTTPError: HTTP Error 407: Proxy Authentication Required</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">See reply log for Python traceback.</font> </p>
<br> <br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">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:</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Blast web server appear to be down and that is the reply log:</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Traceback from web service request:</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Traceback (most recent call last):</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 31, in __init__</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> self._setup(serviceName, opalURL, sessionData)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 84, in _setup</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> resp = self.appServicePort.getAppMetadata(req)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/AppService_client.py", line 40, in getAppMetadata</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> response = self.binding.Receive(getAppMetadataResponse.typecode)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 531, in Receive</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> self.ReceiveSOAP(**kw)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 416, in ReceiveSOAP</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> 'Response is "%s", not "text/xml"' % self.reply_headers.type)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">TypeError: Response is "text/html", not "text/xml"</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Typically, if you get a TypeError, it's a problem on the remote server</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">and it should be fixed shortly. If you get a different error or</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">get TypeError consistently for more than a day, please report the</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">problem using the Report a Bug... entry in the Help menu. Please</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">include the traceback printed above as part of the problem description.</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Traceback from Blast request:</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Traceback (most recent call last):</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/blastpdb/Parser.py", line 519, in _initBlast</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> self.opal = OpalService(service)</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 43, in __init__</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3"> raise NonChimeraError("Web service appears "</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">NonChimeraError: Web service appears to be down. See Reply Log for more details.</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Typically, if you get a TypeError, it's a problem on the remote server</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">and it should be fixed shortly. If you get a different error or</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">get TypeError consistently for more than a day, please report the</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">problem using the Report a Bug... entry in the Help menu. Please</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">include the traceback printed above as part of the problem description.</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Blast web service appears to be down. See Reply Log for more details.</font> </p>
<br> <br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Any help on this matter would be appreciated</font> </p>
<br>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Best wishes</font> </p>
<p style="margin-top: 0; margin-bottom: 0">
<font face="Monaco" size="3">Mahmoud</font> </p>
<br> <font face="Monaco" STYLE="font-size: 12pt"><br>************************************
<BR>Mahmoud E. Soliman
<BR>B.Pharm, M.Pharm, MPhil/PhD (Bath, UK)
<BR>Senior Lecturer - Pharmaceutical Chemistry
<BR>School of Pharmacy and Pharmacology
<BR>Faculty of Health Science
<BR>University of KwaZulu Natal
<BR>Westville Campus
<BR>Private Bag X54001
<BR>Durban
<BR>4000
<BR>South Africa
<BR>Tel. 0312607413
<BR>***********************************
<BR>Mahmoud E. Soliman (PhD)
<BR>Computational Chemistry & Modeling
<BR>Department of Chemistry
<BR>University of Bath
<BR>Bath
<BR>BA2 7AY
<BR>United Kingdom
<BR><a href="http://people.bath.ac.uk/mess20/
">http://people.bath.ac.uk/mess20/
</a><BR><a href="http://www.bath.ac.uk/person/812559
">http://www.bath.ac.uk/person/812559
</a><BR>
<BR>**********************************
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