<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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...<div><br></div><div>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.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><div><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><div><div>On Jan 13, 2012, at 5:59 AM, Mahmoud Soliman wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div style="line-height: normal; margin-left: 4px; margin-right: 4px; margin-bottom: 1px; margin-top: 4px; font-variant: normal"><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Dear support,</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <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> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">1- When I am trying to fetch ID via UniProt, I get the following bug:</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"><class 'urllib2.HTTPError'> Exception in Tk callback</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> Function: <function command at 0x10a113848> (type: <type 'function'>)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> Args: ()</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Traceback (innermost last):</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <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> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> return apply(self.func, args)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> getattr(s, buttonFuncName(txt))()</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> self.Apply()</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/chimera/fetch.py", line 210, in Apply</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> func(code, **kw)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/ChimeraExtension.py", line 27, in showUniprotSeq</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> self.module().showUniprotSeq(ident)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 291, in showUniprotSeq</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> acc = mapUniprotNameID(ident)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 61, in mapUniprotNameID</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> response = urllib2.urlopen(request)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 126, in urlopen</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> return _opener.open(url, data, timeout)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 400, in open</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> response = meth(req, response)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 513, in http_response</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> 'http', request, response, code, msg, hdrs)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 438, in error</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> return self._call_chain(*args)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 372, in _call_chain</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> result = func(*args)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"><class 'urllib2.HTTPError'>: HTTP Error 407: Proxy Authentication Required</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">HTTPError: HTTP Error 407: Proxy Authentication Required</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">See reply log for Python traceback.</font> </div> <br> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <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> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Blast web server appear to be down and that is the reply log:</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Traceback from web service request:</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Traceback (most recent call last):</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 31, in __init__</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> self._setup(serviceName, opalURL, sessionData)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 84, in _setup</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> resp = self.appServicePort.getAppMetadata(req)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/AppService_client.py", line 40, in getAppMetadata</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> response = self.binding.Receive(getAppMetadataResponse.typecode)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 531, in Receive</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> self.ReceiveSOAP(**kw)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 416, in ReceiveSOAP</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> 'Response is "%s", not "text/xml"' % self.reply_headers.type)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">TypeError: Response is "text/html", not "text/xml"</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Typically, if you get a TypeError, it's a problem on the remote server</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">and it should be fixed shortly. If you get a different error or</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">get TypeError consistently for more than a day, please report the</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">problem using the Report a Bug... entry in the Help menu. Please</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">include the traceback printed above as part of the problem description.</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Traceback from Blast request:</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Traceback (most recent call last):</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/blastpdb/Parser.py", line 519, in _initBlast</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> self.opal = OpalService(service)</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 43, in __init__</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3"> raise NonChimeraError("Web service appears "</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">NonChimeraError: Web service appears to be down. See Reply Log for more details.</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Typically, if you get a TypeError, it's a problem on the remote server</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">and it should be fixed shortly. If you get a different error or</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">get TypeError consistently for more than a day, please report the</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">problem using the Report a Bug... entry in the Help menu. Please</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">include the traceback printed above as part of the problem description.</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Blast web service appears to be down. See Reply Log for more details.</font> </div> <br> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Any help on this matter would be appreciated</font> </div> <br><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Best wishes</font> </div><div style="margin-top: 0px; margin-bottom: 0px; "> <font face="Monaco" size="3">Mahmoud</font> </div> </div></blockquote></div></div><br><br><div apple-content-edited="true"> </div><br></body></html>