[Chimera-users] modeller chimera interface

[Mahmoud Soliman]

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 

************************************
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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