[Chimera-users] modeller chimera interface

[Mahmoud Soliman]

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

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

>>> 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 -- 
> >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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