On Fri, Jan 13, 2012 at 5:54 PM, <chimera-users-request@cgl.ucsf.edu> wrote:

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Today's Topics:

1. issue in the installation (kaushlesh mishra)
2. Fwd: Re: issue in the installation (Greg Couch)
3. going through saved scenes (Bala subramanian)
4. modeller chimera interface (Mahmoud Soliman)

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Message: 1
Date: Thu, 12 Jan 2012 19:37:50 +0530
From: kaushlesh mishra <kaushelesh.mishra@gmail.com>
To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu>
Subject: [Chimera-users] issue in the installation
Message-ID:
<CAOMCm+pMFrOJfGnk6v7-+ULpVs8XMJDC+6RW1eqZkZj_k03qGw@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,
I?ve tried hardly to intall the last Chimera version for Windows (chimera
1.5.3), but at the phyton execution time, I have this message: "Unable
to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe
Create process failed; code 14001"
Ifound this error and it possible solution in internet, without any
success. Could you help me?

--
Regards

Kaushlesh Mishra

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Message: 2
Date: Thu, 12 Jan 2012 13:11:59 -0800
From: Greg Couch <gregc@cgl.ucsf.edu>
To: Chimera-users@cgl.ucsf.edu
Subject: [Chimera-users] Fwd: Re: issue in the installation
Message-ID: <4F0F4C9F.8050703@cgl.ucsf.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

FYI

-------- Original Message --------
Subject: Re: [Chimera-users] issue in the installation
Date: Thu, 12 Jan 2012 12:58:39 -0800
From: Greg Couch <gregc@cgl.ucsf.edu>
To: kaushlesh mishra <kaushelesh.mishra@gmail.com>

On 01/12/2012 06:07 AM, kaushlesh mishra wrote:
> Hi, I?ve tried hardly to intall the last Chimera version for Windows
> (chimera 1.5.3), but at the phyton execution time, I have this
> message: "Unable to execute file: C\Archivos de programa\Chimera
> 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this
> error and it possible solution in internet, without any success. Could
> you help me?

Hello,

The last time I saw this, it was because the computer didn't have the
Microsoft Visual Studio 2008 runtime installed. Please try installing
the runtime from Microsoft at
http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en
<http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en>
and then see if the chimera installation works.

HTH,

Greg

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Message: 3
Date: Fri, 13 Jan 2012 16:04:46 +0100
From: Bala subramanian <bala.biophysics@gmail.com>
To: chimera-users BB <chimera-users@cgl.ucsf.edu>
Subject: [Chimera-users] going through saved scenes
Message-ID:
<CA+WPOVPrOLSe8zKHFG4rz6QGSoqq7AwmdNNoDXOsfR_q33EbQA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Friends,
I save several scenes with 'scene name 01, scene name 02' etc. I wanted to
go through the saved scenes one by one and record a movie. But i dnt know
how to do it. Please enlighten me on this.

I tried fly command to go through the scenes in succession with 'fly 01 02
03' but it throws me the following error

IndexError: list index out of range

File "/home/cbala/.local/UCSF-Chimera-2012-01-12/share/Fly/fly.py", line
73, in view_parameters
for mid,xf in positions[pnames[0]][5].items():

Thanks,
--
C. Balasubramanian
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Message: 4
Date: Fri, 13 Jan 2012 15:59:07 +0200
From: "Mahmoud Soliman" <soliman@ukzn.ac.za>
To: <chimera-users@cgl.ucsf.edu>
Cc: chimera-bugs@cgl.ucsf.edu
Subject: [Chimera-users] modeller chimera interface
Message-ID: <4F1054CB02000083000B18A7@dbnsmtp.ukzn.ac.za>
Content-Type: text/plain; charset="us-ascii"

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

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

Please find our Email Disclaimer here: http://www.ukzn.ac.za/disclaimer/
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