Regards all,
i wanted to calculate the calculate the Electrostatics potential associated
with a specific part of the protein and differentiate from the other part
of protein. How can it Possible . is there any method apart from MD to plot
a graph of both to diffrentiate Quantitatively the The Potential
Thanks in advance
Ankush Sharma
On Fri, Jan 13, 2012 at 5:54 PM, <chimera-users-request at 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Jan 2012 19:37:50 +0530
> From: kaushlesh mishra <kaushelesh.mishra at gmail.com>
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] issue in the installation
> Message-ID:
> <CAOMCm+pMFrOJfGnk6v7-+ULpVs8XMJDC+6RW1eqZkZj_k03qGw at 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
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Jan 2012 13:11:59 -0800
> From: Greg Couch <gregc at cgl.ucsf.edu>
> To: Chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Fwd: Re: issue in the installation
> Message-ID: <4F0F4C9F.8050703 at 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 at cgl.ucsf.edu>
> To: kaushlesh mishra <kaushelesh.mishra at 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 at gmail.com>
> To: chimera-users BB <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] going through saved scenes
> Message-ID:
> <CA+WPOVPrOLSe8zKHFG4rz6QGSoqq7AwmdNNoDXOsfR_q33EbQA at 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 at ukzn.ac.za>
> To: <chimera-users at cgl.ucsf.edu>
> Cc: chimera-bugs at cgl.ucsf.edu
> Subject: [Chimera-users] modeller chimera interface
> Message-ID: <4F1054CB02000083000B18A7 at 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
>
> **********************************
>
>
>
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> End of Chimera-users Digest, Vol 105, Issue 14
> **********************************************
>
--
Regards
Ankush Sharma
Doctoral student in Computational Biology
Second University of Naples & Centro Ricerche Oncologiche
di Mercogliano
Email ID : ankush.sharma at unina2.it
Phone: +39 331 831 6370
*P** Please do not print this email unless it is absolutely necessary.
Spread environmental awareness.*
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