Regards all,<br><br>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<br>
<br>Thanks in advance <br>Ankush Sharma<br><br><div class="gmail_quote">On Fri, Jan 13, 2012 at 5:54 PM, <span dir="ltr"><<a href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. issue in the installation (kaushlesh mishra)<br>
2. Fwd: Re: issue in the installation (Greg Couch)<br>
3. going through saved scenes (Bala subramanian)<br>
4. modeller chimera interface (Mahmoud Soliman)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 12 Jan 2012 19:37:50 +0530<br>
From: kaushlesh mishra <<a href="mailto:kaushelesh.mishra@gmail.com">kaushelesh.mishra@gmail.com</a>><br>
To: "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
Subject: [Chimera-users] issue in the installation<br>
Message-ID:<br>
<<a href="mailto:CAOMCm%2BpMFrOJfGnk6v7-%2BULpVs8XMJDC%2B6RW1eqZkZj_k03qGw@mail.gmail.com">CAOMCm+pMFrOJfGnk6v7-+ULpVs8XMJDC+6RW1eqZkZj_k03qGw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi,<br>
I?ve tried hardly to intall the last Chimera version for Windows (chimera<br>
1.5.3), but at the phyton execution time, I have this message: "Unable<br>
to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe<br>
Create process failed; code 14001"<br>
Ifound this error and it possible solution in internet, without any<br>
success. Could you help me?<br>
<br>
--<br>
Regards<br>
<br>
Kaushlesh Mishra<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 12 Jan 2012 13:11:59 -0800<br>
From: Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>><br>
To: <a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
Subject: [Chimera-users] Fwd: Re: issue in the installation<br>
Message-ID: <<a href="mailto:4F0F4C9F.8050703@cgl.ucsf.edu">4F0F4C9F.8050703@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br>
<br>
FYI<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] issue in the installation<br>
Date: Thu, 12 Jan 2012 12:58:39 -0800<br>
From: Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>><br>
To: kaushlesh mishra <<a href="mailto:kaushelesh.mishra@gmail.com">kaushelesh.mishra@gmail.com</a>><br>
<br>
<br>
<br>
On 01/12/2012 06:07 AM, kaushlesh mishra wrote:<br>
> Hi, I?ve tried hardly to intall the last Chimera version for Windows<br>
> (chimera 1.5.3), but at the phyton execution time, I have this<br>
> message: "Unable to execute file: C\Archivos de programa\Chimera<br>
> 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this<br>
> error and it possible solution in internet, without any success. Could<br>
> you help me?<br>
<br>
Hello,<br>
<br>
The last time I saw this, it was because the computer didn't have the<br>
Microsoft Visual Studio 2008 runtime installed. Please try installing<br>
the runtime from Microsoft at<br>
<a href="http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en" target="_blank">http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en</a><br>
<<a href="http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en" target="_blank">http://www.microsoft.com/downloads/en/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en</a>><br>
and then see if the chimera installation works.<br>
<br>
HTH,<br>
<br>
Greg<br>
<br>
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<br>
Message: 3<br>
Date: Fri, 13 Jan 2012 16:04:46 +0100<br>
From: Bala subramanian <<a href="mailto:bala.biophysics@gmail.com">bala.biophysics@gmail.com</a>><br>
To: chimera-users BB <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
Subject: [Chimera-users] going through saved scenes<br>
Message-ID:<br>
<<a href="mailto:CA%2BWPOVPrOLSe8zKHFG4rz6QGSoqq7AwmdNNoDXOsfR_q33EbQA@mail.gmail.com">CA+WPOVPrOLSe8zKHFG4rz6QGSoqq7AwmdNNoDXOsfR_q33EbQA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Friends,<br>
I save several scenes with 'scene name 01, scene name 02' etc. I wanted to<br>
go through the saved scenes one by one and record a movie. But i dnt know<br>
how to do it. Please enlighten me on this.<br>
<br>
I tried fly command to go through the scenes in succession with 'fly 01 02<br>
03' but it throws me the following error<br>
<br>
<br>
IndexError: list index out of range<br>
<br>
File "/home/cbala/.local/UCSF-Chimera-2012-01-12/share/Fly/fly.py", line<br>
73, in view_parameters<br>
for mid,xf in positions[pnames[0]][5].items():<br>
<br>
Thanks,<br>
--<br>
C. Balasubramanian<br>
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<br>
Message: 4<br>
Date: Fri, 13 Jan 2012 15:59:07 +0200<br>
From: "Mahmoud Soliman" <<a href="mailto:soliman@ukzn.ac.za">soliman@ukzn.ac.za</a>><br>
To: <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
Cc: <a href="mailto:chimera-bugs@cgl.ucsf.edu">chimera-bugs@cgl.ucsf.edu</a><br>
Subject: [Chimera-users] modeller chimera interface<br>
Message-ID: <<a href="mailto:4F1054CB02000083000B18A7@dbnsmtp.ukzn.ac.za">4F1054CB02000083000B18A7@dbnsmtp.ukzn.ac.za</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
<br>
Dear support,<br>
<br>
I am actually using Chimera as a GUI for modeller and I came across this nice video tutorial (<a href="http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/" target="_blank">http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/</a>) but I keep getting some bugs at different stages as follow:<br>
<br>
1- When I am trying to fetch ID via UniProt, I get the following bug:<br>
<br>
<class 'urllib2.HTTPError'> Exception in Tk callback<br>
Function: <function command at 0x10a113848> (type: <type 'function'>)<br>
Args: ()<br>
Traceback (innermost last):<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__<br>
return apply(self.func, args)<br>
File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 449, in command<br>
getattr(s, buttonFuncName(txt))()<br>
File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 700, in OK<br>
self.Apply()<br>
File "/Applications/Chimera.app/Contents/Resources/share/chimera/fetch.py", line 210, in Apply<br>
func(code, **kw)<br>
File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/ChimeraExtension.py", line 27, in showUniprotSeq<br>
self.module().showUniprotSeq(ident)<br>
File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 291, in showUniprotSeq<br>
acc = mapUniprotNameID(ident)<br>
File "/Applications/Chimera.app/Contents/Resources/share/SeqAnnotations/__init__.py", line 61, in mapUniprotNameID<br>
response = urllib2.urlopen(request)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 126, in urlopen<br>
return _opener.open(url, data, timeout)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 400, in open<br>
response = meth(req, response)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 513, in http_response<br>
'http', request, response, code, msg, hdrs)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 438, in error<br>
return self._call_chain(*args)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 372, in _call_chain<br>
result = func(*args)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default<br>
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)<br>
<class 'urllib2.HTTPError'>: HTTP Error 407: Proxy Authentication Required<br>
<br>
HTTPError: HTTP Error 407: Proxy Authentication Required<br>
<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 521, in http_error_default<br>
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)<br>
<br>
See reply log for Python traceback.<br>
<br>
<br>
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:<br>
<br>
Blast web server appear to be down and that is the reply log:<br>
Traceback from web service request:<br>
Traceback (most recent call last):<br>
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 31, in __init__<br>
self._setup(serviceName, opalURL, sessionData)<br>
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 84, in _setup<br>
resp = self.appServicePort.getAppMetadata(req)<br>
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/AppService_client.py", line 40, in getAppMetadata<br>
response = self.binding.Receive(getAppMetadataResponse.typecode)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 531, in Receive<br>
self.ReceiveSOAP(**kw)<br>
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/ZSI/client.py", line 416, in ReceiveSOAP<br>
'Response is "%s", not "text/xml"' % self.reply_headers.type)<br>
TypeError: Response is "text/html", not "text/xml"<br>
<br>
Typically, if you get a TypeError, it's a problem on the remote server<br>
and it should be fixed shortly. If you get a different error or<br>
get TypeError consistently for more than a day, please report the<br>
problem using the Report a Bug... entry in the Help menu. Please<br>
include the traceback printed above as part of the problem description.<br>
Traceback from Blast request:<br>
Traceback (most recent call last):<br>
File "/Applications/Chimera.app/Contents/Resources/share/blastpdb/Parser.py", line 519, in _initBlast<br>
self.opal = OpalService(service)<br>
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 43, in __init__<br>
raise NonChimeraError("Web service appears "<br>
NonChimeraError: Web service appears to be down. See Reply Log for more details.<br>
<br>
Typically, if you get a TypeError, it's a problem on the remote server<br>
and it should be fixed shortly. If you get a different error or<br>
get TypeError consistently for more than a day, please report the<br>
problem using the Report a Bug... entry in the Help menu. Please<br>
include the traceback printed above as part of the problem description.<br>
Blast web service appears to be down. See Reply Log for more details.<br>
<br>
<br>
Any help on this matter would be appreciated<br>
<br>
Best wishes<br>
Mahmoud<br>
<br>
************************************<br>
Mahmoud E. Soliman<br>
B.Pharm, M.Pharm, MPhil/PhD (Bath, UK)<br>
Senior Lecturer - Pharmaceutical Chemistry<br>
School of Pharmacy and Pharmacology<br>
Faculty of Health Science<br>
University of KwaZulu Natal<br>
Westville Campus<br>
Private Bag X54001<br>
Durban<br>
4000<br>
South Africa<br>
Tel. <a href="tel:0312607413" value="+390312607413">0312607413</a><br>
***********************************<br>
Mahmoud E. Soliman (PhD)<br>
Computational Chemistry & Modeling<br>
Department of Chemistry<br>
University of Bath<br>
Bath<br>
BA2 7AY<br>
United Kingdom<br>
<a href="http://people.bath.ac.uk/mess20/" target="_blank">http://people.bath.ac.uk/mess20/</a><br>
<a href="http://www.bath.ac.uk/person/812559" target="_blank">http://www.bath.ac.uk/person/812559</a><br>
<br>
**********************************<br>
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End of Chimera-users Digest, Vol 105, Issue 14<br>
**********************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Regards<br>Ankush Sharma<div>Doctoral student in Computational Biology</div><div>Second University of Naples & Centro Ricerche Oncologiche<br>di Mercogliano</div><div>
Email ID : <a href="mailto:ankush.sharma@unina2.it" target="_blank">ankush.sharma@unina2.it</a><br>Phone: +39 331 831 6370<br><span style="font-family:'Kristen ITC';color:rgb(0,38,17);font-size:9pt"><br><br></span><span style="font-family:'Kristen ITC';color:rgb(0,38,17);font-size:9pt"></span><br>
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