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<p class="MsoNormal"><span lang="EN-US">Hi all,</span></p>
<p class="MsoNormal"><span lang="EN-US">When running pdb2pqr and APBS in chimera, I got some problems.
</span></p>
<p class="MsoListParagraph" style="margin-left:18.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1">
<![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">When running PDB2PQR, it came in the ReplyLog at first with “Model 0 (dimer.pdb) appears to be a protein without secondary structure assignments”. I don’t know what does it mean. Is there anything I should do
before running pdb2pqr?</span></p>
<p class="MsoListParagraph" style="margin-left:18.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1">
<![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">I tried to calculate the electrostatic surface of my protein with APBS, but the execution ran for about half an hour and had no stop. So I cite the traceback as below. I want to know why it happened. Is there’s
anything wrong in the settings? I didn’t change any parameters in the options.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks</span></p>
<p class="MsoNormal"><span lang="EN-US">Yinglu</span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Exception in thread Thread-47:</span></p>
<p class="MsoNormal"><span lang="EN-US">Traceback (most recent call last):</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 801, in __bootstrap_inner</span></p>
<p class="MsoNormal"><span lang="EN-US"> self.run()</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 754, in run</span></p>
<p class="MsoNormal"><span lang="EN-US"> self.__target(*self.__args, **self.__kwargs)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\share\WebServices\opal_client.py", line 205, in _queryStatusInThread</span></p>
<p class="MsoNormal"><span lang="EN-US"> status = self.sudsClient.service.queryStatus(jobID)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 521, in __call__</span></p>
<p class="MsoNormal"><span lang="EN-US"> return client.invoke(args, kwargs)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 581, in invoke</span></p>
<p class="MsoNormal"><span lang="EN-US"> result = self.send(soapenv)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 613, in send</span></p>
<p class="MsoNormal"><span lang="EN-US"> reply = self.options.transport.send(request)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 66, in send</span></p>
<p class="MsoNormal"><span lang="EN-US"> return HttpTransport.send(self, request)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 82, in send</span></p>
<p class="MsoNormal"><span lang="EN-US"> fp = self.u2open(u2request)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 132, in u2open</span></p>
<p class="MsoNormal"><span lang="EN-US"> return url.open(u2request, timeout=tm)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 429, in open</span></p>
<p class="MsoNormal"><span lang="EN-US"> response = self._open(req, data)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 447, in _open</span></p>
<p class="MsoNormal"><span lang="EN-US"> '_open', req)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 407, in _call_chain</span></p>
<p class="MsoNormal"><span lang="EN-US"> result = func(*args)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1228, in http_open</span></p>
<p class="MsoNormal"><span lang="EN-US"> return self.do_open(httplib.HTTPConnection, req)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1201, in do_open</span></p>
<p class="MsoNormal"><span lang="EN-US"> r = h.getresponse(buffering=True)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 1121, in getresponse</span></p>
<p class="MsoNormal"><span lang="EN-US"> response.begin()</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 438, in begin</span></p>
<p class="MsoNormal"><span lang="EN-US"> version, status, reason = self._read_status()</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 394, in _read_status</span></p>
<p class="MsoNormal"><span lang="EN-US"> line = self.fp.readline(_MAXLINE + 1)</span></p>
<p class="MsoNormal"><span lang="EN-US"> File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\socket.py", line 480, in readline</span></p>
<p class="MsoNormal"><span lang="EN-US"> data = self._sock.recv(self._rbufsize)</span></p>
<p class="MsoNormal"><span lang="EN-US">timeout: timed out</span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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