[Chimera-users] Problems when using pdb2pqr and APBS calculation

[Elaine Meng]

Hi Yinglu,
1. "protein without secondary structure assignments" is only an information message that Chimera is calculating helix and sheet for ribbon display since the input file did not say which parts are helix and sheet.  It is not an error and it has nothing to do with PDB2PQR, which is not affected by helix/sheet assignments.

2. the PDB2PQR and APBS tools in Chimera do not run calculations inside of Chimera.  Instead they use outside web services which are provided by a different group (not ours)...  see the help pages for details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>

So it is possible that the web service might be down sometimes, making the calculation "time out" so you don't get any results.  However, I tried them both just now and both services ran successfully.

As mentioned in the APBS help page (link above), make sure that when you run the APBS calculation you use the new model that was generated from PDB2PQR as the input to APBS.  Do not use the original model you opened first, because it does not have charges.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 3, 2020, at 3:33 AM, Chen Yinglu <ylchen94 at outlook.com> wrote:
> 
> Hi all,
> When running pdb2pqr and APBS in chimera, I got some problems.
> 1.     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?
> 2.     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.
>  
> Thanks
> Yinglu
>  
> Exception in thread Thread-47:
> Traceback (most recent call last):
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 801, in __bootstrap_inner
>     self.run()
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\threading.py", line 754, in run
>     self.__target(*self.__args, **self.__kwargs)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\share\WebServices\opal_client.py", line 205, in _queryStatusInThread
>     status = self.sudsClient.service.queryStatus(jobID)
>   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__
>     return client.invoke(args, kwargs)
>   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
>     result = self.send(soapenv)
>   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
>     reply = self.options.transport.send(request)
>   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
>     return HttpTransport.send(self, request)
>   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
>     fp = self.u2open(u2request)
>   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
>     return url.open(u2request, timeout=tm)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 429, in open
>     response = self._open(req, data)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 447, in _open
>     '_open', req)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 407, in _call_chain
>     result = func(*args)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1228, in http_open
>     return self.do_open(httplib.HTTPConnection, req)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\urllib2.py", line 1201, in do_open
>     r = h.getresponse(buffering=True)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 1121, in getresponse
>     response.begin()
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 438, in begin
>     version, status, reason = self._read_status()
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\httplib.py", line 394, in _read_status
>     line = self.fp.readline(_MAXLINE + 1)
>   File "C:\Program Files (x86)\Chimera 1.13.1rc\bin\lib\socket.py", line 480, in readline
>     data = self._sock.recv(self._rbufsize)
> timeout: timed out