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<p style="margin-top:0;margin-bottom:0">Hi there,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I'm experimenting with Jalview <i>as Javascript</i> talking to Chimera over the latter's REST server.</p>
<p style="margin-top:0;margin-bottom:0">The first few 'list models' commands work fine, but when I send a command 'open cifID:4zhp' I (usually but not always) get an error '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces below as to
the reason for this? Thanks.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Chimera 1.12 (build 41481) on OSX Sierra 10.12.6.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<div>REST server on host 127.0.0.1 port 53135</div>
<div>127.0.0.1 - - [01/Feb/2019 10:06:14] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 -</div>
<div>Traceback (most recent call last):</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread</div>
<div> callable()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run</div>
<div> _run(q, h, args)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 163, in _run</div>
<div> replyobj.error(str(v) + '\n')</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 637, in error</div>
<div> _replyStack[-1].error(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine</div>
<div> self.write(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write</div>
<div> self.f.write(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write</div>
<div> self.flush()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush</div>
<div> self._sock.sendall(view[write_offset:write_offset+buffer_size])</div>
<div>error: [Errno 32] Broken pipe</div>
<div>thread callback:</div>
<div>error: [Errno 32] Broken pipe</div>
<div><br>
</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush</div>
<div> self._sock.sendall(view[write_offset:write_offset+buffer_size])</div>
<div><br>
</div>
<div>See reply log for Python traceback.</div>
<div><br>
</div>
<div><br>
</div>
<div>----------------------------------------</div>
<div>Exception happened during processing of request from ('127.0.0.1', 53326)</div>
<div>Traceback (most recent call last):</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock</div>
<div> self.process_request(request, client_address)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request</div>
<div> self.finish_request(request, client_address)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request</div>
<div> self.RequestHandlerClass(request, client_address, self)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__</div>
<div> self.finish()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish</div>
<div> self.wfile.close()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close</div>
<div> self.flush()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush</div>
<div> self._sock.sendall(view[write_offset:write_offset+buffer_size])</div>
<div>error: [Errno 32] Broken pipe</div>
<div>----------------------------------------</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 -</div>
<div>Traceback (most recent call last):</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread</div>
<div> callable()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run</div>
<div> _run(q, h, args)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 159, in _run</div>
<div> chimera.runCommand(cmd)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2750, in runCommand</div>
<div> makeCommand(*args, **kw)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 69, in makeCommand</div>
<div> f(c, args)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py", line 20, in command</div>
<div> self.module("cmdline").process(cmdName, args)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 12, in process</div>
<div> doList(args)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 543, in doList</div>
<div> doExtensionFunc(func, otherArgs, **kwargs)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 451, in doExtensionFunc</div>
<div> extFunc(*tuple(processedArgs), **kw)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 192, in listr</div>
<div> replyobj.info(info)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 625, in info</div>
<div> _replyStack[-1].info(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 202, in message</div>
<div> self.writeLine(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine</div>
<div> self.write(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write</div>
<div> self.f.write(s)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write</div>
<div> self.flush()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush</div>
<div> self._sock.sendall(view[write_offset:write_offset+buffer_size])</div>
<div>error: [Errno 32] Broken pipe</div>
<div>thread callback:</div>
<div>error: [Errno 32] Broken pipe</div>
<div><br>
</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush</div>
<div> self._sock.sendall(view[write_offset:write_offset+buffer_size])</div>
<div><br>
</div>
<div>See reply log for Python traceback.</div>
<div><br>
</div>
<div><br>
</div>
<div>----------------------------------------</div>
<div>Exception happened during processing of request from ('127.0.0.1', 53329)</div>
<div>Traceback (most recent call last):</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock</div>
<div> self.process_request(request, client_address)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request</div>
<div> self.finish_request(request, client_address)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request</div>
<div> self.RequestHandlerClass(request, client_address, self)</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__</div>
<div> self.finish()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish</div>
<div> self.wfile.close()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close</div>
<div> self.flush()</div>
<div> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush</div>
<div> self._sock.sendall(view[write_offset:write_offset+buffer_size])</div>
<div>error: [Errno 32] Broken pipe</div>
<div>----------------------------------------</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -</div>
<div>127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -</div>
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