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Hi,</div>
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<br>
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With your helpful hints, I have a version of Jalview interacting with ChimeraX in the same way it can already with Chimera, over the REST interface.</div>
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Functionality includes loading structures, aligning, colouring, raising labels on structure on mouseover in Jalview, and exchange of residue features/attributes.</div>
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<br>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I have just one interaction not working yet: highlighting residues in Jalview when a selection is made in ChimeraX.</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"> - Jalview starts listening for ChimeraX selections with (e.g.)</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
<p style="margin: 0px; font: 12px Menlo; margin: 0px"> info notify start selection jalview prefix SelectionChanged url
<a href="http://localhost:49981/jalview/chimera1">http://localhost:49981/jalview/chimera1</a></p>
<p style="margin: 0px; font: 12px Menlo; margin: 0px"></p>
</span></div>
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<span style="margin: 0px"> - user makes a selection in ChimeraX</span></div>
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<span style="margin: 0px"> - ChimeraX sends GET?chimerax_notification=</span><span style="font-family: Menlo; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal;">SelectionChangedselection+changed</span></div>
<div style="margin: 0px; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif">
<span style="margin: 0px"> - Jalview send 'i</span><span style="font-family: Menlo; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal;">nfo selection level residue'</span></div>
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<span style="margin: 0px"> - no response / timeout; ChimeraX log reports 'broken pipe error'</span></div>
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<span style="margin: 0px"><br>
</span></div>
<div style="margin: 0px; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif">
<span style="margin: 0px"><span>Exception happened during processing of request from ('127.0.0.1', 50714)<br>
</span>
<div>Traceback (most recent call last):<br>
</div>
<div>File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 316, in _handle_request_noblock<br>
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<div>self.process_request(request, client_address)<br>
</div>
<div>File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 347, in process_request<br>
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<div>self.finish_request(request, client_address)<br>
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<div>File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 360, in finish_request<br>
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<div>self.RequestHandlerClass(request, client_address, self)<br>
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<div>File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 720, in __init__<br>
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<div>self.handle()<br>
</div>
<div>File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 426, in handle<br>
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<div>self.handle_one_request()<br>
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<div>File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 414, in handle_one_request<br>
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<div>method()<br>
</div>
<div>File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 97, in do_GET<br>
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<div>self._run(args)<br>
</div>
<div>File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 174, in _run<br>
</div>
<div>self.wfile.write(data)<br>
</div>
<div>File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 799, in write<br>
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<div>self._sock.sendall(b)<br>
</div>
<span>BrokenPipeError: [Errno 32] Broken pipe</span><br>
</span></div>
<br>
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NB this is all before a response has been sent to the 'SelectionChanged' message.</div>
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Any idea what the problem is here please?</div>
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Do I need to reply to the first message before sending another?</div>
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The same mechanism does work ok with Chimera.</div>
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Thanks,</div>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Mungo</div>
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p.s. <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I noticed the 'listinfo' <span style="font-family: Calibri, Arial, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">command (</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; background-color: rgb(255, 255, 255); display: inline !important">undocumented)</span>
seems to behave like 'info'. Should I continue to use 'list' or switch to 'info'?</span>
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<strong style="letter-spacing:1.2px; font-size:14px">Mungo Carstairs</strong><br>
Jalview Computational Scientist</p>
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The Barton Group<br>
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