[chimerax-users] ChimeraX and REST service interoperation

[Mungo Carstairs (Staff)]

With ChimeraX version 0.91 (2019-12-11) on MacOS Sierra 10.12.6


________________________________
From: Mungo Carstairs (Staff)
Sent: 16 January 2020 11:02
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: ChimeraX and REST service interoperation

Hi,

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.
Functionality includes loading structures, aligning, colouring, raising labels on structure on mouseover in Jalview, and exchange of residue features/attributes.

I have just one interaction not working yet: highlighting residues in Jalview when a selection is made in ChimeraX.
 - Jalview starts listening for ChimeraX selections with (e.g.)

  info notify start selection jalview prefix SelectionChanged url http://localhost:49981/jalview/chimera1

 - user makes a selection in ChimeraX
 - ChimeraX sends GET?chimerax_notification=SelectionChangedselection+changed
 - Jalview send 'info selection level residue'
 - no response / timeout; ChimeraX log reports 'broken pipe error'

Exception happened during processing of request from ('127.0.0.1', 50714)
Traceback (most recent call last):
File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 316, in _handle_request_noblock
self.process_request(request, client_address)
File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 347, in process_request
self.finish_request(request, client_address)
File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 360, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 720, in __init__
self.handle()
File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 426, in handle
self.handle_one_request()
File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 414, in handle_one_request
method()
File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 97, in do_GET
self._run(args)
File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 174, in _run
self.wfile.write(data)
File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 799, in write
self._sock.sendall(b)
BrokenPipeError: [Errno 32] Broken pipe

NB this is all before a response has been sent to the 'SelectionChanged' message.
Any idea what the problem is here please?
Do I need to reply to the first message before sending another?
The same mechanism does work ok with Chimera.

Thanks,

Mungo

p.s. I noticed the 'listinfo' command (undocumented) seems to behave like 'info'. Should I continue to use 'list' or switch to 'info'?

  *



[University of Dundee shield logo]<http://uod.ac.uk/sig-home>

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org<http://www.jalview.org>

www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
g.m.carstairs at dundee.ac.uk<mailto:g.m.carstairs at dundee.ac.uk>

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