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'?


			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 www.compbio.dundee.ac.uk g.m.carstairs@dundee.ac.uk


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