Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#4587 closed defect (fixed)

Python shell: ERROR:tornado.general:Uncaught exception in zmqstream callback

Reported by: Tristan Croll Owned by: pett
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
This started happening again while I was messing around in the shell... once it's happened, shell interaction is pretty much broken for the remainder of the session. Not sure what triggered it... the only thing of note that I can think of is that it started soon after I came back after leaving it alone for an hour-long meeting. Seems pretty clearly an iPython bug.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/mystery_helix/class1b_26A.mrc
> format mrc

Opened class1b_26A.mrc as #1, grid size 400,400,400, pixel 0.999, shown at
level 0.0224, step 2, values float32  
ERROR:tornado.general:Uncaught exception in ZMQStream callback  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event  
event_f()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 214, in <lambda>  
self.schedule(lambda : self._really_send(*args, **kwargs))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 222, in _really_send  
self.socket.send_multipart(msg, *args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/socket.py", line 62, in send_multipart  
self.message_sent += 1  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 604, in __set__  
self.set(obj, value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 593, in set  
obj._notify_trait(self.name, old_value, new_value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait  
self.notify_change(Bunch(  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1227, in notify_change  
return self._notify_observers(change)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers  
c(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch  
ident, msg = self.session.recv(self.iopub_socket, copy=False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/jupyter_client/session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 246, in __getattr__  
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,  
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket  
ERROR:tornado.general:Uncaught exception in zmqstream callback  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events  
self._handle_recv()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv  
self._run_callback(callback, msg)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event  
event_f()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 214, in <lambda>  
self.schedule(lambda : self._really_send(*args, **kwargs))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 222, in _really_send  
self.socket.send_multipart(msg, *args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/socket.py", line 62, in send_multipart  
self.message_sent += 1  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 604, in __set__  
self.set(obj, value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 593, in set  
obj._notify_trait(self.name, old_value, new_value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait  
self.notify_change(Bunch(  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1227, in notify_change  
return self._notify_observers(change)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers  
c(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch  
ident, msg = self.session.recv(self.iopub_socket, copy=False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/jupyter_client/session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 246, in __getattr__  
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,  
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket  
ERROR:asyncio:Exception in callback BaseAsyncIOLoop._handle_events(122, 1)  
handle: <Handle BaseAsyncIOLoop._handle_events(122, 1)>  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/asyncio/events.py", line 81, in
_run  
self._context.run(self._callback, *self._args)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/tornado/platform/asyncio.py", line 189, in _handle_events  
handler_func(fileobj, events)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events  
self._handle_recv()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv  
self._run_callback(callback, msg)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event  
event_f()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 214, in <lambda>  
self.schedule(lambda : self._really_send(*args, **kwargs))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 222, in _really_send  
self.socket.send_multipart(msg, *args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/socket.py", line 62, in send_multipart  
self.message_sent += 1  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 604, in __set__  
self.set(obj, value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 593, in set  
obj._notify_trait(self.name, old_value, new_value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait  
self.notify_change(Bunch(  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1227, in notify_change  
return self._notify_observers(change)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers  
c(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch  
ident, msg = self.session.recv(self.iopub_socket, copy=False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/jupyter_client/session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 246, in __getattr__  
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,  
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket  




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        9.0G         38G        388M         14G         52G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.12
    ChimeraX-AtomicLibrary: 3.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103310726
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-DevelExtras: 0.4.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.dev38
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.2
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (6)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → General Controls
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Python shell: ERROR:tornado.general:Uncaught exception in zmqstream callback

comment:2 by pett, 4 years ago

Googling around seems to indicate that this is likely a problem with ipykernel. We ship ipykernel 5.3.4 and the current version is 5.5.4, so we should definitely upgrade after we make the 1.2.x release.

comment:3 by pett, 4 years ago

Tomorrow's daily build will have the latest qtconsole and friends. We'll see what kind of chaos ensues.

comment:4 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

The updated versions seem functional under extremely limited testing. Since this bug is not easily reproducible, we will just have to see if it pops up again to not.

in reply to:  5 ; comment:5 by Tristan Croll, 4 years ago 

Still happening in daily build 1.3.dev202106051310 (2021-06-05 13:10:38 UTC), I'm afraid.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 17 May 2021 23:44
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4587: Python shell: ERROR:tornado.general:Uncaught exception in zmqstream callback

#4587: Python shell: ERROR:tornado.general:Uncaught exception in zmqstream
callback
---------------------------------------+----------------------------
          Reporter:  Tristan Croll     |      Owner:  Eric Pettersen
              Type:  defect            |     Status:  closed
          Priority:  normal            |  Milestone:
         Component:  General Controls  |    Version:
        Resolution:  fixed             |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 The updated versions seem functional under extremely limited testing.
 Since this bug is not easily reproducible, we will just have to see if it
 pops up again to not.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4587#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:6 by pett, 4 years ago

Sorry to hear that. ipykernel is now version 5.5.5. Given our inability to reliably reproduce this problem, I don't know that there's much we can do about it except hope that future updates quash it.

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