Opened 6 months ago
Closed 6 months ago
#17539 closed defect (can't reproduce)
Crash in event loop under remote control
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-212-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00007f09937fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select
File "/usr/lib/ucsf-chimerax/lib/python3.9/socketserver.py", line 232 in serve_forever
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/rest_server/server.py", line 79 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/tasks.py", line 213 in _run_thread
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007f0a2129d740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
> remotecontrol rest start port 54121
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
REST server started on host 127.0.0.1 port 54121
Visit http://127.0.0.1:54121/cmdline.html for CLI interface
> open "/mnt/6DD846FD42AEAF77/BkmB1 refinment/BKmB1/maps and model
> 04112025/outputcombinedJ323J393J394/outputcombinedJ323J393J394_raw.cif"
> format mmcif
Summary of feedback from opening /mnt/6DD846FD42AEAF77/BkmB1
refinment/BKmB1/maps and model
04112025/outputcombinedJ323J393J394/outputcombinedJ323J393J394_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for outputcombinedJ323J393J394_raw.cif #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 AB | No description available
8 | No description available
9 | No description available
A | No description available
AA | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> style stick
Changed 35422 atom styles
> show cartoons
> hide atoms
> select /AB:1-2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /7:1-2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /7:1-2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /8:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /8:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /9:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /9:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /9:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /AA:1-2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /AC:1-2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /B:1-153
1210 atoms, 1233 bonds, 153 residues, 1 model selected
> select /C:1-152
1203 atoms, 1226 bonds, 152 residues, 1 model selected
> select /D:1-152
1202 atoms, 1225 bonds, 152 residues, 1 model selected
> select /E:1-32
250 atoms, 254 bonds, 32 residues, 1 model selected
> select /F:1-522
4177 atoms, 4274 bonds, 522 residues, 1 model selected
> select /G:1-191
1483 atoms, 1511 bonds, 191 residues, 1 model selected
> select /H:1-485
3884 atoms, 3975 bonds, 485 residues, 1 model selected
> select /I:1-129
1023 atoms, 1045 bonds, 129 residues, 1 model selected
> select /J:1-427
3425 atoms, 3505 bonds, 427 residues, 1 model selected
> select /K:1-455
3671 atoms, 3758 bonds, 455 residues, 1 model selected
> select /J:1-427
3425 atoms, 3505 bonds, 427 residues, 1 model selected
> select /L:1-194
1500 atoms, 1528 bonds, 194 residues, 1 model selected
> select /M:1-195
1508 atoms, 1536 bonds, 195 residues, 1 model selected
> select /N:1-194
1496 atoms, 1524 bonds, 194 residues, 1 model selected
> select /O:1-100
814 atoms, 831 bonds, 100 residues, 1 model selected
> select /P:1-24
190 atoms, 190 bonds, 24 residues, 1 model selected
> select /Q:1-42
340 atoms, 346 bonds, 42 residues, 1 model selected
> select /R:1-51
417 atoms, 431 bonds, 51 residues, 1 model selected
> select /S:1-53
441 atoms, 457 bonds, 53 residues, 1 model selected
> select /R:1-51
417 atoms, 431 bonds, 51 residues, 1 model selected
> select /S:1-53
441 atoms, 457 bonds, 53 residues, 1 model selected
> select /T:1-53
435 atoms, 450 bonds, 53 residues, 1 model selected
> select /U:1-46
340 atoms, 344 bonds, 46 residues, 1 model selected
> select /V:1-49
373 atoms, 377 bonds, 49 residues, 1 model selected
> select /W:1-47
347 atoms, 351 bonds, 47 residues, 1 model selected
> select /X:1-52
429 atoms, 444 bonds, 52 residues, 1 model selected
> select /Y:1-45
340 atoms, 344 bonds, 45 residues, 1 model selected
> select /Z:1-51
404 atoms, 413 bonds, 51 residues, 1 model selected
> select /a:1-62
489 atoms, 499 bonds, 62 residues, 1 model selected
> select /b:1-60
466 atoms, 474 bonds, 60 residues, 1 model selected
Falling back to using screens root_visual.
> select /b:1-60
466 atoms, 474 bonds, 60 residues, 1 model selected
> select /c:1-58
457 atoms, 467 bonds, 58 residues, 1 model selected
> select /d:1-22
160 atoms, 161 bonds, 22 residues, 1 model selected
> select /e:1-15
116 atoms, 119 bonds, 15 residues, 1 model selected
> select /f:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> select /g:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> select /h:1-3
25 atoms, 24 bonds, 3 residues, 1 model selected
> select /i:1-3
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /j:1-3
20 atoms, 20 bonds, 3 residues, 1 model selected
> select /k:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> combine #outputcombinedJ323J393J394 chain #X#F#D#N
Expected a keyword
> combine /X /F /D /N
> hide #1 models
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/mnt/6DD846FD42AEAF77/BkmB1
> refinment/BKmB1/RebuildModel_59/refined_composite.pdb"
Summary of feedback from opening /mnt/6DD846FD42AEAF77/BkmB1
refinment/BKmB1/RebuildModel_59/refined_composite.pdb
---
warning | Ignored bad PDB record found on line 35597
Chain information for refined_composite.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 AB | No description available
8 | No description available
9 | No description available
A a | No description available
AA | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
OpenGL version: 3.3.0 NVIDIA 470.256.02
OpenGL renderer: Quadro K5200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:0
Manufacturer: LENOVO
Model: 30B9001PUS
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
Cache Size: 30720 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 39Gi 18Gi 149Mi 4.7Gi 22Gi
Swap: 99Gi 21Gi 78Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK110GL [Quadro K5200] [10de:103c] (rev a1)
Subsystem: NVIDIA Corporation GK110GL [Quadro K5200] [10de:1095]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop under remote control |
comment:2 by , 6 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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