Opened 6 months ago

Closed 6 months ago

Last modified 6 months ago

#17525 closed defect (can't reproduce)

Crash in Qt event loop after opening EMDB entry

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202502131209 (2025-02-13 12:09:28 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x000075dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 320 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 765 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 768 in get
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1678 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\core\tasks.py", line 300 in _run_function
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004178 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004628 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000018ec (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000078bc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007620 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002434 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007e74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003d84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002eb4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002198 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007d3c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006534 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002e98 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000018e4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000013e4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003cc8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004f74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001d90 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005678 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a80 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000080bc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00007db8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\util\connection.py", line 73 in create_connection
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\connection.py", line 198 in _new_conn
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\connection.py", line 276 in connect
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 979 in send
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1041 in _send_output
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1281 in endheaders
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\connection.py", line 445 in request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\connectionpool.py", line 493 in _make_request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\connectionpool.py", line 787 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\poolmanager.py", line 443 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\_request_methods.py", line 182 in request_encode_url
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\urllib3\_request_methods.py", line 135 in request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\cxservices\rest.py", line 206 in request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\cxservices\rest.py", line 228 in GET
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\cxservices\api_client.py", line 341 in request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\cxservices\api_client.py", line 151 in __call_api
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\multiprocessing\pool.py", line 125 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002f64 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\ssl.py", line 1346 in do_handshake
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\ssl.py", line 1075 in _create
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\ssl.py", line 517 in wrap_socket
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1458 in connect
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 979 in send
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1041 in _send_output
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1281 in endheaders
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1332 in _send_request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\http\client.py", line 1286 in request
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\urllib\request.py", line 1348 in do_open
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\urllib\request.py", line 1391 in https_open
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\urllib\request.py", line 496 in _call_chain
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\urllib\request.py", line 536 in _open
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\urllib\request.py", line 519 in open
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\urllib\request.py", line 216 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006ed0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x0000530c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202502131209\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.dev202502131209 (2025-02-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> open 25428 fromDatabase emdb


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502131209 (2025-02-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 561.03
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: XPS 15 9520
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,834,945,024
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.0.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202502131209
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.7
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.12
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.17.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.2.2
    lz4: 4.4.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.2.1
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.1.3
    sphinx-autodoc-typehints: 3.0.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (4)

comment:1 by Eric Pettersen, 6 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash opening EMDB entry

comment:2 by Tom Goddard, 6 months ago

Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash opening EMDB entry → Crash in Qt event loop after opening EMDB entry

No indication of why it crashed.

comment:3 by Eric Pettersen, 6 months ago

I think this happened while opening the map file, since the map information had not made it into the log -- perhaps after the file itself had been opened but before the log's rate-limiting timer had gone off to actually put the info in the log.

comment:4 by Tom Goddard, 6 months ago

The Python traceback shows it is in the event loop so it definitely has finished fetching the file and opening it. You may be right that the map info was not logged yet because of the rate limiting timer. But it is in the event loop and so either the user did some clicking or dragging with the user interface and hit a Qt bug, or Qt had some corrupted state from previous operations, or it has something to do with the Toolshed reload thread -- we see so many crash reports where that thread is present, it could be that code uses Qt which would have a good chance of crashing. I've asked Greg to look into that to no avail.

Note: See TracTickets for help on using tickets.