Opened 4 years ago

Closed 4 years ago

#5936 closed defect (can't reproduce)

Crash after volume level command

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-89-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fb73effd700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb73f7fe700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb73ffff700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/selectors.py", line 416 in select
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75cff9700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75d7fa700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75dffb700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75e7fc700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75effd700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75f7fe700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb75ffff700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb798ff9700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb7997fa700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb799ffb700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb79a7fc700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb79affd700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb79b7fe700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb79bfff700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb7b8d75700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb7b9576700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007fb881a97740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/cns-obrien/TypeIC_dsDNA_structure/dsDNA_foc_2-coot-0_1-11-22.pdb

Chain information for dsDNA_foc_2-coot-0_1-11-22.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C E F G H | No description available  
D | No description available  
I | No description available  
J K | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> hide atoms

> show cartoons

> set bgColor white

> open /home/cns-
> obrien/TypeIC_dsDNA_structure/cryosparc_P16_J118_004_volume_map_sharp.mrc

Opened cryosparc_P16_J118_004_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 1.1, shown at level 0.567, step 2, values float32  

> close #2

> open /home/cns-
> obrien/TypeIC_dsDNA_structure/cryosparc_P16_J118_004_volume_map.mrc

Opened cryosparc_P16_J118_004_volume_map.mrc as #2, grid size 420,420,420,
pixel 1.1, shown at level 0.0821, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.283

> volume #2 level 1.059

> close #2

> open /home/cns-
> obrien/TypeIC_dsDNA_structure/cryosparc_P16_J118_004_volume_map.mrc

Opened cryosparc_P16_J118_004_volume_map.mrc as #2, grid size 420,420,420,
pixel 1.1, shown at level 0.0821, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.4416

> volume #2 level 0.9665


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 460.91.03
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           78Gi        32Gi       5.5Gi       129Mi        40Gi        44Gi
	Swap:          63Gi        16Gi        47Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)	
	Subsystem: PNY GP104 [GeForce GTX 1080] [196e:119e]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash after volume level command

comment:2 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Crash appears to be in Qt event loop. But actually there are about 15 threads, all the others being in multiprocessing thread workers. The Python faulthandler tracebacks don't seem to indicate which thread crashed. So it is not clear if the thread in the event loop crashed. But there is no other thread in ChimeraX Python code.

Possibly it is a graphics driver crash. But the graphics gtx 1080 (8 Gb) should have plenty of memory and map being displayed was not particularly large 420 by 420 by 420. Oddly the user opened that map, adjust the level, closed it, then opened it again and adjusted the level.

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