Opened 3 years ago
Closed 3 years ago
#8693 closed defect (can't reproduce)
Crash in event loop
| 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: Windows-10-10.0.19045
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.
Windows fatal exception: code 0xc0000374
Thread 0x00000a70 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000db0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000199c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
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 "C:/Users/shirn/Desktop/45 degree/30%Ethanol/100ns.pdb"
Summary of feedback from opening C:/Users/shirn/Desktop/45
degree/30%Ethanol/100ns.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 100ns.pdb #1
---
Chain | Description
A | No description available
> select #1
5982 atoms, 6054 bonds, 386 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 interModel false relax false distSlop 3.0 angleSlop 30.0
> saltOnly true reveal true retainCurrent true log true
Finding intramodel H-bonds
Using precise constraint criteria
Models used:
1 100ns.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 41 NZ /A GLU 53 OE1 /A LYS 41 1HZ 2.717 1.695
/A ARG 50 NH1 /A ASP 103 OD2 /A ARG 50 2HH1 2.671 1.639
/A ARG 50 NH2 /A ASP 103 OD1 /A ARG 50 2HH2 2.984 1.964
/A ARG 92 NE /A ASP 79 OD1 /A ARG 92 HE 2.875 1.868
/A ARG 92 NH1 /A ASP 79 OD2 /A ARG 92 1HH1 2.765 1.856
/A ARG 95 NH1 /A GLU 68 OE2 /A ARG 95 1HH1 2.726 1.848
/A LYS 108 NZ /A ASP 103 OD1 /A LYS 108 2HZ 2.938 1.910
/A LYS 109 NZ /A ASP 385 OD2 /A LYS 109 1HZ 2.721 1.719
/A ARG 130 NH2 /A GLU 126 OE1 /A ARG 130 1HH2 2.832 1.874
/A LYS 152 NZ /A ASP 149 OD1 /A LYS 152 3HZ 2.767 1.751
/A LYS 177 NZ /A ASP 298 OD2 /A LYS 177 1HZ 2.976 1.986
/A ARG 225 NE /A GLU 217 OE2 /A ARG 225 HE 2.784 1.812
/A ARG 225 NH1 /A GLU 217 OE1 /A ARG 225 1HH1 2.947 1.933
/A LYS 249 NZ /A GLU 235 OE2 /A LYS 249 2HZ 3.068 2.113
/A ARG 283 NE /A ASP 348 OD1 /A ARG 283 HE 2.854 1.925
/A ARG 283 NH2 /A ASP 346 OD1 /A ARG 283 2HH2 2.590 1.591
/A ARG 293 NE /A ASP 289 OD2 /A ARG 293 HE 2.769 1.771
/A ARG 293 NH1 /A ASP 289 OD2 /A ARG 293 1HH1 2.864 1.881
/A ARG 362 NH1 /A ASP 359 OD1 /A ARG 362 1HH1 2.867 1.928
19 hydrogen bonds found
> hbonds sel dashes 6 interModel false relax false distSlop 3.0 angleSlop 30.0
> saltOnly true reveal true retainCurrent true log true
Finding intramodel H-bonds
Using precise constraint criteria
Models used:
1 100ns.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A LYS 41 NZ /A GLU 53 OE1 /A LYS 41 1HZ 2.717 1.695
/A ARG 50 NH1 /A ASP 103 OD2 /A ARG 50 2HH1 2.671 1.639
/A ARG 50 NH2 /A ASP 103 OD1 /A ARG 50 2HH2 2.984 1.964
/A ARG 92 NE /A ASP 79 OD1 /A ARG 92 HE 2.875 1.868
/A ARG 92 NH1 /A ASP 79 OD2 /A ARG 92 1HH1 2.765 1.856
/A ARG 95 NH1 /A GLU 68 OE2 /A ARG 95 1HH1 2.726 1.848
/A LYS 108 NZ /A ASP 103 OD1 /A LYS 108 2HZ 2.938 1.910
/A LYS 109 NZ /A ASP 385 OD2 /A LYS 109 1HZ 2.721 1.719
/A ARG 130 NH2 /A GLU 126 OE1 /A ARG 130 1HH2 2.832 1.874
/A LYS 152 NZ /A ASP 149 OD1 /A LYS 152 3HZ 2.767 1.751
/A LYS 177 NZ /A ASP 298 OD2 /A LYS 177 1HZ 2.976 1.986
/A ARG 225 NE /A GLU 217 OE2 /A ARG 225 HE 2.784 1.812
/A ARG 225 NH1 /A GLU 217 OE1 /A ARG 225 1HH1 2.947 1.933
/A LYS 249 NZ /A GLU 235 OE2 /A LYS 249 2HZ 3.068 2.113
/A ARG 283 NE /A ASP 348 OD1 /A ARG 283 HE 2.854 1.925
/A ARG 283 NH2 /A ASP 346 OD1 /A ARG 283 2HH2 2.590 1.591
/A ARG 293 NE /A ASP 289 OD2 /A ARG 293 HE 2.769 1.771
/A ARG 293 NH1 /A ASP 289 OD2 /A ARG 293 1HH1 2.864 1.881
/A ARG 362 NH1 /A ASP 359 OD1 /A ARG 362 1HH1 2.867 1.928
19 hydrogen bonds found
> close session
> open "C:/Users/shirn/Desktop/25 degree celcius/G210C IN 30%
> methanol/100ns.pdb"
Summary of feedback from opening C:/Users/shirn/Desktop/25 degree
celcius/G210C IN 30% methanol/100ns.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK YASARA *************************************************************
Ignored bad PDB record found on line 2
REMARK YASARA * *
Ignored bad PDB record found on line 3
REMARK YASARA * Y A S A R A *
Ignored bad PDB record found on line 4
REMARK YASARA * *
Ignored bad PDB record found on line 5
REMARK YASARA * Yet Another Scientific Artificial Reality Application *
14 messages similar to the above omitted
Chain information for 100ns.pdb #1
---
Chain | Description
A | No description available
> select #1
5982 atoms, 6054 bonds, 386 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 interModel false relax false distSlop 3.0 angleSlop 30.0
> saltOnly true reveal true retainCurrent true log true
Finding intramodel H-bonds
Using precise constraint criteria
Models used:
1 100ns.pdb
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 92 NE /A ASP 79 OD1 /A ARG 92 HE 2.809 1.823
/A ARG 92 NH1 /A ASP 79 OD2 /A ARG 92 1HH1 2.800 1.864
/A ARG 95 NE /A GLU 68 OE1 /A ARG 95 HE 2.811 1.945
/A ARG 123 NH2 /A GLU 126 OE2 /A ARG 123 1HH2 2.761 1.772
/A LYS 152 NZ /A ASP 149 OD2 /A LYS 152 1HZ 2.814 1.838
/A LYS 177 NZ /A ASP 298 OD2 /A LYS 177 2HZ 2.631 1.613
/A LYS 185 NZ /A GLU 235 OE2 /A LYS 185 2HZ 2.939 1.977
/A ARG 225 NE /A GLU 217 OE2 /A ARG 225 HE 2.788 1.814
/A ARG 225 NH1 /A GLU 217 OE1 /A ARG 225 1HH1 2.837 1.892
/A ARG 283 NH2 /A ASP 359 OD1 /A ARG 283 1HH2 2.780 1.852
/A LYS 324 NZ /A ASP 334 OD1 /A LYS 324 3HZ 2.769 1.813
/A LYS 361 NZ /A ASP 359 OD2 /A LYS 361 3HZ 2.753 1.828
/A ARG 362 NH2 /A ASP 351 OD1 /A ARG 362 2HH2 2.785 1.843
13 hydrogen bonds found
> hbonds sel dashes 6 interModel false relax false distSlop 3.0 angleSlop 30.0
> saltOnly true reveal true retainCurrent true log true
Finding intramodel H-bonds
Using precise constraint criteria
Models used:
1 100ns.pdb
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 92 NE /A ASP 79 OD1 /A ARG 92 HE 2.809 1.823
/A ARG 92 NH1 /A ASP 79 OD2 /A ARG 92 1HH1 2.800 1.864
/A ARG 95 NE /A GLU 68 OE1 /A ARG 95 HE 2.811 1.945
/A ARG 123 NH2 /A GLU 126 OE2 /A ARG 123 1HH2 2.761 1.772
/A LYS 152 NZ /A ASP 149 OD2 /A LYS 152 1HZ 2.814 1.838
/A LYS 177 NZ /A ASP 298 OD2 /A LYS 177 2HZ 2.631 1.613
/A LYS 185 NZ /A GLU 235 OE2 /A LYS 185 2HZ 2.939 1.977
/A ARG 225 NE /A GLU 217 OE2 /A ARG 225 HE 2.788 1.814
/A ARG 225 NH1 /A GLU 217 OE1 /A ARG 225 1HH1 2.837 1.892
/A ARG 283 NH2 /A ASP 359 OD1 /A ARG 283 1HH2 2.780 1.852
/A LYS 324 NZ /A ASP 334 OD1 /A LYS 324 3HZ 2.769 1.813
/A LYS 361 NZ /A ASP 359 OD2 /A LYS 361 3HZ 2.753 1.828
/A ARG 362 NH2 /A ASP 351 OD1 /A ARG 362 2HH2 2.785 1.843
13 hydrogen bonds found
===== 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 526.86
OpenGL renderer: NVIDIA GeForce GTX 1660 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z590 UD
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 17,041,100,800
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700KF @ 3.60GHz
OSLanguage: en-US
Locale: ('en_MY', 'cp1252')
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-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-ItemsInspection: 1.0
ChimeraX-Label: 1.1
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
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
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
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
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
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
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
Send2Trash: 1.8.0
SEQCROW: 1.5.10
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
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.