![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16985 closed defect (can't reproduce)
Crash processing timer
| 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: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 73000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 1453,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-02-28 16:06:28.7158 +0800",
"codeSigningMonitor" : 1,
"incident" : "391771DC-8768-4F9F-8F7F-507E057D83B4",
"pid" : 36858,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-27 22:06:32.3421 +0800",
"procStartAbsTime" : 1012937844228,
"procExitAbsTime" : 1769905502163,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FE9CD0D9-0778-5FF3-A549-C97ED3F6241C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4831F70F-7116-9D1A-7512-5ABDFD405025",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "689ED439-C619-40AA-B34E-FCFCA531F02C",
"wakeTime" : 21231,
"sleepWakeUUID" : "D6B190AE-B3D1-4C85-962D-E04F9D406740",
"sip" : "enabled",
"vmRegionInfo" : "0x94 is not in any region. Bytes before following region: 4297314156\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10023d000-10023e000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000094","rawCodes":[1,148],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000094"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":36858},
"vmregioninfo" : "0x94 is not in any region. Bytes before following region: 4297314156\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10023d000-10023e000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
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}
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/zhengtao/Downloads/weev/pcdh10/RealSpaceRefine_7/ev71-pcdh10-remumber.pdb
Summary of feedback from opening
/Users/zhengtao/Downloads/weev/pcdh10/RealSpaceRefine_7/ev71-pcdh10-remumber.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 19
ASP A 22 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO A 39 SER A 41 5
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 63 CYS A 67 1
5
Start residue of secondary structure not found: HELIX 4 4 ILE C 19 ASP C 22 1
4
Start residue of secondary structure not found: HELIX 5 5 ILE C 27 LYS C 29 5
3
48 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 U 4 GLY D 98 LYS D 100 0
Start residue of secondary structure not found: SHEET 2 U 4 PHE D 103 ALA D
106 -1 N LEU D 105 O GLY D 98
Start residue of secondary structure not found: SHEET 3 U 4 ILE D 46 VAL D 50
-1 N ILE D 48 O LEU D 104
Start residue of secondary structure not found: SHEET 4 U 4 ILE D 34 TRP D 38
-1 N TRP D 38 O ARG D 47
Start residue of secondary structure not found: SHEET 1 V 3 ILE D 86 SER D 89
0
Start residue of secondary structure not found: SHEET 2 V 3 SER D 113 THR D
119 -1 N SER D 117 O ALA D 87
1 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 W 2 LYS D 151 TYR D 158
0
Start residue of secondary structure not found: SHEET 2 W 2 LEU D 264 VAL D
271 -1 N VAL D 271 O LYS D 151
Start residue of secondary structure not found: SHEET 1 X 3 GLY D 256 LEU D
258 0
Start residue of secondary structure not found: SHEET 2 X 3 ILE D 169 ARG D
173 -1 N MET D 171 O GLY D 256
Start residue of secondary structure not found: SHEET 3 X 3 TRP D 239 PHE D
241 -1 N VAL D 240 O HIS D 172
Start residue of secondary structure not found: SHEET 1 Y 3 SER D 210 SER D
215 0
5 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 AA 3 THR D 296 LYS D 302
-1 N THR D 300 O THR D 310
Start residue of secondary structure not found: SHEET 3 AA 3 LEU D 329 TRP D
333 -1 N VAL D 332 O THR D 299
Start residue of secondary structure not found: SHEET 1 AL 2 GLY H 17 CYS H 19
0
Start residue of secondary structure not found: SHEET 2 AL 2 CYS H 28 SER H 30
-1 N SER H 30 O GLY H 17
End residue of secondary structure not found: SHEET 1 AM 4 GLY H 98 LYS H 100
0
Start residue of secondary structure not found: SHEET 2 AM 4 PHE H 103 GLN H
107 -1 N LEU H 105 O GLY H 98
Start residue of secondary structure not found: SHEET 3 AM 4 SER H 45 VAL H 50
-1 N ILE H 48 O LEU H 104
Start residue of secondary structure not found: SHEET 4 AM 4 ILE H 34 TRP H 38
-1 N TRP H 38 O ARG H 47
Start residue of secondary structure not found: SHEET 1 AN 2 SER H 71 HIS H 74
0
Start residue of secondary structure not found: SHEET 2 AN 2 ASP H 77 GLU H 80
-1 N LYS H 79 O PHE H 72
3 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 AP 2 LYS H 151 TYR H 158
0
Start residue of secondary structure not found: SHEET 2 AP 2 LEU H 264 VAL H
271 -1 N VAL H 271 O LYS H 151
Start residue of secondary structure not found: SHEET 1 AQ 3 GLY H 256 LEU H
258 0
Start residue of secondary structure not found: SHEET 2 AQ 3 ILE H 169 ARG H
173 -1 N MET H 171 O GLY H 256
Start residue of secondary structure not found: SHEET 3 AQ 3 TRP H 239 PHE H
241 -1 N VAL H 240 O HIS H 172
Start residue of secondary structure not found: SHEET 1 AR 3 SER H 210 SER H
215 0
5 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 AT 3 THR H 296 LYS H 302
-1 N THR H 300 O THR H 310
Start residue of secondary structure not found: SHEET 3 AT 3 LEU H 329 TRP H
333 -1 N VAL H 332 O THR H 299
Start residue of secondary structure not found: SHEET 1 BG 2 GLY L 17 CYS L 19
0
Start residue of secondary structure not found: SHEET 2 BG 2 CYS L 28 SER L 30
-1 N SER L 30 O GLY L 17
Start residue of secondary structure not found: SHEET 1 BH 4 ILE L 34 TRP L 38
0
Start residue of secondary structure not found: SHEET 2 BH 4 ILE L 46 VAL L 50
-1 N GLN L 49 O GLU L 35
7 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 BK 2 LYS L 151 TYR L 158
0
Start residue of secondary structure not found: SHEET 2 BK 2 LEU L 264 VAL L
271 -1 N VAL L 271 O LYS L 151
Start residue of secondary structure not found: SHEET 1 BL 2 ILE L 169 MET L
171 0
Start residue of secondary structure not found: SHEET 2 BL 2 GLY L 256 LEU L
258 -1 N LEU L 258 O ILE L 169
Start residue of secondary structure not found: SHEET 1 BM 3 SER L 210 SER L
215 0
Start residue of secondary structure not found: SHEET 2 BM 3 ASN L 199 CYS L
204 -1 N CYS L 204 O SER L 210
4 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 BO 4 THR L 296 LYS L 302
-1 N THR L 300 O THR L 310
Start residue of secondary structure not found: SHEET 3 BO 4 LEU L 329 TRP L
333 -1 N VAL L 332 O THR L 299
Start residue of secondary structure not found: SHEET 4 BO 4 VAL L 339 VAL L
341 -1 N VAL L 341 O LEU L 329
Start residue of secondary structure not found: SHEET 1 BZ 2 GLY P 17 CYS P 19
0
Start residue of secondary structure not found: SHEET 2 BZ 2 CYS P 28 SER P 30
-1 N SER P 30 O GLY P 17
Start residue of secondary structure not found: SHEET 1 CA 4 ILE P 34 TRP P 38
0
8 messages similar to the above omitted
End residue of secondary structure not found: SHEET 1 CD 2 LYS P 151 TYR P 158
0
Start residue of secondary structure not found: SHEET 2 CD 2 LEU P 264 VAL P
271 -1 N VAL P 271 O LYS P 151
Start residue of secondary structure not found: SHEET 1 CE 3 GLY P 256 LEU P
258 0
Start residue of secondary structure not found: SHEET 2 CE 3 ILE P 169 ARG P
173 -1 N MET P 171 O GLY P 256
Start residue of secondary structure not found: SHEET 3 CE 3 TRP P 239 PHE P
241 -1 N VAL P 240 O HIS P 172
Start residue of secondary structure not found: SHEET 1 CF 3 THR P 211 SER P
215 0
5 messages similar to the above omitted
End residue of secondary structure not found: SHEET 2 CH 3 THR P 296 ARG P 301
-1 N THR P 300 O THR P 310
Start residue of secondary structure not found: SHEET 3 CH 3 GLU P 330 TRP P
333 -1 N VAL P 332 O THR P 299
Cannot find LINK/SSBOND residue CYS (67 )
Cannot find LINK/SSBOND residue CYS (67 )
Cannot find LINK/SSBOND residue CYS (67 )
Cannot find LINK/SSBOND residue CYS (67 )
Cannot find LINK/SSBOND residue CYS (127 )
23 messages similar to the above omitted
Chain information for ev71-pcdh10-remumber.pdb #1
---
Chain | Description
A C E G | No description available
B F J N | No description available
D H L P | No description available
I K M O | No description available
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3CH/A
Chip: Unknown
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 1天6小时29分钟
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
27B1:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash processing timer |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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