id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16985	Crash processing timer	chimerax-bug-report@…	Eric Pettersen	"{{{
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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},
  ""reportNotes"" : [
  ""PC register does not match crashing frame (0x0 vs 0x7FF89BEB6A84)""
]
}


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:
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    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
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    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
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    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
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    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
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    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
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    jedi: 0.18.1
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    kiwisolver: 1.4.2
    line-profiler: 3.4.0
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    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
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    packaging: 21.0
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    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
}}}
"	defect	closed	normal		Core		can't reproduce						all	ChimeraX