Opened 3 years ago

Closed 3 years ago

#8380 closed defect (can't reproduce)

Crash reading PDB file

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 340000,
  "procLaunch" : "2023-01-27 19:14:57.8556 -0500",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "iMac20,1",
  "procStartAbsTime" : 348860600424038,
  "coalitionID" : 18575,
  "osVersion" : {
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    "build" : "21G217",
    "releaseType" : "User"
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  "captureTime" : "2023-01-27 19:16:44.6302 -0500",
  "incident" : "591C7FD9-BF7F-4A43-9DE9-F63D0498185C",
  "bug_type" : "309",
  "pid" : 29228,
  "procExitAbsTime" : 348967365980264,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.2.5.app\/Contents\/MacOS\/ChimeraX",
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "32B92764-D6ED-98B5-6E04-ED6E4F302E3E",
  "bridgeVersion" : {"build":"20P420","train":"7.0"},
  "sip" : "enabled",
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  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
  "vmregioninfo" : "0x8 is not in any region.  Bytes before following region: 140737488105464\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      VM_ALLOCATE              7ffffffc3000-7ffffffc4000 [    4K] r-x\/r-x SM=ALI  ",
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  "faultingThread" : 0,
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Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/meganmayer/Dropbox (HMS)/bGSDM Pore Paper/Model Building/meta-
> bGSDM/20230117_meta-pore-model-complete-
> sheets/Lipsome_C31_P34_J910_004_6pt03_bGSDM_Bact31mer_v2.pdb"

Summary of feedback from opening /Users/meganmayer/Dropbox (HMS)/bGSDM Pore
Paper/Model Building/meta-bGSDM/20230117_meta-pore-model-complete-
sheets/Lipsome_C31_P34_J910_004_6pt03_bGSDM_Bact31mer_v2.pdb  
---  
warning | Ignored bad PDB record found on line 56360  
END  
  
Chain information for Lipsome_C31_P34_J910_004_6pt03_bGSDM_Bact31mer_v2.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e | No description
available  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.3 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 4 days 1:00

Graphics/Displays:

    AMD Radeon Pro 5300:

      Chipset Model: AMD Radeon Pro 5300
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0047
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XL-012
      Option ROM Version: 113-D322A1XL-012
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
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    ChimeraX-BasicActions: 1.1
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    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
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    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
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    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
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    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
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    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
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    ChimeraX-PDB: 2.4.1
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    ChimeraX-PresetMgr: 1.0.1
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    ChimeraX-ReadPbonds: 1.0
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    ChimeraX-ResidueFit: 1.0
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    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
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    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
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    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-Storm: 1.0
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    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
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    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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
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    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
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    kiwisolver: 1.3.1
    line-profiler: 2.1.2
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    MarkupSafe: 2.0.1
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    openvr: 1.14.1501
    packaging: 20.9
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    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
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    ptyprocess: 0.7.0
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    PyOpenGL-accelerate: 3.1.5
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    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash reading PDB file

comment:2 by Eric Pettersen, 3 years ago

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

1.2.5

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