Must run from installer

[zstuwdc@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
The software needs to be opened from the installation package every time. Once it is closed, it will disappear.
Process:               ChimeraX [5560]
Path:                  /private/var/folders/*/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier:            edu.ucsf.cgl.ChimeraX
Version:               1.5.0 (1.5.0.0)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           ChimeraX [5560]
User ID:               501

Date/Time:             2023-02-27 16:56:10.934 +0800
OS Version:            macOS 11.4 (20F71)
Report Version:        12
Anonymous UUID:        9869FB5A-22BD-CC6F-FFE0-90CEBF50417F

Sleep/Wake UUID:       6C835A13-8CD6-43E6-9E61-975C2C71D656

Time Awake Since Boot: 62000 seconds
Time Since Wake:       14000 seconds

System Integrity Protection: enabled

Crashed Thread:        0

Exception Type:        EXC_BAD_ACCESS (SIGBUS)
Exception Codes:       KERN_MEMORY_ERROR at 0x000000011af0dac0
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0x11af0dac0:
    __LINKEDIT                  11aef0000-11aef4000    [   16K] r--/r-- SM=NUL  /usr/lib/dyld
--> mapped file                 11aef4000-124c5c000    [157.4M] r-x/rwx SM=COW  Object_id=e61551f5
    mapped file                 124c5c000-1252e8000    [ 6704K] rw-/rwx SM=COW  Object_id=e27c12f5

Thread 0 Crashed:
0   ???                           	0x00007fff204da92e 0 + 140733735348526
1   ???                           	0x00007fff203edbe5 0 + 140733734378469
2   ???                           	0x00007fff2054ed7d 0 + 140733735824765
3   ChimeraX                      	000000000000000000 0 + 0
4   ???                           	0x0000000118ea56d7 0 + 4712978135
5   ???                           	0x00000001189c5fdc 0 + 4707868636
6   ???                           	0x0000000116198655 0 + 4665738837
7   ???                           	0x000000010cab71dc 0 + 4507529692
8   ???                           	0x000000010cbf15b1 0 + 4508816817
9   ???                           	0x000000010cb94d4e 0 + 4508437838
10  ???                           	0x000000010cbb72b0 0 + 4508578480
11  ???                           	0x000000010cbb758f 0 + 4508579215
12  ???                           	0x000000010cbb749b 0 + 4508578971
13  ???                           	0x000000010ca2ddc8 0 + 4506967496
14  ???                           	0x00007fff20524f5d 0 + 140733735653213

Thread 1:
0   ???                           	0x00007fff204d6cde 0 + 140733735333086
1   ???                           	0x000000010d9b923f 0 + 4523266623
2   ???                           	0x00007fff205098fc 0 + 140733735540988
3   ???                           	0x00007fff20505443 0 + 140733735523395

Thread 2:
0   ???                           	0x00007fff20505420 0 + 140733735523360

Thread 3:
0   ???                           	0x00007fff20505420 0 + 140733735523360

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x000000011aeb3e00  rcx: 0x00007f9d0c955a58  rdx: 0x0000000000000000
  rdi: 0x0000000000000103  rsi: 0x000000000000000a  rbp: 0x00007f9d0c955a80  rsp: 0x00007f9d0c955a58
   r8: 0x00007f9d0c955f48   r9: 0x79c20489345d5e48  r10: 0x000000011aeb3e00  r11: 0x0000000000000246
  r12: 0x0000000000000103  r13: 0x000060000285d600  r14: 0x000000000000000a  r15: 0x0000000000000016
  rip: 0x00007fff204da92e  rfl: 0x0000000000000246  cr2: 0x00007f9d0c955f48
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133

Thread 0 instruction stream not available.

Thread 0 last branch register state not available.


Binary Images:
                 0 - 0xffffffffffffffff +ChimeraX (???) /private/var/folders/*/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
       0x11addc000 -        0x11ae77fff  dyld (852)  /usr/lib/dyld

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=848K resident=0K(0%) swapped_out_or_unallocated=848K(100%)
Writable regions: Total=679.2M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=679.2M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Activity Tracing                   256K        1 
Foundation                          16K        1 
Kernel Alloc Once                    8K        1 
MALLOC                           216.8M      190 
MALLOC guard page                   32K        8 
MALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
STACK GUARD                         12K        3 
Stack                             9752K        4 
Stack Guard                       56.0M        1 
VM_ALLOCATE                       64.0M        6 
VM_ALLOCATE (reserved)              12K        1         reserved VM address space (unallocated)
__DATA                             224K        2 
__DATA_CONST                        32K        1 
__LINKEDIT                         240K        2 
__TEXT                             624K        1 
dylib                             3620K       12 
dylib (reserved)                   572K       72         reserved VM address space (unallocated)
mapped file                      364.2M      286 
shared memory                      752K       14 
===========                     =======  ======= 
TOTAL                              1.1G      608 
TOTAL, minus reserved VM space   716.2M      608 



Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-16.4.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 429.120.4.0.0
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 105 days 11:23

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

Hi,

Once you open the .dmg file, do you run ChimeraX from there or do you copy it somewhere first? It is not designed to be run from the .dmg (though that will _usually_ work), but rather it should be copied somewhere permanent and run from there. After copying you can remove the .dmg.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab