Opened 2 years ago

Closed 2 years ago

#9994 closed defect (nonchimerax)

ChimeraX hangs saving a session, macOS Sonoma

Reported by: maf95@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Eric Pettersen, Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.7.dev202310140743 (2023-10-14 07:43:20 UTC)
Description
(Describe the actions that caused this problem to occur here)
1. Open .html script with PDB files.
2. Adjust model view to vertical.
3. Tried saving snapshot of the scene by going to "File" --> Save.
4. ChimeraX becomes unresponsive.
5. Force quit after 45 seconds of no response.
6. Submitted error report to Apple. The issue, according to that message, is that there was a "hang."


Log:
UCSF ChimeraX version: 1.7.dev202310140743 (2023-10-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
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: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 18 hours, 50 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      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


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.0
    Babel: 2.13.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.3.0
    ChimeraX-AddCharge: 1.5.12
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49
    ChimeraX-AtomicLibrary: 11.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.4
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202310140743
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    contourpy: 1.1.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.0
    filelock: 3.9.0
    fonttools: 4.43.1
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.4.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    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: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.11.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.0
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.6
    wcwidth: 0.2.8
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (17)

comment:1 by Tom Goddard, 2 years ago

Cc: Eric Pettersen Tom Goddard added
Component: Unassigned → Platform
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ChimeraX hangs saving a session, macOS Sonoma

This is a follow-up to #9991.

What do you mean by "snapshot" in your statement "tried saving snapshot of the scene"? Do you mean you tried to save a ChimeraX session or an image file? What location did you try to save the file to? Mac restricts access to Documents, Downloads and Desktop. You might try saving to /Users/yourusername to see if that is the problem.

Zach could you try saving a session on macOS Sonoma and see if it hangs for you?

comment:2 by maf95@…, 2 years ago 

I was originally trying to save a JPEG of the window, but it doesn’t seem to matter too much as the hang is occurring before I can interact with the window that opens after selecting “save” from the file dropdown menu. When the window for saving opens, it is trying to save to User/markfrank/Desktop. I checked my security settings and ChimeraX does have access to Downloads, Desktop, and Documents folder.

I did not have any issues when I was previously on macOS Ventura.


--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 2:33 PM
To: Frank, Mark Allen <maf95@psu.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma (was: ChimeraX bug report submission)
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+--------------------------
          Reporter:  maf95@…   |      Owner:  Zach Pearson
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------------
Changes (by Tom Goddard):

 * cc: pett, Tom Goddard (added)
 * component:  Unassigned => Platform
 * owner:  (none) => Zach Pearson
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => assigned
 * summary:  ChimeraX bug report submission => ChimeraX hangs saving a
     session, macOS Sonoma

Comment:

 This is a follow-up to #9991.

 What do you mean by "snapshot" in your statement "tried saving snapshot of
 the scene"?  Do you mean you tried to save a ChimeraX session or an image
 file?  What location did you try to save the file to?  Mac restricts
 access to Documents, Downloads and Desktop.  You might try saving to
 /Users/yourusername to see if that is the problem.

 Zach could you try saving a session on macOS Sonoma and see if it hangs
 for you?
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A1&data=05%7C01%7Cmaf95%40psu.edu%7Cf150cf9c50bc40dac97308dbce765aa3%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330779952742643%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rWxljTbGwc3tYbdGjRqnVcU%2FHqswT%2BZT0yF1D%2FASULQ%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:1>>
ChimeraX <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Cmaf95%40psu.edu%7Cf150cf9c50bc40dac97308dbce765aa3%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330779952742643%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8yFoZOvVHTl6Yge9KQlibVWrIrR5iD3j1cmJAD3WtVw%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker

comment:3 by Zach Pearson, 2 years ago

I rebuilt ChimeraX just last night. Today, I'm able to save sessions OK without hangs.

comment:4 by Zach Pearson, 2 years ago 

Well we’re not exactly out of the woods yet. I just tried saving a session of what I happened to be working on, but getting a copy of the script you ran would be helpful too, since I can see if I can reproduce your exact conditions and if that fails for me we have a bug to work on. 

— Zach

comment:5 by maf95@…, 2 years ago 

I just tried the following and got the same issue.


  1.  Open ChimeraX from Spotlight search.
  2.  In command line, I typed: open 6wlb
  3.  Go to File and select save
  4.  Hang (spinning beachball on macOS) • Force Quit required




--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: Zach Pearson <zjp@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 2:45 PM
To: Frank, Mark Allen <maf95@psu.edu>
Cc: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Eric Pettersen <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
Well we’re not exactly out of the woods yet. I just tried saving a session of what I happened to be working on, but getting a copy of the script you ran would be helpful too, since I can see if I can reproduce your exact conditions and if that fails for me we have a bug to work on.

— Zach

On Oct 16, 2023, at 11:42, Frank, Mark Allen <maf95@psu.edu> wrote:

Hi Zach,
Thank you. This sounds promising. I am still seeing the latest daily build as October 14, 2023 [version 1.7.dev202310140743 (2023-10-14)].

I’ll keep my eyes open for this next build and see if it resolves the issue for me. I suspect it will.

--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>>
Date: Monday, October 16, 2023 at 2:38 PM
To: Frank, Mark Allen <maf95@psu.edu<mailto:maf95@psu.edu>>, zjp@cgl.ucsf.edu<mailto:zjp@cgl.ucsf.edu> <zjp@cgl.ucsf.edu<mailto:zjp@cgl.ucsf.edu>>
Cc: goddard@cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu> <goddard@cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu>>, pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu> <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+--------------------------
          Reporter:  maf95@…   |      Owner:  Zach Pearson
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------------
Comment (by Zach Pearson):

 I rebuilt ChimeraX just last night. Today, I'm able to save sessions OK
 without hangs.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A3&data=05%7C01%7Cmaf95%40psu.edu%7C048105ca5f4c4929303808dbce772768%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330783385128040%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SDpsc0O6dMykpaw4Co5aR7MX%2FnUdZenxVjOOS3QWz3c%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:3>>
ChimeraX <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Cmaf95%40psu.edu%7C048105ca5f4c4929303808dbce772768%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330783385128040%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AYoE7XA0KIvp47axTaUJYLnISGIKwLs7gUWaP6oPDVI%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker

comment:6 by Zach Pearson, 2 years ago

I was able to follow that procedure on my developer build from last night. It's plausible that a new developer build will help you. You have a build from the 14th. On that day I committed a fix to a bug that was introduced by relicensing for our PyPI library ​here, where there was some duplicate code introduced to a dozen or so files. It's possible the build succeeded despite the bad code but it causes a crash at runtime. Can you download a new daily build and try it?

comment:7 by Tom Goddard, 2 years ago

That commit you mention Zach is code that would only run after saving a file. So it doesn't seem too likely to me that it is the problem since Mark reports that the dialog hangs before he tries to save any file. To me it looks more like a Mac file system problem, for instance, there is an external disk connected that is not responding, or something like DropBox which has virtual folder which is not responding.

How about if you save your file using the ChimeraX save command?

save ~/Desktop/test.jpg

I guess that will work, and this is just an issue with the Qt window toolkit save file dialog being hung.

comment:8 by maf95@…, 2 years ago 

Running the command was successful and I now see a JPEG of the screen.

For convenience the command is posted again below:
save ~/Desktop/test.jpg


--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 3:03 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Frank, Mark Allen <maf95@psu.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+--------------------------
          Reporter:  maf95@…   |      Owner:  Zach Pearson
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------------
Comment (by Tom Goddard):

 That commit you mention Zach is code that would only run after saving a
 file.  So it doesn't seem too likely to me that it is the problem since
 Mark reports that the dialog hangs before he tries to save any file.  To
 me it looks more like a Mac file system problem, for instance, there is an
 external disk connected that is not responding, or something like DropBox
 which has virtual folder which is not responding.

 How about if you save your file using the ChimeraX save command?

    save ~/Desktop/test.jpg

 I guess that will work, and this is just an issue with the Qt window
 toolkit save file dialog being hung.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A7&data=05%7C01%7Cmaf95%40psu.edu%7Cac3529def0384ca542f108dbce7aa3f0%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330798356387975%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SRujKPV0RLjmELfCTEQGwiqzT%2FVV6p0XcQaPDrUFJYc%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:7>>
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comment:9 by Tom Goddard, 2 years ago

If it is something related to the daily build you are using, you don't need to wait until tomorrow's daily build, you could just try the ChimeraX 1.6.1 current release version.

comment:10 by maf95@…, 2 years ago 

This problem also occurs in 1.1.6.

Again, you can bypass the problem with the save command.

--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 3:07 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Frank, Mark Allen <maf95@psu.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+--------------------------
          Reporter:  maf95@…   |      Owner:  Zach Pearson
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------------
Comment (by Tom Goddard):

 If it is something related to the daily build you are using, you don't
 need to wait until tomorrow's daily build, you could just try the ChimeraX
 1.6.1 current release version.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A9&data=05%7C01%7Cmaf95%40psu.edu%7Cc6195b7f6c434248c05108dbce7b1dee%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330800402502840%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Q8ylY6ey9tZudGXiVdiUurs7uwCDzgafRd4byV2s%2F%2Fo%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:9>>
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comment:11 by maf95@…, 2 years ago 

*version 1.6.1
My bad!

--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 3:07 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Frank, Mark Allen <maf95@psu.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+--------------------------
          Reporter:  maf95@…   |      Owner:  Zach Pearson
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------------
Comment (by Tom Goddard):

 If it is something related to the daily build you are using, you don't
 need to wait until tomorrow's daily build, you could just try the ChimeraX
 1.6.1 current release version.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A9&data=05%7C01%7Cmaf95%40psu.edu%7Cc6195b7f6c434248c05108dbce7b1dee%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330800402502840%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Q8ylY6ey9tZudGXiVdiUurs7uwCDzgafRd4byV2s%2F%2Fo%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:9>>
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comment:12 by Tom Goddard, 2 years ago

Thanks for all the testing.

I more strongly suspect now that it is something wrong with your macOS file system, and the Qt window toolkit not handling the file system not responding when it tries to list files on your Desktop.

You say the Save dialog is trying to start showing your Desktop. Let's see if it has to do with restricted access to the desktop. Enter the ChimeraX command

cd ~/

to change the current working directory to your home directory instead of the Desktop and then try showing the Save dialog.

comment:13 by Tom Goddard, 2 years ago

The test in the previous comment will make the Save dialog open showing your home directory instead of the Desktop and macOS doesn't restrict access to that.

comment:14 by maf95@…, 2 years ago 

I can confirm that it appears the file system was the issue. When I cd up one level in my directory to Users/markfrank, I can now save different files.

I wonder if the fact many of my desktop files are in the cloud could be causing a hang when Qt tries to list the files. Perhaps downloading everything is another workaround. For now though, it appears this problem has been resolved. At the very least, I now have two workarounds.

Thank you for your help.

--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 3:14 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Frank, Mark Allen <maf95@psu.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+--------------------------
          Reporter:  maf95@…   |      Owner:  Zach Pearson
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+--------------------------
Comment (by Tom Goddard):

 Thanks for all the testing.

 I more strongly suspect now that it is something wrong with your macOS
 file system, and the Qt window toolkit not handling the file system not
 responding when it tries to list files on your Desktop.

 You say the Save dialog is trying to start showing your Desktop.  Let's
 see if it has to do with restricted access to the desktop.  Enter the
 ChimeraX command

     cd ~/

 to change the current working directory to your home directory instead of
 the Desktop and then try showing the Save dialog.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A12&data=05%7C01%7Cmaf95%40psu.edu%7Ca7283dfc8dd04bb36a0408dbce7c0c7e%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330804405221707%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1ZpMDnWSKFccHEDpXV5u4CR6ttLHPJACmCHWCjbET%2FY%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:12>>
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comment:15 by Tom Goddard, 2 years ago

Cc: Zach Pearson added; Tom Goddard removed
Owner: changed from Zach Pearson to Tom Goddard

Good.

You say many of your Desktop files are in the cloud. That probably is the problem. What do you mean they are in the cloud? What service allows you to put cloud located files on your Desktop? Understanding this will help us advise other users if they encounter the same problem.

comment:16 by maf95@…, 2 years ago 

To clarify:
Desktop is a folder that, at least on my Mac, automatically syncs to iCloud. In comparison, Users/markfrank is a local storage folder and is not in iCloud.

Again, I am not 100% certain but I suspect that is the case.

This may be informative:  https://support.apple.com/en-gb/HT206985#:~:text=Find%20your%20Desktop%20and%20Documents,automatically%20stored%20in%20iCloud%20too.

--
Mark A. Frank
Ph.D.  Candidate
Nixon Lab
319 South Frear Laboratory
Department of Biochemistry and Molecular Biology
The Pennsylvania State University


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, October 16, 2023 at 3:27 PM
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Frank, Mark Allen <maf95@psu.edu>
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #9994: ChimeraX hangs saving a session, macOS Sonoma
#9994: ChimeraX hangs saving a session, macOS Sonoma
-------------------------------+-------------------------
          Reporter:  maf95@…   |      Owner:  Tom Goddard
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+-------------------------
Changes (by Tom Goddard):

 * cc: Tom Goddard (removed)
 * cc: Zach Pearson (added)
 * owner:  Zach Pearson => Tom Goddard

Comment:

 Good.

 You say many of your Desktop files are in the cloud.  That probably is the
 problem.  What do you mean they are in the cloud?  What service allows you
 to put cloud located files on your Desktop?  Understanding this will help
 us advise other users if they encounter the same problem.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9994%23comment%3A15&data=05%7C01%7Cmaf95%40psu.edu%7C124b28f1b10b4b6d179308dbce7defba%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638330812509996240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SgQqztPAzQ0BZ9pDOT4uf618OKzBNYRceXGAdZtzuS4%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9994#comment:15>>
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comment:17 by Tom Goddard, 2 years ago

Resolution: → nonchimerax
Status: assigned → closed

Seems it was a non-responsive file system causing the file browser not to appear.

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