Opened 6 months ago

Closed 6 months ago

#17735 closed defect (fixed)

xr is None

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: VR Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505160006 (2025-05-16 00:06:03 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202505160006 (2025-05-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "D:\showcase\Nucleus Segmentation\cancerOrg_Nuc_mito_chimerax.cxs"
> format session

Opened fullNuc_mito.mrc as #1, grid size 2750,1938,70, pixel 5,5,10, shown at
step 1, values float32  
Opened nuc_seg_smoothed_scaled_chimerax.mrc as #2, grid size 2120,1412,67,
pixel 5,5,10, shown at level 0.844, step 1, values int16  
Opened mito_seg_smoothed_scaled_chimerax.mrc as #4, grid size 1097,930,69,
pixel 5,5,10, shown at level 5e-05, step 1, values uint8  
Log from Thu Jan 30 17:43:34 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/fullNuc_mito.mrc

Summary of feedback from opening
E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/fullNuc_mito.mrc  
---  
note | E:\Eli\Cancer_organoid\Jan2025\Full_nuc_mito_SEM\fullNuc_mito.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened fullNuc_mito.mrc as #1, grid size 2750,1938,70, pixel 1,1,1, shown at
step 1, values float32  

> open C:/Users/CryoEM/Downloads/nuc_seg_smoothed_scaled_chimerax.mrc

Opened nuc_seg_smoothed_scaled_chimerax.mrc as #2, grid size 2120,1412,67,
pixel 5,5,10, shown at level 1, step 4, values int16  

> volume #2 level 0.8439

> view orient

> volume #1 level 2.268e+04,0 level 3.797e+04,0.8 level 4.574e+04,1

> ui tool show "Map Coordinates"

> view orient

> volume #2 color #757552

> save
> E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/cancerOrg_Nuc_mito_chimerax.cxs
> includeMaps true

> open E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/mito_seg_amira.mrc

Summary of feedback from opening
E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/mito_seg_amira.mrc  
---  
note | E:\Eli\Cancer_organoid\Jan2025\Full_nuc_mito_SEM\mito_seg_amira.mrc: invalid cell angles 0,0,0 must be between 0 and 180.  
  
Opened mito_seg_amira.mrc as #3, grid size 2750,1938,70, pixel 1,1,1, shown at
step 1, values uint8  

> volume #3 region 0,0,0,2749,1937,69 step 4

[Repeated 1 time(s)]

> surface #1 smooth factor 0.3 iterations 20

Expected a keyword  

> surface smooth #1 factor 0.3 iterations 20

No surfaces specified  

> surface smooth #3 factor 0.3 iterations 20

> surface smooth #3 factor 0.3 iterations 30

> hide #4 models

> show #4 models

> hide #4 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> close #4

> surface smooth #3 factor 0.3 iterations 40

> hide #4 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> surface smooth #3 factor 0.4 iterations 40

> hide #5 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> close #5

> close #4

> volume mask #3 surfaces #6

Opened mito_seg_amira.mrc masked as #4, grid size 1097,930,69, pixel 5,5,10,
shown at step 1, values uint8  

> volume #3 change image level 0,0 level 0.1,0.8 level 1,1

> close #3

> close #6

> save
> E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/mito_seg_smoothed_scaled_chimerax.mrc
> models #4

> hide #!4 models

> show #!4 models

> show #!1 models

> show #!2 models

> volume #2 step 1

> save
> E:/Eli/Cancer_organoid/Jan2025/Full_nuc_mito_SEM/cancerOrg_Nuc_mito_chimerax.cxs
> includeMaps true

——— End of log from Thu Jan 30 17:43:34 2025 ———

> view name session-start

opened ChimeraX session  

> xr false

> xr true

> mousemode setting zoom speed 0.2

started OpenXR rendering SonySRD System, render size 3840 by 2160  

> VIEW

Unknown command: VIEW  

> view

[Repeated 1 time(s)]

> xr true

> xr false

> mousemode setting zoom speed 1

> xr false

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site-
packages\chimerax\vive\xr.py", line 87, in vr  
stop_vr(session, simplify_graphics)  
File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site-
packages\chimerax\vive\xr.py", line 444, in stop_vr  
cpos = c.mono_camera_position()  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site-
packages\chimerax\vive\xr.py", line 657, in mono_camera_position  
xr_fov = xr.field_of_view[eye]  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'field_of_view'  
  
AttributeError: 'NoneType' object has no attribute 'field_of_view'  
  
File "C:\Program Files\ChimeraX 1.10rc202505160007\bin\Lib\site-
packages\chimerax\vive\xr.py", line 657, in mono_camera_position  
xr_fov = xr.field_of_view[eye]  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_TW.cp950
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: W790 WS
OS: Microsoft Windows 11 專業版 (Build 26100)
Memory: 274,484,432,896
MaxProcessMemory: 137,438,953,344
CPU: 24 Intel(R) Xeon(R) w5-2455X
OSLanguage: zh-TW

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.3
    build: 1.2.2.post1
    certifi: 2025.4.26
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.6
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202505160006
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    platformdirs: 4.2.2
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.5
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.13.2
    typing_extensions: 4.12.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1
    zipp: 3.19.2

Change History (3)

comment:1 by Eric Pettersen, 6 months ago

Component: Unassigned → VR
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → xr is None

comment:2 by Tom Goddard, 6 months ago

The user enabled OpenXR then turned it off, then turned it off a second time when it wasn't on. Looks like the code needs some check when OpenXR is turned off when it is not actually enabled but has been turned off before so the OpenXR camera exists. Test a fix on Windows.

comment:3 by Tom Goddard, 6 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made "xr off" do nothing if the openxr camera is not the current camera.

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