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Opened 11 days ago
Closed 11 days ago
#19054 closed defect (duplicate)
Segger: bounding_grid() missing 1 required positional argument: 'cube'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-84-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9.dev202410080811 (2024-10-08 08:11:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9.dev202410080811 (2024-10-08)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/naveen/Desktop/Env 1872/ModelAndRawMap.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 986, in restore_snapshot
sp = r.make_surface()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface
grid = bounding_grid(xyz, grid_spacing, pad)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: bounding_grid() missing 1 required positional argument: 'cube'
opened ChimeraX session
> open "/home/naveen/Desktop/Env 1872/ModelAndRawMap.cxs"
Error opening map "/home/naveen/Desktop/Env 1872/ModelAndRawMap.cxs": File
ModelAndRawMap.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 986, in restore_snapshot
sp = r.make_surface()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface
grid = bounding_grid(xyz, grid_spacing, pad)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: bounding_grid() missing 1 required positional argument: 'cube'
opened ChimeraX session
> open "/home/naveen/Desktop/Env 1872/Fab-Map-Colored3X.cxs"
Error opening map "/home/naveen/Desktop/Env 1872/ModelAndRawMap.cxs": File
ModelAndRawMap.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 986, in restore_snapshot
sp = r.make_surface()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface
grid = bounding_grid(xyz, grid_spacing, pad)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: bounding_grid() missing 1 required positional argument: 'cube'
opened ChimeraX session
> open "/home/naveen/Desktop/Env 1872/Fab-Map-Colored3X.cxs" format session
Error opening map "/home/naveen/Desktop/Env 1872/ModelAndRawMap.cxs": File
ModelAndRawMap.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 986, in restore_snapshot
sp = r.make_surface()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface
grid = bounding_grid(xyz, grid_spacing, pad)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: bounding_grid() missing 1 required positional argument: 'cube'
opened ChimeraX session
> open "/home/naveen/Desktop/Env 1872/Fab-Map-Colored3X.cxs" format session
Error opening map "/home/naveen/Desktop/Env 1872/ModelAndRawMap.cxs": File
ModelAndRawMap.cxs, format mrc
MRC header value nsymbt (875113504) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 986, in restore_snapshot
sp = r.make_surface()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/segger/regions.py", line 1173, in make_surface
vertices, normals, triangles, level = gaussian_surface(pts, weights, res,
level = 0.1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/surface/gaussian.py", line 31, in gaussian_surface
grid = bounding_grid(xyz, grid_spacing, pad)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: bounding_grid() missing 1 required positional argument: 'cube'
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 535.230.02
OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_AU.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 5950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 22Gi 9.2Gi 631Mi 94Gi 107Gi
Swap: 2.0Gi 0.0Ki 2.0Gi
Graphics:
3a:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3080 12GB] [10de:220a] (rev a1)
Subsystem: ASUSTeK Computer Inc. Device [1043:8887]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 2.4.1
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.14
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.7
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.3.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202410080811
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.5
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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
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-Label: 1.1.11
ChimeraX-LinuxSupport: 1.0.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.2.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.13
ChimeraX-Shape: 1.0.1
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.6
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
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: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.4
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.1
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 11 days ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Segger: bounding_grid() missing 1 required positional argument: 'cube' |
comment:2 by , 11 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Was fixed in ChimeraX 1.9.