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#19397 closed defect (nonchimerax)

surface dust: ArrayMemoryError

Reported by:	chimerax-bug-report@…	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:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/ioo23a/Downloads/emd_29377.map/emd_29377.map

Opened emd_29377.map as #1, grid size 460,460,460, pixel 0.939, shown at level
4.45, step 2, values float32  

> volume #1 step 1

> lighting soft

> set bgColor white

> ui tool show "Hide Dust"

Invalid texture upload for 0x206bc6e48e0 layer=0 mip=0  

[Repeated 2 time(s)]

> surface dust #1 size 5.63

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\dustgui.py", line 241, in _dust  
run(self.session, cmd, log = log_command)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\sop.py", line 339, in surface_dust  
dust.hide_dust(s, metric, size, auto_update = update)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\dust.py", line 24, in hide_dust  
hide_surface_dust(s, metric, limit, auto_update, use_cached_geometry)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\dust.py", line 40, in hide_surface_dust  
m = b.triangle_mask(metric, limit)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\dust.py", line 164, in triangle_mask  
mask = self.mask_array()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\dust.py", line 272, in mask_array  
self.tmask = empty((self.triangle_count,), bool)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 4.77 MiB for an
array with shape (5001288,) and data type bool  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 4.77 MiB for an
array with shape (5001288,) and data type bool  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\surface\dust.py", line 272, in mask_array  
self.tmask = empty((self.triangle_count,), bool)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> surface dust #1 size 5.63

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 655, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 311, in mouse_drag  
self._rotate(axis, angle)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 403, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 1035, in rotate  
center = self.center_of_rotation  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 716, in _get_cofr  
cofr = self._compute_center_of_rotation()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 743, in _compute_center_of_rotation  
p = self._front_center_cofr()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 811, in _front_center_cofr  
cr = self._front_center_point() # Can be None  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 820, in _front_center_point  
p = self.picked_object(0.5 * w, 0.5 * h, max_transparent_layers = 0,
exclude=View.unpickable)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 839, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 871, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1074, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1091, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1138, in first_intercept  
pd = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1074, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1091, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1100, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1360, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 56.3 MiB for an
array with shape (4921032, 3) and data type int32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 56.3 MiB for an
array with shape (4921032, 3) and data type int32  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1360, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 839, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\view.py", line 871, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1074, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1091, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1138, in first_intercept  
pd = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1074, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1091, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1069, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1100, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1360, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 37.5 MiB for an
array with shape (4921032,) and data type int64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 37.5 MiB for an
array with shape (4921032,) and data type int64  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1360, in masked_triangles  
return ta if tm is None else ta[tm,:]  
~~^^^^^^  
  
See log for complete Python traceback.  
  

Invalid texture upload for 0x206bc6e48e0 layer=0 mip=0  

[Repeated 3 time(s)]




OpenGL version: 3.3.0 Core Profile Context 23.19.21.02.240903
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 14 7435 2-in-1
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 7,816,343,552
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 7530U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.10.1
    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-maskChains: 1.4
    ChimeraX-MatchMaker: 2.2.2
    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: 1.1.3
    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: 1.2.1
    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: 1.45.2
    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: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 2.1.1
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 2.2.6
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    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
    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
    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: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    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
    tomlkit: 0.13.2
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 weeks ago

Component:	Unassigned → Volume Data
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → surface dust: ArrayMemoryError

comment:2 by Tom Goddard, 2 weeks ago

Resolution:	→ nonchimerax
Status:	assigned → closed

User opened a 0.5 GB map on a Windows 11 machine with 8 GB, showed hide dust and got an error probably from Qt "Invalid texture upload for 0x206bc6e48e0 layer=0 mip=0" and then trying to hide dust allocated a 5 MB array which failed.

Puzzling how it can fail with so little data open and on such a tiny allocation.

These out of memory errors on small allocations are always on Windows.

AMD graphics driver from 2023.

Best guess is that some other allocation has most of the memory used. Greg says page file on Windows is supposedly half of physical memory size by default.

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