volume splitbyzone: ArrayMemoryError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
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 "D:\\\A_Hu lab\\\G6P\\\C_CryoData\\\JHZ\\\ZWQ20250910
> dimer\\\20251015-J818\\\lmng-fit-3-to818-coot-0.pdb"

Chain information for lmng-fit-3-to818-coot-0.pdb #1  
---  
Chain | Description  
B C | No description available  
  

> set bgColor white

> open "D:/A_Hu lab/G6P/C_CryoData/JHZ/ZWQ20250910
> dimer/20251015-J818/cryosparc_P50_J818_004_volume_map_sharp.mrc"

Opened cryosparc_P50_J818_004_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.85, shown at level 0.0852, step 2, values float32  

> volume #2 level 0.3506

> volume #2 step 1

> volume #2 level 0.4012

Alignment identifier is 1  

> select /B-C:7

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select /B-C:7-41

590 atoms, 610 bonds, 70 residues, 1 model selected  

> hide #!2 models

> color sel red

> select /B-C:46

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:46-72

394 atoms, 398 bonds, 54 residues, 1 model selected  

> color sel orange

> select /B-C:7

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select /B-C:7-41

590 atoms, 610 bonds, 70 residues, 1 model selected  

> color sel orange red

> select /B-C:77

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /B-C:77-95

306 atoms, 314 bonds, 38 residues, 1 model selected  

> color sel yellow

> select /B-C:100

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select /B-C:100-128

458 atoms, 478 bonds, 58 residues, 1 model selected  

> color sel lime

> select /B-C:131

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:131-161

452 atoms, 464 bonds, 62 residues, 1 model selected  

> color sel forest green

> select /B-C:165

28 atoms, 30 bonds, 2 residues, 1 model selected  

> select /B-C:165-186

328 atoms, 332 bonds, 44 residues, 1 model selected  

> color sel cyan

> select /B-C:224

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:224-254

510 atoms, 528 bonds, 62 residues, 1 model selected  

> color sel light sea green

> select /B-C:259

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select /B-C:259-289

418 atoms, 420 bonds, 62 residues, 1 model selected  

> color sel cornflower blue

> select /B-C:299

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:299-320

354 atoms, 362 bonds, 44 residues, 1 model selected  

> color sel hot pink

> select /B-C:328

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /B-C:328-356

436 atoms, 448 bonds, 58 residues, 1 model selected  

> color sel magenta

> select /B-C:359

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:359-390

446 atoms, 456 bonds, 64 residues, 1 model selected  

> color sel light gray

> select /B-C:393

28 atoms, 30 bonds, 2 residues, 1 model selected  

> select /B-C:393-414

340 atoms, 352 bonds, 44 residues, 1 model selected  

> color sel black

> color sel dim gray

> select clear

> save "D:/A_Hu lab/G6P/F_Draft/20251025/dimer tms.cxs"

> rainbow

> color #1 light gray

> rainbow

> show #!2 models

> color zone #2 near #1 distance 2.5

> volume #2 level 0.3949

> volume splitbyzone #2

Traceback (most recent call last):  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 378, in split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 321, in split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 125. MiB for an
array with shape (320, 320, 320) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 125. MiB for an
array with shape (320, 320, 320) and data type float32  
  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> volume splitbyzone #2

Traceback (most recent call last):  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\cmd_line\tool.py",
line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 378, in split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 321, in split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 125. MiB for an
array with shape (320, 320, 320) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 125. MiB for an
array with shape (320, 320, 320) and data type float32  
  
File "D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 341, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4255
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: Vivobook_ASUSLaptop X3400PA_K3400PA
OS: Microsoft Windows 11 家庭中文版 (Build 26200)
Memory: 16,856,469,504
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-11300H @ 3.10GHz
OSLanguage: zh-CN

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-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
    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: 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
    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

[Tom Goddard]

Volume splitbyzone makes a separate copy of a volume for every color. So it is easy to run out of memory if you don't know what you are doing. And on Windows running out of memory is very common.