id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17286 volume splitbyzone: ArrayMemoryError parthodas@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.9rc202410300406 (2024-10-30 04:06:08 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: 1.9rc202410300406 (2024-10-30) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\parth\Downloads\cryosparc_P16_J227_003_volume_map_sharp.mrc > format mrc Opened cryosparc_P16_J227_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.92, shown at level 0.182, step 2, values float32 > volume #1 step 1 > set bgColor white > volume flip #1 axis z Opened cryosparc_P16_J227_003_volume_map_sharp.mrc z flip as #2, grid size 400,400,400, pixel 0.92, shown at step 1, values float32 > close #1 > volume #2 color #919191 > set bgColor white > graphics silhouettes true > open C:/Users/parth/Downloads/4p1y.pdb 4p1y.pdb title: Crystal structure of staphylococcal γ-hemolysin prepore [more info...] Chain information for 4p1y.pdb #1 --- Chain | Description | UniProt A C E G | LUKF | Q931F3_STAAM 2-300 B D F H | γ-hemolysin component A | HLGA_STAAM 13-280 > ui mousemode right ""translate selected models"" Drag select of 34011 atoms, 12 pseudobonds > view matrix models #1,1,0,0,174.05,0,1,0,116.72,0,0,1,-22.391 > view matrix models #1,1,0,0,223.22,0,1,0,137.18,0,0,1,267.93 > view matrix models #1,1,0,0,228.55,0,1,0,139.33,0,0,1,265.09 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.8449,-0.53073,0.066938,247.64,0.52109,0.84485,0.12124,174.18,-0.1209,-0.067554,0.99036,262.3 > fitmap #1 inMap #2 Fit molecule 4p1y.pdb (#1) to map cryosparc_P16_J227_003_volume_map_sharp.mrc z flip (#2) using 34011 atoms average map value = 0.1675, steps = 112 shifted from previous position = 8.4 rotated from previous position = 10.2 degrees atoms outside contour = 19523, contour level = 0.18172 Position of 4p1y.pdb (#1) relative to cryosparc_P16_J227_003_volume_map_sharp.mrc z flip (#2) coordinates: Matrix rotation and translation 0.90228263 -0.43114505 -0.00008249 249.43489782 0.43114504 0.90228263 -0.00011042 161.28248239 0.00012204 0.00006406 0.99999999 270.64265331 Axis 0.00020235 -0.00023719 0.99999995 Axis point -231.25393629 630.82635392 0.00000000 Rotation angle (degrees) 25.54025071 Shift along axis 270.65485806 > hide sel atoms > show sel cartoons > select clear > color #1 #9f9feeff > ui tool show ""Color Zone"" > color zone #2 near #1 distance 5.52 > volume splitbyzone #2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site- packages\chimerax\surface\colorzonegui.py"", line 253, in _split_map run(self.session, cmd) File ""C:\Program Files\ChimeraX 1.9rc202410300406\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 1.9rc202410300406\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9rc202410300406\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 ""C:\Program Files\ChimeraX 1.9rc202410300406\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 ""C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site- packages\chimerax\surface\colorzone.py"", line 362, in split_zones_by_color g = masked_grid_data(sg, mask, m) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site- packages\chimerax\map_data\arrays.py"", line 345, in masked_grid_data putmask(masked, mask == mask_value, matrix) numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an array with shape (400, 400, 400) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an array with shape (400, 400, 400) and data type float32 File ""C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site- packages\chimerax\map_data\arrays.py"", line 345, in masked_grid_data putmask(masked, mask == mask_value, matrix) See log for complete Python traceback. > fitmap #1 inMap #2 Fit molecule 4p1y.pdb (#1) to map cryosparc_P16_J227_003_volume_map_sharp.mrc z flip (#2) using 34011 atoms average map value = 0.1675, steps = 28 shifted from previous position = 0.0239 rotated from previous position = 0.0201 degrees atoms outside contour = 19517, contour level = 0.18172 Position of 4p1y.pdb (#1) relative to cryosparc_P16_J227_003_volume_map_sharp.mrc z flip (#2) coordinates: Matrix rotation and translation 0.90219684 -0.43132453 0.00014795 249.46435436 0.43132455 0.90219679 -0.00028491 161.28689697 -0.00001059 0.00032086 0.99999995 270.62846817 Axis 0.00070222 0.00018379 0.99999974 Axis point -230.90108180 630.28417987 0.00000000 Rotation angle (degrees) 25.55165540 Shift along axis 270.83321841 > surface dust #2 size 9.2 > color zone #2 near #1 distance 5.52 > volume splitbyzone #2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site- packages\chimerax\surface\colorzonegui.py"", line 253, in _split_map run(self.session, cmd) File ""C:\Program Files\ChimeraX 1.9rc202410300406\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 1.9rc202410300406\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9rc202410300406\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 ""C:\Program Files\ChimeraX 1.9rc202410300406\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 ""C:\Program Files\ChimeraX 1.9rc202410300406\bin\Lib\site- packages\chimerax\surface\colorzone.py"", line 362, in split_zones_by_color g = masked_grid_data(sg, mask, m) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9rc202410300406\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 244. MiB for an array with shape (400, 400, 400) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 244. MiB for an array with shape (400, 400, 400) and data type float32 File ""C:\Program Files\ChimeraX 1.9rc202410300406\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 27.20.100.8681 OpenGL renderer: Intel(R) UHD Graphics 620 OpenGL vendor: Intel Python: 3.11.4 Locale: en_IN.cp1252 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: windows Manufacturer: ASUSTeK COMPUTER INC. Model: VivoBook_ASUSLaptop X409FA_X409FA OS: Microsoft Windows 10 Home Single Language (Build 19045) Memory: 8,434,266,112 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz OSLanguage: en-US Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 2.4.1 auditwheel: 6.1.0 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.post1 charset-normalizer: 3.4.0 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: 2.16.1 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: 14.1.11 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: 1.4.0 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: 1.9rc202410300406 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-Dicom: 1.2.5 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-KVFinder: 1.2 ChimeraX-Label: 1.1.11 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-ModelArchive: 1.0 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-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 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: 1.6.1 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.2.2 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 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-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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.5 contourpy: 1.3.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.7 decorator: 5.1.1 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: 3.0.2 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 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 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: 3.2.0 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 pywin32: 306 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 WMI: 1.5.1 }}} " defect closed normal Volume Data limitation all ChimeraX