id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19283 MemoryError processing surface chimerax-bug-report@… Tom Goddard "{{{ 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 ""F:\\\PBMC SELEX\\\Results\\\MD > simulation\\\apt5-CD35\\\apt5complex.pdb"" Summary of feedback from opening F:\\\PBMC SELEX\\\Results\\\MD simulation\\\apt5-CD35\\\apt5complex.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Number: 3 Ignored bad PDB record found on line 2 REMARK Ligand: lig_68fc9bea19dfb.pdb Ignored bad PDB record found on line 3 REMARK Contact: 0 0 0 Ignored bad PDB record found on line 4 REMARK Score: -289.02 Ignored bad PDB record found on line 5 REMARK RMSD: 135.73 Chain information for apt5complex.pdb #1 --- Chain | Description ? | No description available A | No description available Computing secondary structure > set bgColor white > nucleotides fill > style nucleic stick Changed 1973 atom styles > nucleotides stubs > nucleotides fill > style nucleic stick Changed 1973 atom styles > select /A 14975 atoms, 15427 bonds, 1945 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for apt5complex.pdb_A SES surface #1.1: minimum, -21.82, mean -1.68, maximum 10.96 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for apt5complex.pdb_A SES surface #1.1: minimum, -21.82, mean -1.68, maximum 10.96 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for apt5complex.pdb_A SES surface #1.1: minimum, -21.82, mean -1.68, maximum 10.96 To also show corresponding color key, enter the above coulombic command and add key true > select add #1 16948 atoms, 17637 bonds, 2041 residues, 2 models selected > select subtract #1 1 model selected > select add #1 16948 atoms, 17637 bonds, 2041 residues, 2 models selected > hide #!1 models > show #!1 models Traceback (most recent call last): File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\model_panel\tool.py"", line 214, in lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar)) ^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\model_panel\tool.py"", line 255, in _fill_tree self._get_info(model, all_selected_models, part_selected_models) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\model_panel\tool.py"", line 356, in _get_info bg_color = self._model_color(obj) ^^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\model_panel\tool.py"", line 401, in _model_color return model.overall_color ^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\atomic\molsurf.py"", line 404, in _get_overall_color return self.color if vc is None or len(vc) == 0 else most_common_color(vc) ^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\colors.py"", line 825, in most_common_color unique, indices, counts = unique(as32, return_index=True, return_counts=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\numpy\lib\arraysetops.py"", line 274, in unique ret = _unique1d(ar, return_index, return_inverse, return_counts, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\numpy\lib\arraysetops.py"", line 333, in _unique1d perm = ar.argsort(kind='mergesort' if return_index else 'quicksort') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ MemoryError Error processing trigger ""new frame"": MemoryError File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\numpy\lib\arraysetops.py"", line 333, in _unique1d perm = ar.argsort(kind='mergesort' if return_index else 'quicksort') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Unable to allocate 9.07 MiB for an array with shape (792276, 3) and data type int32 Traceback (most recent call last): File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\view.py"", line 259, in _draw_scene draw_opaque(r, opaque_drawings) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 1559, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 1572, in _draw_multiple d.draw(renderer, draw_pass) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 784, in draw self.draw_self(renderer, draw_pass) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 791, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 815, in _draw_geometry self._update_buffers() File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 942, in _update_buffers dss.update_element_buffer(ta, style, tmsel, em) File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 1788, in update_element_buffer e = self.masked_elements(triangles, style, triangle_mask, edge_mask) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\graphics\drawing.py"", line 1816, in masked_elements ta = ta[tmask, :] ~~^^^^^^^^^^ numpy.core._exceptions._ArrayMemoryError: Unable to allocate 9.07 MiB for an array with shape (792276, 3) and data type int32 OpenGL version: 3.3.0 NVIDIA 560.94 OpenGL renderer: NVIDIA GeForce RTX 3070 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation 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 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 }}} " defect assigned normal Graphics Eric Pettersen all ChimeraX