id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20485 Crash in glBufferSubData martakubanska@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.7.8-x86_64-i386-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics. Fatal Python error: Aborted Current thread 0x00007ff85f891a00 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1769 in set_multishadow_view File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 251 in _draw_scene File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in 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unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 3120K 8 \nCG image 676K 66 \nColorSync 264K 30 \nCoreAnimation 2944K 177 \nCoreGraphics 16K 3 \nCoreMedia Capture Data 6188K 4 \nCoreServices 624K 2 \nCoreUI image data 5268K 68 \nFoundation 52K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 951.3M 339 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 744.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 160K 40 \nStack 200.8M 41 \nStack Guard 56.0M 1 \nVM_ALLOCATE 308.5M 234 \n__CTF 824 1 \n__DATA 48.3M 860 \n__DATA_CONST 52.2M 499 \n__DATA_DIRTY 1868K 243 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 228.3M 197 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 1.0G 853 \ndyld private memory 772K 4 \nmapped file 268.4M 80 \nshared memory 3028K 37 \n=========== ======= ======= \nTOTAL 4.2G 3826 \nTOTAL, minus reserved VM space 3.2G 3826 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""ea5a64043517955ad9cfa0223a836ce74dbf8680"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""62c73fd17cce0d1b0bcb8a02"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""651482b98d79034dd899e383"" }, ""deploymentId"" : 240000212 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 > artiax start Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho > open > /Users/makubanska/figures_thesis/thesis_results/sta_core63/lists/motl_core_v63_6_8_somemissalignedremoved.em > format motl Opened Particle list motl_core_v63_6_8_somemissalignedremoved.em with 12088 particles. > ui mousemode right ""delete selected particles"" > save > /Users/makubanska/figures_thesis/thesis_results/sta_core63/lists/motl_core_v63_6_8_somemissalignedremoved_502.em > partlist #1.2.1 > open > /Users/makubanska/thesis_viva_presentation/ref_composite_thesis_forbackprojections_correctlyrotated.mrc Opened ref_composite_thesis_forbackprojections_correctlyrotated.mrc as #2, grid size 220,220,220, pixel 1, shown at level 0.945, step 1, values float32 1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652 > artiax colormap #1.2.1.3 cross_correlation palette crest minValue > 0.10220000147819519 maxValue 0.6520000100135803 transparency 0.0 1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652 > artiax colormap #1.2.1.3 cross_correlation palette crest minValue > 0.3640095293521881 maxValue 0.6520000100135803 transparency 0.0 1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652 > artiax colormap #1.2.1.3 cross_correlation palette crest minValue > 0.3640095293521881 maxValue 0.4462925238268716 transparency 0.0 > artiax particles #1.2.1 radius 0.1 > artiax particles #1.2.1 axesSize 0.1 > artiax attach #2 toParticleList #1.2.1 Opened ref_composite_thesis_forbackprojections_correctlyrotated.mrc as #1.2.1.1.1, grid size 220,220,220, pixel 1, shown at level 0.945, step 1, values float32 > volume #1.2.1.1.1 capFaces false 1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652 > artiax colormap #1.2.1.3 cross_correlation palette crest minValue > 0.33408844045230324 maxValue 0.4462925238268716 transparency 0.0 1832 atoms, 1832 residues, atom legacy_x range 0 to 0 > artiax colormap #1.2.1.3 legacy_x palette crest minValue 0.0 maxValue 0.0 > transparency 0.0 1832 atoms, 1832 residues, atom tomo_number range 502 to 502 > artiax colormap #1.2.1.3 tomo_number palette crest minValue 502.0 maxValue > 502.0 transparency 0.0 1832 atoms, 1832 residues, atom psi range -86.7 to 245 > artiax colormap #1.2.1.3 psi palette crest minValue -86.6886978149414 > maxValue 244.8070068359375 transparency 0.0 1832 atoms, 1832 residues, atom psi range -86.7 to 245 > artiax colormap #1.2.1.3 psi palette crest minValue 55.380889892578125 > maxValue 244.8070068359375 transparency 0.0 1832 atoms, 1832 residues, atom psi range -86.7 to 245 > artiax colormap #1.2.1.3 psi palette crest minValue 55.380889892578125 > maxValue 114.01278323218935 transparency 0.0 > ui mousemode right select Drag select of axes, 1 of 1832 instances, 1 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select Drag select of axes, 1 of 1831 instances, surfaces, 1 of 1831 instances, 1 atoms Drag select of axes, 1 of 1831 instances, surfaces, 2 of 1831 instances, 1 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select Drag select of axes, 1 of 1829 instances, 1 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select > artiax view xy Drag select of surfaces, 1 of 1828 instances Drag select of axes, 1 of 1828 instances, 1 atoms Drag select of axes, 1 of 1828 instances, surfaces, 3 of 1828 instances, 1 atoms > select add #1.2.1.2 3 atoms, 3 residues, 2 models selected > select clear Drag select of axes, 1 of 1828 instances, surfaces, 3 of 1828 instances, 1 atoms > select #1.2.1.2 1 model selected Drag select of axes, 2 of 1828 instances, surfaces, 2 of 1828 instances, 2 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select Drag select of axes, 2 of 1826 instances, surfaces, 2 of 1826 instances, 2 atoms > ui mousemode right ""delete selected particles"" > artiax view xy > artiax view xz > artiax view yz > artiax view xy > ui mousemode right select Drag select of axes, 2 of 1824 instances, surfaces, 1 of 1824 instances, 2 atoms > select add #1.2.1.2 2 atoms, 2 residues, 2 models selected Drag select of axes, 1 of 1824 instances, surfaces, 1 of 1824 instances, 1 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select Drag select of axes, 1 of 1823 instances, surfaces, 1 of 1823 instances, 1 atoms Drag select of axes, 1 of 1823 instances, 1 atoms > select clear Drag select of axes, 1 of 1823 instances, surfaces, 1 of 1823 instances, 1 atoms > select clear Drag select of surfaces, 1 of 1823 instances Drag select of axes, 3 of 1823 instances, surfaces, 2 of 1823 instances, 3 atoms > select clear Drag select of axes, 2 of 1823 instances, surfaces, 1 of 1823 instances, 2 atoms > select clear Drag select of axes, 2 of 1823 instances, surfaces, 1 of 1823 instances, 2 atoms > select add #1.2.1.2 2 atoms, 2 residues, 2 models selected Drag select of axes, 1 of 1823 instances, surfaces, 1 of 1823 instances, 1 atoms Drag select of surfaces, 1 of 1823 instances > ui mousemode right ""delete selected particles"" > ui mousemode right select Drag select of axes, 1 of 1822 instances, surfaces, 1 of 1822 instances, 1 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select Drag select of axes, 1 of 1821 instances, surfaces, 1 of 1821 instances, 1 atoms > ui mousemode right ""delete selected particles"" > ui mousemode right select > artiax view xy Drag select of axes, 3 of 1820 instances, surfaces, 4 of 1820 instances, 3 atoms > select #1.2.1.2 1 model selected Drag select of axes, 1 of 1820 instances, surfaces, 1 of 1820 instances, 1 atoms > ui mousemode right ""delete selected particles"" > artiax particles #1.2.1 surfaceLevel 0.45492 > artiax view xy > save > /Users/makubanska/figures_thesis/thesis_results/sta_core63/lists/motl_core_v63_6_8_somemissalignedremoved_502.em > partlist #1.2.1 > open > /Users/makubanska/thesis_viva_presentation/PBS_reprojected_502/502_bin4_MemBrain_seg_v10_alpha.mrc Opened 502_bin4_MemBrain_seg_v10_alpha.mrc as #2, grid size 1024,1024,550, pixel 7.88,7.88,7.88, shown at step 1, values int8 > volume #2 color #cfd3db color #ffffb3 color #ffffb3 > volume #2 region 0,0,0,1023,1023,549 step 4 > hide #!1.2.1 models > close #2 > open > /Users/makubanska/thesis_viva_presentation/PBS_reprojected_502/502_bin4_MemBrain_seg_v10_alpha.mrc Opened 502_bin4_MemBrain_seg_v10_alpha.mrc as #2, grid size 1024,1024,550, pixel 7.88,7.88,7.88, shown at step 1, values int8 > volume #2 region 0,0,0,1023,1023,549 step 4 > volume #2 change image level 0,0 level 0.1,0.8 level 1,1 > volume #2 level 0.9838 > volume #2 step 8 > volume #2 level 0.2262 > show #!1.2.1 models > hide #!1.2.1 models > volume #2 step 4 > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > volume #2 color #cfd3db > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models > show #!1.2.1 models > lighting soft > set bgColor white > hide #!1.2.1 models > show #!1.2.1 models > hide #!1.2.1 models ===== Log before crash end ===== 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 OpenGL version: 4.1 INTEL-20.7.3 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0) OS Loader Version: 577.140.2~30 Software: System Software Overview: System Version: macOS 13.7.8 (22H730) Kernel Version: Darwin 22.6.0 Time since boot: 43 minutes, 20 seconds Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PA302W: Resolution: 2560 x 1600 UI Looks like: 2560 x 1600 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 66105741TW Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: ff.c8 Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 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: 2023.11.17 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-ArtiaX: 0.1 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 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 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 pandas: 2.3.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 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 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 21.0.0 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 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 starfile: 0.5.13 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 }}} " defect closed normal Graphics nonchimerax all ChimeraX