id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18269 Crash moving window between screens yaxin.dai@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #10000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode surface cap false; surface style solid; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10 > position cofr; color ##~num_residues cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ydai/Documents/MD_data_analysis/humanV263noM_shortC_NaK389_charmm36m_pH74/complex_0ns.pdb Summary of feedback from opening /Users/ydai/Documents/MD_data_analysis/humanV263noM_shortC_NaK389_charmm36m_pH74/complex_0ns.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX complex_0ns.pdb title: Title t= 0.00000 step= 0 [more info...] Chain information for complex_0ns.pdb #1 --- Chain | Description A | No description available Non-standard residues in complex_0ns.pdb #1 --- ABU — (ABU) HSD — (HSD) SOD — (SOD) Computing secondary structure > open > /Users/ydai/Documents/MD_data_analysis/humanV263noM_shortC_NaK389_charmm36m_pH74/complex.xtc Replaced existing frames of complex_0ns.pdb #1 with 2501 new frames > select :213 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > close session > open > /Users/ydai/Documents/PHENIX/vGAT/RealSpaceRefine_214/hvGATRef214_coot_1Na1water.pdb Summary of feedback from opening /Users/ydai/Documents/PHENIX/vGAT/RealSpaceRefine_214/hvGATRef214_coot_1Na1water.pdb --- warning | End residue of secondary structure not found: HELIX 18 18 TRP A 487 VAL A 532 1 46 Chain information for hvGATRef214_coot_1Na1water.pdb #1 --- Chain | Description A | No description available > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 6492 atoms, 6579 bonds, 411 residues, 1 model selected > show sel surfaces > hide sel atoms > hide sel cartoons > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /A PRO 114 H2 bonded to atom that should not have hydrogens (/A PRO 114 N) > set bgColor white > view sel > ui tool show ""Side View"" > close session > open > /Users/ydai/Documents/MD_data_analysis/humanV263noM_shortC_NaK351_charmm36m_pH74/complex_0ns.pdb Summary of feedback from opening /Users/ydai/Documents/MD_data_analysis/humanV263noM_shortC_NaK351_charmm36m_pH74/complex_0ns.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX complex_0ns.pdb title: Title t= 0.00000 step= 0 [more info...] Chain information for complex_0ns.pdb #1 --- Chain | Description A | No description available Non-standard residues in complex_0ns.pdb #1 --- ABU — (ABU) HSD — (HSD) SOD — (SOD) Computing secondary structure > open > /Users/ydai/Documents/MD_data_analysis/humanV263noM_shortC_NaK351_charmm36m_pH74/complex.xtc Replaced existing frames of complex_0ns.pdb #1 with 2501 new frames > open > /Users/ydai/Documents/PHENIX/vGAT/RealSpaceRefine_219/humanV263NoM_refined_219_NaK351.pdb Summary of feedback from opening /Users/ydai/Documents/PHENIX/vGAT/RealSpaceRefine_219/humanV263NoM_refined_219_NaK351.pdb --- warnings | Start residue of secondary structure not found: HELIX 7 7 MET A 263 ASP A 291 1 29 End residue of secondary structure not found: HELIX 18 18 TRP A 487 VAL A 532 1 46 Chain information for humanV263NoM_refined_219_NaK351.pdb #2 --- Chain | Description A | No description available > mmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker complex_0ns.pdb, chain A (#1) with humanV263NoM_refined_219_NaK351.pdb, chain A (#2), sequence alignment score = 2043.9 RMSD between 404 pruned atom pairs is 0.625 angstroms; (across all 410 pairs: 0.704) > hide #1 models > select #2/A:351 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > show #1 models > select #2/A:130 17 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > hide #2 models > close session > open > /Users/ydai/Documents/SV2A/LEV_UB1_cryosparc_P233_J111_004_volume_map_sharp.mrc Opened LEV_UB1_cryosparc_P233_J111_004_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.974, shown at level 0.0901, step 1, values float32 > volume #1 level 0.209 > lighting flat > lighting gentle > surface dust #1 size 9.74 > volume #1 level 0.2769 > volume #1 level 0.2996 > volume #1 color #d6d6d6 > volume #1 color silver > volume #1 level 0.3335 > save /Users/ydai/Documents/SV2A/LEV_UB1.png width 1000 height 1000 > supersample 3 > volume #1 color #d6d6d6 > save /Users/ydai/Documents/SV2A/LEV_UB1.png width 1000 height 1000 > supersample 3 > open > /Users/ydai/Documents/SV2A/LEV_UB1_cryosparc_P233_J111_004_volume_map_half_A.mrc Opened LEV_UB1_cryosparc_P233_J111_004_volume_map_half_A.mrc as #2, grid size 256,256,256, pixel 0.974, shown at level 0.0964, step 1, values float32 > volume #2 level 0.2144 > volume #2 level 0.2699 > volume #2 level 0.2474 > volume #2 level 0.23 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #10000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode surface cap false; surface style solid; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10 > position cofr; color ##~num_residues cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: MK183LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 22 days, 18 hours, 5 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR QHD: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 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: 1.58.8 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: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 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-Clipper: 0.24.0 ChimeraX-clix: 0.2.1 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: 1.9 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: 1.2.6 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-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 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: 1.5.18 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: 1.6.2 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: 3.5.6 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 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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 MolecularDynamicsViewer: 1.6 more-itertools: 10.3.0 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: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 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 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 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 sniffio: 1.3.1 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 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX