id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9106 Crash opening mmCIF kirshner1@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6 (2023-03-23 07:59:11 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Entered command ""open 3ubx"" Fatal Python error: Segmentation fault Thread 0x0000700009c07000 (most recent call first): File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700012e46000 (most recent call first): File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00000001104ee600 (most recent call first): File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py"", line 43 in open File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in remember_data_format File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 465 in collated_open File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 194 in provider_open File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/manager.py"", line 198 in open_data File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py"", line 97 in fetch File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in remember_data_format File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 464 in collated_open File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 154 in provider_open File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 284 in event_loop File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File 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All rights reserved. How to cite UCSF ChimeraX > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/a6nlu0_p1.pdb format pdb Summary of feedback from opening /Users/kirshner1/Library/CloudStorage/OneDrive- LLNL/Documents/yue/quantum/a6nlu0_p1.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: 238.9 0.000 0.000 Ignored bad PDB record found on line 3 REMARK Name = LIG_min.pdb Ignored bad PDB record found on line 5 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 6 REMARK 1 A between atoms: C1_1 and O1_5 Ignored bad PDB record found on line 7 REMARK 2 A between atoms: O1_5 and C2_6 57 messages similar to the above omitted > hide #1 models > show #1 models > select add #1 65 atoms, 71 bonds, 1 residue, 1 model selected > select subtract #1 Nothing selected > ui mousemode right rotate > ui mousemode right select > ui mousemode right rotate > close session > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/a6nlu0.cxs format session opened ChimeraX session > close session > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/a6nmz2_com_min.pdb format pdb Chain information for a6nmz2_com_min.pdb #1 --- Chain | Description ? | No description available > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/A6NMZ2_p1.pdb Summary of feedback from opening /Users/kirshner1/Library/CloudStorage/OneDrive- LLNL/Documents/yue/quantum/A6NMZ2_p1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK VINA RESULT: 234.4 0.000 0.000 Ignored bad PDB record found on line 2 REMARK Name = LIG_min.pdb Ignored bad PDB record found on line 3 REMARK 7 active torsions: Ignored bad PDB record found on line 4 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 5 REMARK 1 A between atoms: C4_9 and C5_10 6 messages similar to the above omitted > surface > ui tool show ""Side View"" > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting simple > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes false > surface cap false > select add #1/?:83 15 atoms, 14 bonds, 1 residue, 1 model selected > select clear > save /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/a6nmz2_com_min.cxs > surface hidePatches > select #1/?:9 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 164 atoms, 163 bonds, 11 residues, 2 models selected > select up 1273 atoms, 1280 bonds, 79 residues, 2 models selected > ~display sel > hide sel cartoons > select #1/?:82 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 164 atoms, 163 bonds, 11 residues, 2 models selected > ~display sel > hide sel cartoons > select #1/?:150 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 190 atoms, 191 bonds, 11 residues, 2 models selected > ~display sel > hide sel cartoons > select #1/?:144 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 128 atoms, 128 bonds, 8 residues, 2 models selected > hide sel atoms > hide sel cartoons > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 48 atoms, 53 bonds, 1 residue, 1 model selected > select down 2 atoms, 1 bond, 1 residue, 1 model selected > select #1/?:80 13 atoms, 12 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/?:92 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 77 atoms, 77 bonds, 4 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #1/?:115 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 181 atoms, 180 bonds, 11 residues, 2 models selected > select up 1273 atoms, 1280 bonds, 79 residues, 2 models selected > hide sel atoms > hide sel cartoons > close session > surface cap true > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/a6nmz2_com_min.cxs format session > surface cap false opened ChimeraX session > ui mousemode right zoom > surface hidePatches > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/sp_A6NMZ2_SNTAN_HUMA.00_xxsBL62.COMPLEX.1_2_0.1k2h_A.pdb Chain information for sp_A6NMZ2_SNTAN_HUMA.00_xxsBL62.COMPLEX.1_2_0.1k2h_A.pdb #3 --- Chain | Description ? | No description available > select sidechain 3820 atoms, 3532 bonds, 316 residues, 2 models selected > display sel > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #2 models > show #2 models > hide #2 models > close session > surface cap true > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/a6nmz2_com_min.cxs format session > surface cap false opened ChimeraX session > close session > surface cap true > open /Users/kirshner1/Library/CloudStorage/OneDrive- > LLNL/Documents/yue/quantum/sp_P14324_FPPS_HUMAN.17_xxsBL62.COMPLEX.2_1_0.4p0v_A.pdb Chain information for sp_P14324_FPPS_HUMAN.17_xxsBL62.COMPLEX.2_1_0.4p0v_A.pdb #1 --- Chain | Description ? | No description available > ui mousemode right ""rotate selected models"" > close session > open 3ubx ===== Log before crash end ===== Log: You can double click a model's Name or ID in the model panel to edit those fields Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129) UCSF ChimeraX version: 1.6 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX 2023-05-31 12:12:42,861 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129)'))': /cxservices/api/v1/chimerax/updates?uuid=157f8010-670d-5e80-b4c4-a935acbc3820&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.6 2023-05-31 12:12:42,905 WARNING Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129)'))': /cxservices/api/v1/chimerax/updates?uuid=157f8010-670d-5e80-b4c4-a935acbc3820&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.6 OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6.5 (21G531) Kernel Version: Darwin 21.6.0 Time since boot: 39 days 23:11 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1.1 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Input/Output worksforme all ChimeraX