id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10153 Segger: library not loaded: libsz.2.dylib rposert@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.1-arm64-arm-64bit ChimeraX Version: 1.7rc202311140124 (2023-11-14 01:24:52 UTC) Description Attempting to save a `.seg` file results in the error (in log). To reproduce: 1) Open a `.mrc` map 2) Segment the map using default settings 3) From Segger pane, File > Save segmentation Log: > ui mousemode right zoom > volume defaultvalues initialColors > #00a4c2,#fbbd00,#a00000,#ea7100,#007d31,#1d1f5e UCSF ChimeraX version: 1.7rc202311140124 (2023-11-14) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ""Segment Map"" > open /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc Summary of feedback from opening /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc --- notes | open kw {} Opened cryosparc_P312_J95_map.mrc as #1, grid size 128,128,128, pixel 3.4, shown at level 0.103, step 1, values float32 > select #1 2 models selected No segmentation chosen [Repeated 1 time(s)] > open /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc Summary of feedback from opening /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc --- notes | open kw {} Opened cryosparc_P312_J95_map.mrc as #2, grid size 128,128,128, pixel 3.4, shown at level 0.103, step 1, values float32 > close #2 No segmentation chosen > open /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc Summary of feedback from opening /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc --- notes | open kw {} Opened cryosparc_P312_J95_map.mrc as #2, grid size 128,128,128, pixel 3.4, shown at level 0.103, step 1, values float32 > close #2 No segmentation chosen Segmenting cryosparc_P312_J95_map.mrc, density threshold 0.102567 Showing 4 region surfaces 289 watershed regions, grouped to 4 regions Showing cryosparc_P312_J95_map.seg - 4 regions, 4 surfaces > open /Users/rposert/Downloads/cryosparc_P312_J95_map.mrc Summary of feedback from opening /Users/rposert/Downloads/cryosparc_P312_J95_map.mrc --- notes | open kw {} Opened cryosparc_P312_J95_map.mrc as #3, grid size 128,128,128, pixel 3.4, shown at level 0.103, step 1, values float32 > close #3 > save /Users/rposert/Desktop/cryosparc_P312_J95_map.seg models #2 Traceback (most recent call last): File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segment_dialog.py"", line 1152, in SaveSegmentation self.SaveSegmentationAs() File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segment_dialog.py"", line 1163, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segfile.py"", line 160, in show_save_dialog show_save_file_dialog(seg.session, format = 'Segmentation', File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 138, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 62, in display run(session, cmd) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/__init__.py"", line 52, in save save_segmentation(session, path, models = models) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segfile.py"", line 138, in save_segmentation write_segmentation(seg, path) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segfile.py"", line 48, in write_segmentation import tables File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/__init__.py"", line 32, in from .utilsextension import get_hdf5_version as _get_hdf5_version ImportError: dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib Referenced from: /Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/libhdf5.200.dylib Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/usr/lib/libsz.2.dylib' (no such file, not in dyld cache) ImportError: dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib Referenced from: /Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/libhdf5.200.dylib Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/usr/lib/libsz.2.dylib' (no such file, not in dyld cache) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/__init__.py"", line 32, in from .utilsextension import get_hdf5_version as _get_hdf5_version See log for complete Python traceback. > save /Users/rposert/Desktop/cryosparc_P312_J95_map.seg models #2 Traceback (most recent call last): File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segment_dialog.py"", line 1163, in SaveSegmentationAs segfile.show_save_dialog(smod, self.path_changed_cb) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segfile.py"", line 160, in show_save_dialog show_save_file_dialog(seg.session, format = 'Segmentation', File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 138, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 62, in display run(session, cmd) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/__init__.py"", line 52, in save save_segmentation(session, path, models = models) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segfile.py"", line 138, in save_segmentation write_segmentation(seg, path) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/segger/segfile.py"", line 48, in write_segmentation import tables File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/__init__.py"", line 32, in from .utilsextension import get_hdf5_version as _get_hdf5_version ImportError: dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib Referenced from: /Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/libhdf5.200.dylib Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/usr/lib/libsz.2.dylib' (no such file, not in dyld cache) ImportError: dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib Referenced from: /Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/libhdf5.200.dylib Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file), '/usr/lib/libsz.2.dylib' (no such file, not in dyld cache) File ""/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/tables/__init__.py"", line 32, in from .utilsextension import get_hdf5_version as _get_hdf5_version See log for complete Python traceback. OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: Z17500103LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1 (23B74) Kernel Version: Darwin 23.1.0 Time since boot: 7 days, 21 hours, 10 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2723QE: Resolution: 6720 x 3780 UI Looks like: 3360 x 1890 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina 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: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.1 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: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7rc202311140124 ChimeraX-CoreFormats: 1.2 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: 1.4 ChimeraX-DockPrep: 1.1.2 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: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.44.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 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: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.0.0 prompt-toolkit: 3.0.41 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.10 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Volume Data fixed all ChimeraX