id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18177 ffmpeg permission denied, Mac, ChimeraX 1.10 chimerax-bug-report@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/cameronheanue/Downloads/rd1sample4.pdb format pdb Chain information for rd1sample4.pdb #1 --- Chain | Description A | No description available > open /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav1.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav2.dx Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav1.dx as #2.1, grid size 86,100,101, pixel 0.2, shown at level -6,6, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav2.dx as #2.2, grid size 101,142,105, pixel 0.2, shown at level -6,6, step 1, values float32 > volume #2.1 level 0.3447 level 6 > volume #2.2 level 0.2801 level 6 > volume #2.1 level 0.5817 level 6 > open /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav3.dx Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav3.dx as #3, grid size 60,74,64, pixel 0.2, shown at level -6,6, step 1, values float32 > volume #3 level 0.488 level 6 > open /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav4.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav5.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav6.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav7.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav8.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav9.dx > /Users/cameronheanue/Desktop/results_cavity/rd1sample4_surface- > map_grid-0.2_rad1-1.1_rad2-3.6_cav10.dx Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav4.dx as #4.1, grid size 115,74,95, pixel 0.2, shown at level -4,4, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav5.dx as #4.2, grid size 116,59,37, pixel 0.2, shown at level -6,6, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav6.dx as #4.3, grid size 70,55,52, pixel 0.2, shown at level -6,6, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav7.dx as #4.4, grid size 62,63,51, pixel 0.2, shown at level -6,6, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav8.dx as #4.5, grid size 45,44,51, pixel 0.2, shown at level -6,6, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav9.dx as #4.6, grid size 39,61,59, pixel 0.2, shown at level -6,6, step 1, values float32 Opened rd1sample4_surface-map_grid-0.2_rad1-1.1_rad2-3.6_cav10.dx as #4.7, grid size 49,40,37, pixel 0.2, shown at level -6,6, step 1, values float32 > volume #4.1 level 0.2994 level 4 > volume #4.2 level 0.3327 level 6 > close #4.1 > close #4.2 > volume #4.3 level 0.61 level 6 > close #4.3 > volume #4.4 level 0.2994 level 6 > close #4.4 > volume #4.5 level 0.4436 level 6 > close #4.5 > volume #4.6 level 0.4325 level 6 > close #4.6 > volume #4.7 level 0.366 level 6 > close #4.7 > volume #2.1 level 0.5817 level 6 > volume #2.1 level 0.4597 level 6 > volume #2.2 level 0 level 6 > volume #2.1 style mesh > volume #2.1 color #fff7aa color #b2b2b2 > open /Users/cameronheanue/Downloads/8sbb.pdb 8sbb.pdb title: Cryo-em structure of ftalkb [more info...] Chain information for 8sbb.pdb #5 --- Chain | Description A | alkane 1-monooxygenase B | nanobody Non-standard residues in 8sbb.pdb #5 --- D12 — dodecane FE — Fe (III) ion > select add #5 4049 atoms, 4176 bonds, 9 pseudobonds, 502 residues, 2 models selected > select add #1 6940 atoms, 7153 bonds, 9 pseudobonds, 877 residues, 3 models selected > select add #2 6940 atoms, 7153 bonds, 9 pseudobonds, 877 residues, 10 models selected > ui tool show Matchmaker > matchmaker #!5 to #1 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 rd1sample4.pdb, chain A (#1) with 8sbb.pdb, chain A (#5), sequence alignment score = 1114.3 RMSD between 319 pruned atom pairs is 1.103 angstroms; (across all 373 pairs: 1.449) > select subtract #1 4049 atoms, 4176 bonds, 9 pseudobonds, 502 residues, 9 models selected > select subtract #2 4049 atoms, 4176 bonds, 9 pseudobonds, 502 residues, 2 models selected > select add #2.1 4049 atoms, 4176 bonds, 9 pseudobonds, 502 residues, 5 models selected > select subtract #2.1 4049 atoms, 4176 bonds, 9 pseudobonds, 502 residues, 2 models selected > select subtract #5 Nothing selected > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!5 models > color #1 #d7aa5aff > color #1 #89d760ff > color #1 #d92a68ff > color #1 #d95989ff > color #1 #d9608bff > color #1 #ff71a3ff > color #1 #e66693ff > color #1 #e6669395 > color #1 #e66693be > color #1 #e66693b7 > color #1 #e66693b6 > color #1 #e66693b8 > color #1 #de4a76b8 > color #1 #de577db8 > color #1 #de527ab8 > select ::name=""HIS"" 350 atoms, 354 bonds, 35 residues, 2 models selected > color sel & #1 byhetero > select ions 4 atoms, 4 residues, 2 models selected > color sel & #1 byhetero > movie record > turn y 2 180 > wait 180 > movie encode /Users/cameronheanue/Desktop/movie1.mp4 Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 185, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1419, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1394, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 403, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 421, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 340, in run f(s) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1312, in save_spin_movie run(session, cmd) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 537, in run run_command(session, command, **kw) File ""/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/moviecmd.py"", line 202, in movie_encode encode_op(session, output[-1], format, quality, qscale, bitrate, File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/moviecmd.py"", line 260, in encode_op movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'], ""yuv420p"", f['size_restriction'], File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/movie.py"", line 324, in start_encoding self.encoder.run(Status_Reporter()) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/encode.py"", line 232, in run p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py"", line 1026, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py"", line 1950, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: '/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg' PermissionError: [Errno 13] Permission denied: '/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg' File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py"", line 1950, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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 Air Model Identifier: MacBookAir10,1 Model Number: MGNE3LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 14 days, 2 hours, 4 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 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-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 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 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: 1.1.2 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: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 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: 4.4.4 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 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 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 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 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: 4.14.0 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 Platform fixed all ChimeraX