id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14639 Looks like Mac daily build is not notarized goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202402241727 (2024-02-24 17:27:28 UTC) Description When I started this Mac ChimeraX daily build it said it could not be checked for malware and would not open it. Apparently it is not notarized. Log: UCSF ChimeraX version: 1.8.dev202402241727 (2024-02-24) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs format session Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.48, step 1, values float32 Log from Thu Mar 23 18:12:01 2023UCSF ChimeraX version: 1.6.dev202303230058 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs format session Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.48, step 1, values float32 Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.478, step 1, values float32 Log from Thu Mar 23 17:52:16 2023UCSF ChimeraX version: 1.6.dev202303230058 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs format session Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.48, step 1, values float32 Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.478, step 1, values float32 Log from Thu Mar 23 17:41:16 2023UCSF ChimeraX version: 1.6.dev202303230058 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/goddard/ucsf/presentations/paxlovid-vr-mar2023/data/paxlovid.cxs restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.48, step 1, values float32 Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at level 0.478, step 1, values float32 Log from Mon Mar 20 10:30:55 2023UCSF ChimeraX version: 1.6.dev202302100235 (2023-02-10) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7tgr format mmcif fromDatabase pdb 7tgr title: Structure of SARS-CoV-2 main protease in complex with GC376 [more info...] Chain information for 7tgr #1 --- Chain | Description | UniProt A | 3C-like proteinase | R1AB_SARS2 1-304 Non-standard residues in 7tgr #1 --- B1S — (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) K — potassium ion K36 — (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid (GC376) NA — sodium ion 7tgr mmCIF Assemblies --- 1| author_and_software_defined_assembly > ui tool show ""Send to Quest"" > graphics quality atomTriangles 100 > graphics quality bondTriangles 20 > graphics quality ribbonDivisions 10 > open 7tgr fromDatabase eds Summary of feedback from opening 7tgr fetched from eds --- note | Fetching map 7tgr from http://www.ebi.ac.uk/pdbe/coordinates/files/7tgr.ccp4 Opened eds 7tgr as #2, grid size 204,96,80, pixel 0.562,0.551,0.574, shown at level 0.818, step 1, values float32 > volume #2 level 0.7671 > select :166 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select ligand 62 atoms, 63 bonds, 3 residues, 1 model selected > select sel :< 5 263 atoms, 248 bonds, 39 residues, 1 model selected > usage volume cover volume cover volumes [atomBox an atoms specifier] [pad a number] [box box bounds] [x 2 floats] [y 2 floats] [z 2 floats] [fBox box bounds] [fx 2 floats] [fy 2 floats] [fz 2 floats] [iBox box bounds] [ix 2 floats] [iy 2 floats] [iz 2 floats] [useSymmetry true or false] [cellSize cellSize] [step map step] [modelId modelId] — Use symmetry to extend a map to cover a region cellSize: some integers modelId: a model id > volume cover #2 atomBox sel Extended map eds 7tgr to box of size (60, 77, 95), cell size (204, 96, 80) grid points, 4 symmetry operations, 0 points not covered by any symmetry, maximum value difference where symmetric map copies overlap = 1.308e-06 Opened eds 7tgr extended as #3, grid size 60,77,95, pixel 0.562,0.551,0.574, shown at step 1, values float32 > close #3 Drag select of 14 atoms, 32 residues, 9 bonds > select clear > select :B1S 29 atoms, 30 bonds, 1 residue, 1 model selected > select sel :< 4 182 atoms, 179 bonds, 20 residues, 1 model selected > select :B1S :< 3 97 atoms, 98 bonds, 9 residues, 1 model selected > select :B1S :< 5 229 atoms, 223 bonds, 29 residues, 1 model selected > volume cover #2 atomBox sel Extended map eds 7tgr to box of size (58, 50, 47), cell size (204, 96, 80) grid points, 4 symmetry operations, 0 points not covered by any symmetry, maximum value difference where symmetric map copies overlap = 1.308e-06 Opened eds 7tgr extended as #3, grid size 58,50,47, pixel 0.562,0.551,0.574, shown at step 1, values float32 > volume #3 level 0.6057 > volume #3 level 0.4812 > volume zone #3 nearAtoms sel & #1 range 3.44 > volume #3 level 0.3982 > volume #3 level 0.472 > select :166 9 atoms, 8 bonds, 1 residue, 1 model selected > color :166 magenta > color :166 orange > color :166 byhetero > color :B1S pink > graphics quality bondTriangles 20 [Repeated 2 time(s)] > save 7tgr.cxs > close > open 7rfw 7rfw title: Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor [more info...] Chain information for 7rfw #1 --- Chain | Description | UniProt A | 3C-like proteinase | R1AB_SARS2 1-306 Non-standard residues in 7rfw #1 --- 4WI — (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide (PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form) 7rfw mmCIF Assemblies --- 1| author_and_software_defined_assembly > graphics quality bondTriangles 20 > graphics quality Quality 1, atom triangles 100, bond triangles 20, ribbon divisions 10 > color :4WI pink > color :4WI byhetero > select ligand 68 atoms, 70 bonds, 1 residue, 1 model selected > hbonds sel reveal true 7 hydrogen bonds found > color :166 orange > color :166 byhetero > select :21,50 15 atoms, 13 bonds, 2 residues, 1 model selected > show sel > color sel cyan > color sel byhetero > select clear > open 7rfw fromDatabase eds Summary of feedback from opening 7rfw fetched from eds --- note | Fetching map 7rfw from http://www.ebi.ac.uk/pdbe/coordinates/files/7rfw.ccp4 Opened eds 7rfw as #2, grid size 200,96,80, pixel 0.573,0.553,0.568, shown at level 0.885, step 1, values float32 > select :4WI :<5 276 atoms, 276 bonds, 7 pseudobonds, 28 residues, 2 models selected > volume cover #2 near sel Expected a keyword > volume cover #2 atomBox sel Extended map eds 7rfw to box of size (58, 57, 47), cell size (200, 96, 80) grid points, 4 symmetry operations, 0 points not covered by any symmetry, maximum value difference where symmetric map copies overlap = 1.4156e-06 Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at step 1, values float32 > volume #3 level 0.6537 > volume #3 level 0.5574 > volume zone #3 nearAtoms sel & #1 range 3.44 > volume #3 level 0.4804 > select clear > volume #3 color #ffffb24e > volume #3 color #ffffb27f > save paxlovid.cxs > sym #1 assembly 1 Made 2 copies for 7rfw assembly 1 > view > hide #!4.2 models > show #!4.2 models > color #4.2 cornflowerblue ribbons > color #4.2 cornflowerblue > color #4.2:4WI pink > color #4.2:21,50 lime > color #4.2:166 orange lime Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #4.2:166 orange > color #4.1:21,50 lime > color #4 byhetero > save paxlovid.cxs > volume #3 color #ffffff7f > volume #3 color #ffffff80 [Repeated 1 time(s)] > save paxlovid.cxs > save paxlovid.glb > ui tool show ""Send to Quest"" > save /Users/goddard/Desktop/paxlovid.glb Running command: ""/opt/homebrew/bin/adb"" push /Users/goddard/Desktop/paxlovid.glb /sdcard/Android/data/com.UCSF.Lookie/files stdout: adb: error: failed to get feature set: no devices/emulators found stderr: > save /Users/goddard/Desktop/paxlovid.glb Running command: ""/opt/homebrew/bin/adb"" push /Users/goddard/Desktop/paxlovid.glb /sdcard/Android/data/com.UCSF.LookieAR/files stdout: adb: error: failed to get feature set: no devices/emulators found stderr: > save /Users/goddard/Desktop/paxlovid.glb Running command: ""/opt/homebrew/bin/adb"" push /Users/goddard/Desktop/paxlovid.glb /sdcard/Android/data/com.UCSF.LookieAR/files > volume cover #2 atomBox #4.2:4WI :< 5 Extended map eds 7rfw to box of size (58, 57, 47), cell size (200, 96, 80) grid points, 4 symmetry operations, 0 points not covered by any symmetry, maximum value difference where symmetric map copies overlap = 1.4156e-06 Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568, shown at step 1, values float32 > select #4.2:4WI :< 5 288 atoms, 286 bonds, 7 pseudobonds, 30 residues, 4 models selected > volume #5 color #feffff > volume #5 color #feffff7c > volume #5 color #feffff7d Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 1 maps. > hide #!4.1 models > volume zone #5 nearAtoms sel & #4.2 range 3.44 > volume #2 level 0.4977 > volume #5 level 0.4783 > show #!4.1 models > select clear > save paxlovid.cxs [Repeated 1 time(s)] > save /Users/goddard/Desktop/paxlovid.glb Running command: ""/opt/homebrew/bin/adb"" push /Users/goddard/Desktop/paxlovid.glb /sdcard/Android/data/com.UCSF.LookieAR/files > save paxlovid.cxs ——— End of log from Mon Mar 20 10:30:55 2023 ——— opened ChimeraX session > graphics quality atomTriangles 100 > graphics quality ribbonDivisions 2 > graphics quality ribbonDivisions 5 > graphics quality ribbonSides 8 > graphics quality ribbonSides 4 > ~hbonds > graphics quality ribbonSides 8 > graphics quality bondTriangles 20 > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs ——— End of log from Thu Mar 23 17:41:16 2023 ——— opened ChimeraX session > color #4.2 salmon > color #4.2:21,50 lime > color #4.2:4WI pink > color #4.2 byhetero > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.glb > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/images/mpro_nirmatrelvir.png > select #4.2/A:401@C11 1 atom, 1 residue, 1 model selected > select up 68 atoms, 70 bonds, 1 residue, 1 model selected > hbonds sel reveal true 7 hydrogen bonds found > ~hbonds > color #4.2:166 orange > color #4.2 byhetero > select clear > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/images/mpro_nirmatrelvir.png > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.glb > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs ——— End of log from Thu Mar 23 17:52:16 2023 ——— opened ChimeraX session > close #5 > save /Users/goddard/ucsf/presentations/paxlovid-vr- > mar2023/data/mpro_nirmatrelvir.cxs ——— End of log from Thu Mar 23 18:12:01 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 13 days, 2 hours, 9 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 alphashape: 1.3.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.0.3 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.4 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.53 ChimeraX-AtomicLibrary: 12.1.14 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 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: 2.12 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: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 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: 1.8.dev202402241727 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4.2 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: 1.1.1 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: 1.1.9 ChimeraX-ListInfo: 1.2.2 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: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.2 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.2 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.2.1 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-Segmentations: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 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: 1.15 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.4 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-TetraScapeCommand: 0.1 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: 1.35 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-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 click: 8.1.7 click-log: 0.4.0 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.8 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.49.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.2 matplotlib-inline: 0.1.6 msgpack: 1.0.7 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.9.6 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.1 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.8.2 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 Rtree: 1.1.0 scipy: 1.12.0 setuptools: 69.1.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 shapely: 2.0.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 trimesh: 4.0.10 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.42.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Build System nonchimerax chimerax-programmers all ChimeraX