id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16085 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6.9-x86_64-i386-64bit ChimeraX Version: 1.8.dev202401240123 (2024-01-24 01:23:36 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84aeb67c0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 526 in _cursor_position File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 483 in mouse_pause_tracking File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 151 in _redraw_timer_callback File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 276 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 53) {""app_name"":""ChimeraX"",""timestamp"":""2024-10-08 13:05:43.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.6.9 (22G830)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""F505BE0B-BBDF-46BA-AA8A-46B624D53484""} { ""uptime"" : 180000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""iMac18,1"", ""coalitionID"" : 3571, ""osVersion"" : { ""train"" : ""macOS 13.6.9"", ""build"" : ""22G830"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-10-08 13:05:19.1940 -0500"", ""incident"" : ""F505BE0B-BBDF-46BA-AA8A-46B624D53484"", ""pid"" : 13797, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-09-20 12:24:05.1422 -0500"", ""procStartAbsTime"" : 28581505688747, ""procExitAbsTime"" : 183210275599324, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""7C866D01-A3A4-51A6-B6CA-64C18B8FFF6D"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""0FEC3219-7ABA-91C7-FA8E-8E023799E894"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 1686, ""sleepWakeUUID"" : ""8F0F752F-8D52-4856-AD63-E007B2654042"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. 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""logWritingSignature"" : ""923a49e40b26f85f1d89246b11c7f24348b1406c"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000142 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.8.dev202401240123 (2024-01-24) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Nishya/Downloads/6fah.pdb 6fah.pdb title: Molecular basis of the flavin-based electron-bifurcating caffeyl-coa reductase reaction [more info...] Chain information for 6fah.pdb #1 --- Chain | Description | UniProt A E | caffeyl-coa reductase-etf complex subunit care | CARE_ACEWD 1-396 B F | caffeyl-coa reductase-etf complex subunit card | CARD_ACEWD 1-262 C D | caffeyl-coa reductase-etf complex subunit carc | CARC_ACEWD 1-379 Non-standard residues in 6fah.pdb #1 --- FAD — flavin-adenine dinucleotide SF4 — iron/sulfur cluster SO4 — sulfate ion > open ""/Users/Nishya/Desktop/Peters_03_08_24/oxidized/Oxidized_peak1_bead > model/7koe.pdb"" 7koe.pdb title: Electron bifurcating flavoprotein fix/etfabcx [more info...] Chain information for 7koe.pdb #2 --- Chain | Description | UniProt A E | electron transfer flavoprotein, β subunit | Q9X1L6_THEMA 2-285 B F | electron transfer flavoprotein, α subunit | R4P3F4_THEMA 286-623 C G | electron transfer flavoprotein-quinone oxidoreductase fixc | R4P168_THEMA 1-438 D H | ferredoxin-like protein | R4NRM2_THEMA 439-530 Non-standard residues in 7koe.pdb #2 --- FAD — flavin-adenine dinucleotide MQ7 — menaquinone-7 SF4 — iron/sulfur cluster > view > toolshed show > select #1/A#1/E 6001 atoms, 6114 bonds, 17 pseudobonds, 788 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/E Alignment identifier is 1 > select clear > select #1/A:8-396/E:4-396 5863 atoms, 5949 bonds, 782 residues, 1 model selected > select #1/A,E:396 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A,E:226-396 2548 atoms, 2584 bonds, 342 residues, 1 model selected > select #1/A,E:396 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A,E:279-396 1734 atoms, 1760 bonds, 236 residues, 1 model selected > select #1/A,E:247-248 32 atoms, 30 bonds, 4 residues, 1 model selected > select #1/A,E:247-396 2230 atoms, 2260 bonds, 300 residues, 1 model selected > select ::name=""SF4"" 64 atoms, 96 bonds, 8 residues, 2 models selected > hide #!2 models > select add #2 18380 atoms, 18778 bonds, 4 pseudobonds, 2312 residues, 3 models selected > select subtract #2 32 atoms, 48 bonds, 4 residues, 1 model selected > select #1/C#1/D 5929 atoms, 6016 bonds, 767 residues, 1 model selected > hide sel atoms > show sel cartoons > hide sel cartoons > select #1/B#1/F 4046 atoms, 4114 bonds, 526 residues, 1 model selected > hide sel atoms > show sel cartoons > hide sel cartoons > select #1/A#1/E 6001 atoms, 6114 bonds, 17 pseudobonds, 788 residues, 2 models selected > hide sel atoms > hide sel cartoons > show sel cartoons > select ::name=""SF4"" 64 atoms, 96 bonds, 8 residues, 2 models selected > show sel & #!1 atoms > select #1/A,E:72 28 atoms, 30 bonds, 2 residues, 1 model selected > select #1/A,E:72-216 2212 atoms, 2248 bonds, 290 residues, 1 model selected > select clear > select #1/A:8-64/E:4-64 865 atoms, 869 bonds, 118 residues, 1 model selected > select > #1/A,E:71-74,77-78,81-82,104-110,127-132,159-163,182-187,189-192,199-205,210-215,222-226,244-246,259-265,279-282,305-308,336-339,357-361,374-377 1306 atoms, 1288 bonds, 170 residues, 1 model selected > select #1/A:8-64/E:4-64 865 atoms, 869 bonds, 118 residues, 1 model selected > select clear > select #1/A:8-70/E:4-70 959 atoms, 965 bonds, 130 residues, 1 model selected > open /Users/Nishya/Downloads/Av_FixABCX_rsr28.pdb Chain information for Av_FixABCX_rsr28.pdb #3 --- Chain | Description A E | No description available B F | No description available C G | No description available D H | No description available > open /Users/Nishya/Downloads/Av_FixABCX_rsr28.pdb Chain information for Av_FixABCX_rsr28.pdb #4 --- Chain | Description A E | No description available B F | No description available C G | No description available D H | No description available > hide #!3 models > close #3 > close #2 > close #1 > show atoms > show cartoons > hide atoms > view > select ::name=""FAD"" 318 atoms, 348 bonds, 6 residues, 1 model selected > show sel atoms > select ::name=""SF4"" 32 atoms, 72 pseudobonds, 4 residues, 2 models selected > show sel atoms > select clear > select ::name=""CYS"" 240 atoms, 202 bonds, 40 residues, 1 model selected > show sel atoms > show sel cartoons > style sel ball Changed 240 atom styles > color sel yellow > select clear > open ""/Users/Nishya/Desktop/Peters_03_08_24/oxidized/Oxidized_peak1_bead > model/7koe.pdb"" 7koe.pdb title: Electron bifurcating flavoprotein fix/etfabcx [more info...] Chain information for 7koe.pdb #1 --- Chain | Description | UniProt A E | electron transfer flavoprotein, β subunit | Q9X1L6_THEMA 2-285 B F | electron transfer flavoprotein, α subunit | R4P3F4_THEMA 286-623 C G | electron transfer flavoprotein-quinone oxidoreductase fixc | R4P168_THEMA 1-438 D H | ferredoxin-like protein | R4NRM2_THEMA 439-530 Non-standard residues in 7koe.pdb #1 --- FAD — flavin-adenine dinucleotide MQ7 — menaquinone-7 SF4 — iron/sulfur cluster > hide #!4 models > show #!1 cartoons > show #!1 atoms > select add #1 18348 atoms, 18730 bonds, 4 pseudobonds, 2308 residues, 2 models selected > show sel cartoons > show sel atoms > show sel cartoons > hide sel atoms > select ::name=""SF4"" 64 atoms, 48 bonds, 72 pseudobonds, 8 residues, 3 models selected > show sel & #!1 atoms > select ::name=""CYS"" 444 atoms, 374 bonds, 74 residues, 2 models selected > show sel & #!1 atoms > style (#!1 & sel) ball Changed 204 atom styles > color (#!1 & sel) yellow > hide #!1 models > show #!4 models > show #!1 models > hide #!1 models > hide #!4 models > show #!1 models > select clear > view > select ::name=""FAD"" 636 atoms, 696 bonds, 12 residues, 2 models selected > show sel & #!1 atoms > select clear Drag select of 51 atoms, 119 residues, 55 bonds > style sel ball Changed 909 atom styles > show sel target ab > view sel > color sel byelement > ui tool show ""Color Actions"" > color sel byhetero > color sel byelement > color sel bynucleotide > select clear > select ::name=""FAD"" 636 atoms, 696 bonds, 12 residues, 2 models selected > color (#!1 & sel) yellow > color (#!1 & sel) byhetero > select clear Drag select of 74 atoms, 259 residues, 73 bonds ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8.dev202401240123 (2024-01-24) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.7.2 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. 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: iMac Model Identifier: iMac18,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 529.140.2.0.0 OS Loader Version: 577.140.2~22 SMC Version (system): 2.39f40 Software: System Software Overview: System Version: macOS 13.6.9 (22G830) Kernel Version: Darwin 22.6.0 Time since boot: 19 days, 10 hours, 4 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 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: 1.5.15 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.52 ChimeraX-AtomicLibrary: 12.1.7 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: 2.11 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: 1.3.2 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.dev202401240123 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 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: 2.6.2 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: 1.0.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11.1 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: 1.1.2 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: 1.33.5 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 colorama: 0.4.6 comm: 0.2.1 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: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 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: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.3 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.3 MarkupSafe: 2.1.4 matplotlib: 3.8.2 matplotlib-inline: 0.1.6 msgpack: 1.0.7 ndindex: 1.7 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.26.3 openvr: 1.26.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.7 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 Pygments: 2.16.1 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3301 pyparsing: 3.1.1 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.4 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.8.1 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: 1.0.8 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.12.9 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX