id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14687 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.4-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000135ff000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000011e794600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py"", line 58 in _commit_removals File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py"", line 33 in __exit__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py"", line 64 in __iter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py"", line 519 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py"", line 519 in rebuild File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 65 in draw_new_frame File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56) 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All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > open 4YIT Summary of feedback from opening 4YIT fetched from pdb --- notes | Fetching compressed mmCIF 4yit from http://files.rcsb.org/download/4yit.cif Fetching CCD CA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif 4yit title: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA [more info...] Chain information for 4yit #1 --- Chain | Description A D | Meganuclease I-AabMI B | DNA (25-MER) C | DNA (25-MER) E | DNA (25MER) F | DNA (25-MER) Non-standard residues in 4yit #1 --- CA — calcium ion 4yit mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > show cartoons > hide target a > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 6138 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > select /E 485 atoms, 541 bonds, 25 residues, 1 model selected > select /A 2074 atoms, 2106 bonds, 10 pseudobonds, 281 residues, 3 models selected > select /B 506 atoms, 562 bonds, 28 residues, 1 model selected > select /C 524 atoms, 586 bonds, 27 residues, 1 model selected > select add /A 2598 atoms, 2692 bonds, 10 pseudobonds, 308 residues, 3 models selected > select add /B 3104 atoms, 3254 bonds, 10 pseudobonds, 336 residues, 3 models selected > save /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA.pdb selectedOnly > true relModel #1 > close session > open /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA.pdb Summary of feedback from opening /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA.pdb --- warnings | Start residue of secondary structure not found: HELIX 12 12 PRO D 3 GLU D 13 1 11 Start residue of secondary structure not found: HELIX 13 13 HIS D 40 LYS D 42 1 3 Start residue of secondary structure not found: HELIX 14 14 ASP D 43 LYS D 55 1 13 Start residue of secondary structure not found: HELIX 15 15 THR D 73 TYR D 87 1 15 Start residue of secondary structure not found: HELIX 16 16 LYS D 92 ASN D 109 1 18 17 messages similar to the above omitted Cannot find LINK/SSBOND residue ASP (209 ) Cannot find LINK/SSBOND residue GLY (12 ) Cannot find LINK/SSBOND residue GLU (13 ) Cannot find LINK/SSBOND residue ALA (168 ) Cannot find LINK/SSBOND residue GLU (169 ) 4 messages similar to the above omitted Chain information for chainA+DNA.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > select add /B 506 atoms, 562 bonds, 28 residues, 1 model selected > select add /C 1030 atoms, 1148 bonds, 55 residues, 1 model selected > show sel target ab > nucleotides sel fill > cartoon hide sel > select /A 2074 atoms, 2106 bonds, 10 pseudobonds, 281 residues, 3 models selected > select helix 1084 atoms, 1099 bonds, 142 residues, 1 model selected > color sel red > select strand 474 atoms, 478 bonds, 58 residues, 1 model selected > color sel yellow > save /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA_colored.pdb > relModel #1 > open 1lws Summary of feedback from opening 1lws fetched from pdb --- note | Fetching compressed mmCIF 1lws from http://files.rcsb.org/download/1lws.cif 1lws title: Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence [more info...] Chain information for 1lws #2 --- Chain | Description | UniProt A | ENDONUCLEASE PI-SCEI | VATA_YEAST 1-454 B | PI-SceI DNA recognition region top strand | C | PI-SceI DNA recognition region bottom strand | Non-standard residues in 1lws #2 --- CA — calcium ion > ui tool show Matchmaker > matchmaker #!2 to #1/A pairing bs Parameters --- Chain pairing | bs 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 chainA+DNA.pdb, chain A (#1) with 1lws, chain A (#2), sequence alignment score = 47.1 RMSD between 10 pruned atom pairs is 1.368 angstroms; (across all 173 pairs: 28.731) Drag select of 10 residues > select #2/C 682 atoms, 760 bonds, 34 residues, 1 model selected > select add #1/C 1206 atoms, 1346 bonds, 61 residues, 2 models selected > cartoon hide sel > select add #1/B 1712 atoms, 1908 bonds, 89 residues, 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right rotate > lighting soft > lighting simple > lighting full > lighting soft > lighting simple > set bgColor white > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select add #2 5786 atoms, 6130 bonds, 98 pseudobonds, 552 residues, 5 models selected > select subtract #2 1030 atoms, 1148 bonds, 55 residues, 1 model selected > select add #1 3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected > select subtract #1 Nothing selected > select add #1 3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected > select add #2 7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected > select subtract #2 3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected > select add #2 7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected > select subtract #2 3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected > select add #2 7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select subtract #2 3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected > select add #2 7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected > select subtract #1 4756 atoms, 4982 bonds, 98 pseudobonds, 497 residues, 4 models selected > select add #1 7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected > select subtract #1 4756 atoms, 4982 bonds, 98 pseudobonds, 497 residues, 4 models selected > select add #1 7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected > select subtract #1 4756 atoms, 4982 bonds, 98 pseudobonds, 497 residues, 4 models selected > select subtract #2 Nothing selected > log metadata #1 No models had metadata > log chains #1 Chain information for chainA+DNA.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > close #1 > show target m > log metadata #2 Metadata for 1lws #2 --- Title | Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence Citations | Moure, C.M., Gimble, F.S., Quiocho, F.A. (2002). Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Nat.Struct.Biol., 9, 764-770. PMID: 12219083. DOI: 10.1038/nsb840 Duan, X., Gimble, F.S., Quiocho, F.A. (1997). Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell(Cambridge,Mass.), 89, 555-564. DOI: 10.1016/S0092-8674(00)80237-8 Non-standard residue | CA — calcium ion Gene source | Saccharomyces cerevisiae (baker's yeast) Experimental method | X-ray diffraction Resolution | 3.5Å > log chains #2 Chain information for 1lws #2 --- Chain | Description | UniProt A | ENDONUCLEASE PI-SCEI | VATA_YEAST 1-454 B | PI-SceI DNA recognition region top strand | C | PI-SceI DNA recognition region bottom strand | > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show cartoons > view #2 clip false > open /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA_colored.pdb Chain information for chainA+DNA_colored.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > select helix 2087 atoms, 2107 bonds, 268 residues, 2 models selected ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.54 OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine OpenGL vendor: ATI Technologies 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: iMac19,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Memory: 16 GB System Firmware Version: 1731.120.8.0.0 OS Loader Version: 540.120.3~6 SMC Version (system): 2.46f13 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 24 days 22:12 Graphics/Displays: Radeon Pro 575X: Chipset Model: Radeon Pro 575X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c4 ROM Revision: 113-D0008A-042 VBIOS Version: 113-D0008A14GP-003 EFI Driver Version: 01.B1.042 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) 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: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 1.3.2 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: 1.7.1 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: 1.1.3 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: 1.1.8 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: 2.6.1 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: 1.5.14 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: 1.13.1 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: 1.1 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: 1.12.4 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: 1.33.3 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: 0.38 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: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 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: 5.9.5 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: 25.1.2 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: 1.0.8 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: 2023.7.18 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