id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18308 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.5-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 Current thread 0x0000000111429600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 907 in atomspec_atoms File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 627 in _add_model_parts File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 476 in _check File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 470 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 612 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 455 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1004 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1001 in evaluate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1091 in evaluate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 36 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 71 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2499 in _parse_arg File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2640 in _process_positional_arguments File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2864 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 303 in run_matchmaker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 171 in 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.pdb_lib._load_libs, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/DALI > hits/7ml0.cif"" format mmcif 7ml0.cif title: RNA polymerase II pre-initiation complex (PIC1) [more info...] Chain information for 7ml0.cif #1 --- Chain | Description | UniProt 0 | General transcription and DNA repair factor IIH helicase subunit XPD | A0A6A5Q1C1_YEASX 1-778 1 | DNA-directed RNA polymerase subunit | 2 | RNA polymerase II transcription factor B subunit 2 | A0A6A5Q2X3_YEASX 1-513 3 | BJ4_G0050160.mRNA.1.CDS.1 | A0A7I9BTI9_YEASX 1-321 4 | DNA-directed RNA polymerase II subunit RPB4 | 5 | General transcription and DNA repair factor IIH subunit TFB5 | TFB5_YEAST 1-72 6 | General transcription and DNA repair factor IIH subunit SSL1 | 7 | General transcription and DNA repair factor IIH helicase subunit XPB | RAD25_YEAST 1-843 A | DNA-directed RNA polymerase subunit | A0A6A5Q1P2_YEASX 1-1733 B | DNA-directed RNA polymerase subunit beta | A0A6A5Q4H2_YEASX 1-1224 C | DNA-directed RNA polymerase II subunit RPB3 | A0A6A5Q0Z3_YEASX 1-318 D | DNA-directed RNA polymerase II subunit RPB4 | A0A6A5PTI6_YEASX 1-221 E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | A0A6A5Q456_YEASX 1-215 F | DNA-directed RNA polymerases I,II,and III subunit RPABC2 | A0A6L0ZRI7_YEASX 1-155 G | DNA-directed RNA polymerase II subunit RPB7 | A0A6A5Q270_YEASX 1-171 H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | A0A6A5Q8C2_YEASX 1-146 I | DNA-directed RNA polymerase II subunit RPB9 | A0A7I9EWC2_YEASX 1-122 J | DNA-directed RNA polymerases II subunit RPABC5 | A0A6A5Q7Q6_YEASX 1-70 K | DNA-directed RNA polymerase II subunit RPB11 | A0A6A5Q7A1_YEASX 1-120 L | DNA-directed RNA polymerases II subunit RPABC4 | A0A6A5PY05_YEASX 1-70 M | Transcription initiation factor IIB | TF2B_YEAST 1-345 N | non-template strand DNA | O | TATA-box-binding protein | TBP_YEAST 1-240 Q | Transcription initiation factor IIF subunit alpha | T2FA_YEAST 1-735 R | Transcription initiation factor IIF subunit beta | A0A6A5PZ00_YEASX 1-400 T | template strand DNA | W | Transcription initiation factor IIE subunit alpha | A0A6A5PTU5_YEASX 1-482 X | Transcription initiation factor IIE subunit beta | A0A6A5PS93_YEASX 1-328 Non-standard residues in 7ml0.cif #1 --- MG — magnesium ion SF4 — iron/sulfur cluster ZN — zinc ion > split #1 Split 7ml0.cif (#1) into 28 models Chain information for 7ml0.cif 0 #1.1 --- Chain | Description 0 | No description available Chain information for 7ml0.cif 1 #1.2 --- Chain | Description 1 | No description available Chain information for 7ml0.cif 2 #1.3 --- Chain | Description 2 | No description available Chain information for 7ml0.cif 3 #1.4 --- Chain | Description 3 | No description available Chain information for 7ml0.cif 4 #1.5 --- Chain | Description 4 | No description available Chain information for 7ml0.cif 5 #1.6 --- Chain | Description 5 | No description available Chain information for 7ml0.cif 6 #1.7 --- Chain | Description 6 | No description available Chain information for 7ml0.cif 7 #1.8 --- Chain | Description 7 | No description available Chain information for 7ml0.cif A #1.9 --- Chain | Description A | No description available Chain information for 7ml0.cif B #1.10 --- Chain | Description B | No description available Chain information for 7ml0.cif C #1.11 --- Chain | Description C | No description available Chain information for 7ml0.cif D #1.12 --- Chain | Description D | No description available Chain information for 7ml0.cif E #1.13 --- Chain | Description E | No description available Chain information for 7ml0.cif F #1.14 --- Chain | Description F | No description available Chain information for 7ml0.cif G #1.15 --- Chain | Description G | No description available Chain information for 7ml0.cif H #1.16 --- Chain | Description H | No description available Chain information for 7ml0.cif I #1.17 --- Chain | Description I | No description available Chain information for 7ml0.cif J #1.18 --- Chain | Description J | No description available Chain information for 7ml0.cif K #1.19 --- Chain | Description K | No description available Chain information for 7ml0.cif L #1.20 --- Chain | Description L | No description available Chain information for 7ml0.cif M #1.21 --- Chain | Description M | No description available Chain information for 7ml0.cif N #1.22 --- Chain | Description N | No description available Chain information for 7ml0.cif O #1.23 --- Chain | Description O | No description available Chain information for 7ml0.cif Q #1.24 --- Chain | Description Q | No description available Chain information for 7ml0.cif R #1.25 --- Chain | Description R | No description available Chain information for 7ml0.cif T #1.26 --- Chain | Description T | No description available Chain information for 7ml0.cif W #1.27 --- Chain | Description W | No description available Chain information for 7ml0.cif X #1.28 --- Chain | Description X | No description available > show cartoons > hide atoms > select add #1.2 2415 atoms, 2448 bonds, 1 pseudobond, 367 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > select add #1.1 8522 atoms, 8676 bonds, 7 pseudobonds, 1121 residues, 5 models selected > select subtract #1.2 6107 atoms, 6228 bonds, 6 pseudobonds, 754 residues, 3 models selected > select subtract #1.1 Nothing selected > select add #1.2 2415 atoms, 2448 bonds, 1 pseudobond, 367 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1.2/1 Alignment identifier is 1.2/1 > select #1.2/1:639 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.2/1 2415 atoms, 2448 bonds, 1 pseudobond, 367 residues, 2 models selected > select add #1 64214 atoms, 65571 bonds, 108 pseudobonds, 8257 residues, 54 models selected > hide #!1.1 models > select subtract #1 Nothing selected > hide #!1.3 models > hide #!1.4 models > hide #!1.5 models > hide #1.6 models > hide #!1.7 models > hide #!1.8 models > hide #!1.9 models > hide #!1.11 models > select #1.2/1:281 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1.2/1:281-289 85 atoms, 90 bonds, 9 residues, 1 model selected > select #1.2/1:541 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.2/1:541-553 79 atoms, 78 bonds, 13 residues, 1 model selected > select #1.2/1:540 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.2/1:540-639 585 atoms, 591 bonds, 1 pseudobond, 95 residues, 2 models selected > select #1.2/1:591-639 288 atoms, 290 bonds, 49 residues, 1 model selected > select #1.2/1:537-639 600 atoms, 606 bonds, 1 pseudobond, 98 residues, 2 models selected > close #1.11 > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/DALI > hits/2q8g.cif"" 2q8g.cif title: Structure of pyruvate dehydrogenase kinase isoform 1 in complex with glucose- lowering drug AZD7545 [more info...] Chain information for 2q8g.cif #2 --- Chain | Description | UniProt A | [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1 | PDK1_HUMAN 30-436 Non-standard residues in 2q8g.cif #2 --- AZX — 4-[(3-chloro-4-{[(2R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoyl]amino}phenyl)sulfonyl]-N,N-dimethylbenzamide K — potassium ion 2q8g.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly > close #1.9 > close > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/DALI > hits/2q8g.cif"" 2q8g.cif title: Structure of pyruvate dehydrogenase kinase isoform 1 in complex with glucose- lowering drug AZD7545 [more info...] Chain information for 2q8g.cif #1 --- Chain | Description | UniProt A | [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1 | PDK1_HUMAN 30-436 Non-standard residues in 2q8g.cif #1 --- AZX — 4-[(3-chloro-4-{[(2R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoyl]amino}phenyl)sulfonyl]-N,N-dimethylbenzamide K — potassium ion 2q8g.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:41 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:41-197 1268 atoms, 1294 bonds, 1 pseudobond, 155 residues, 2 models selected > select > /A:41-51,58-68,71-95,98-123,131-149,151-203,225-245,269-292,324-333,357-369,404-412 1840 atoms, 1876 bonds, 1 pseudobond, 220 residues, 2 models selected > select clear > select /A:41-246 1583 atoms, 1615 bonds, 2 pseudobonds, 194 residues, 2 models selected > select clear > select /A:41-203 1315 atoms, 1343 bonds, 1 pseudobond, 161 residues, 2 models selected > close > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1 > truncating variants by > themselves/fold_setbp1_201_transcript_1_p_ala75glyfsx3/fold_setbp1_201_transcript_1_p_ala75glyfsx3_model_0.cif"" Chain information for fold_setbp1_201_transcript_1_p_ala75glyfsx3_model_0.cif #1 --- Chain | Description A | . > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1 > truncating variants by > themselves/fold_setbp1_201_transcript_1_p_gly15argfsx47/fold_setbp1_201_transcript_1_p_gly15argfsx47_model_0.cif"" Chain information for fold_setbp1_201_transcript_1_p_gly15argfsx47_model_0.cif #2 --- Chain | Description A | . > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1 > truncating variants by > themselves/fold_setbp1_201_transcript_1_p_ile822tyrfs_13/fold_setbp1_201_transcript_1_p_ile822tyrfs_13_model_0.cif"" Chain information for fold_setbp1_201_transcript_1_p_ile822tyrfs_13_model_0.cif #3 --- Chain | Description A | . > open ""/Users/miguelberbeirasantana/Desktop/setbp1_structure/SETBP1 > truncating variants by > themselves/fold_setbp1_201_transcript_1_p_lys693profs_86/fold_setbp1_201_transcript_1_p_lys693profs_86_model_0.cif"" Chain information for fold_setbp1_201_transcript_1_p_lys693profs_86_model_0.cif #4 --- Chain | Description A | . > ui tool show Matchmaker ===== 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 INTEL-18.8.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine 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: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6.5 (21G531) Kernel Version: Darwin 21.6.0 Time since boot: 3:45 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No 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 all ChimeraX