id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16376 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.1-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 0x000000031a8ee000 (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 0x0000000204f082c0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py"", line 575 in __init__ 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 1613 in remove_deleted_pointers 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 134 in __init__ 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 1455 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2226 in process_changes File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2231 in changes File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 36 in check_for_changes File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py"", line 77 in 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/commands/cli.py"", line 3005 in command_trigger File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 144 in __exit__ 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 2899 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/ui/gui.py"", line 1522 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, 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""deploymentId"" : 240000002 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 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 > open /Users/jeff/Research/phenix/Refine_498/CrTE_refine_498_renum.pdb Summary of feedback from opening /Users/jeff/Research/phenix/Refine_498/CrTE_refine_498_renum.pdb --- warning | Cannot find LINK/SSBOND residue CYS (277 ) Chain information for CrTE_refine_498_renum.pdb #1 --- Chain | Description A | No description available > select ::name=""HOH"" 8 atoms, 8 residues, 1 model selected > show sel atoms > select clear > ui tool show ""Crystal Contacts"" > crystalcontacts #1 3 pairs of asymmetric units of CrTE_refine_498_renum.pdb contact at distance 3.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 17 0 7 0 0 0 0 1 9 0 4 1 0 0 0 1 5 0 4 0 0 0 0 1 > select #2.1 2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected > hide sel cartoons > hide sel atoms > show sel cartoons > show sel atoms > hide sel atoms > select clear > select ::name=""HOH"" 32 atoms, 32 residues, 4 models selected > show sel atoms > select clear > hide atoms > show cartoons > hide cartoons > undo > select #2.2 2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected > hide sel atoms > hide sel cartoons > select #2.3 2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected > hide sel atoms > hide sel cartoons > select clear > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > select ::name=""HOH"" 32 atoms, 32 residues, 4 models selected > show sel atoms > hide sel atoms > color sel bychain > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for CrTE_refine_498_renum.pdb_B SES surface #1.2: minimum, 0.00, mean 0.00, maximum 0.00 Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 7_B SES surface #2.1.2: minimum, 0.00, mean 0.00, maximum 0.00 Coulombic values for CrTE_refine_498_renum.pdb 1 0 0 sym 4_B SES surface #2.2.2: minimum, 0.00, mean 0.00, maximum 0.00 Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 4_B SES surface #2.3.2: minimum, 0.00, mean 0.00, maximum 0.00 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > select clear > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for CrTE_refine_498_renum.pdb_A SES surface #1.3: minimum, -14.22, mean -1.14, maximum 12.95 Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 7_A SES surface #2.1.3: minimum, -14.22, mean -1.14, maximum 12.95 Coulombic values for CrTE_refine_498_renum.pdb 1 0 0 sym 4_A SES surface #2.2.3: minimum, -14.22, mean -1.14, maximum 12.95 Coulombic values for CrTE_refine_498_renum.pdb 0 0 0 sym 4_A SES surface #2.3.3: minimum, -14.22, mean -1.14, maximum 12.95 To also show corresponding color key, enter the above coulombic command and add key true > select #2.2,2.3 2291 atoms, 290 residues, 1 model selected > hide sel surfaces > select #2.2,#2.3 Expected an objects specifier or a keyword > hide sel surfaces > select #2.3 2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected > hide sel surfaces > select clear > hide surfaces > select add #2.2 2299 atoms, 2343 bonds, 1 pseudobond, 298 residues, 2 models selected > select add #2.3 4598 atoms, 4686 bonds, 2 pseudobonds, 596 residues, 6 models selected > close #2.2 > close #2.3 > hide #!2 models > ui tool show ""Selection Inspector"" > setattr =sel p display false Assigning display attribute to 1 item > undo > redo No redo action is available > redo No redo action is available > hide #!2 models > select clear Drag select of 19 residues > ui tool show ""Selection Inspector"" > show sel atoms > hide sel atoms > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2.1/A Alignment identifier is 1 > select #1:266,268,270 26 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > select clear > select #1:138 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select clear > select #1:306 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #1 cornflower blue > select clear > color #!1 byhetero > select clear > color #1 #f7fff8ff > color #1 #f6fff8ff > color #1 #f5fff8ff > color #1 #eefff9ff > color #1 #e7fffbff > color #1 #e2fffcff > color #1 #d5ffffff > color #1 #cbfcffff > color #1 #c9fbffff > color #1 #c2f9ffff > color #1 #baf6ffff > color #1 #b7f5ffff > color #1 #b3f2ffff > color #1 #b2f2ffff > color #1 #aff1ffff > color #1 #acefffff > color #1 #aaefffff > color #1 #a9efffff > color #1 #a8eeffff > color #1 #a7eeffff > color #1 #a5edffff > color #1 #a2ebffff > color #1 #a1eaffff > color #1 #9fe8ffff > color #1 #9fe7ffff > color #1 #9ee6ffff > color #1 #9ee5ffff > color #1 #9de3ffff > color #1 #9de2ffff > color #1 #9de1ffff > color #1 #9de0ffff > color #1 #9dddffff > color #1 #9ddcffff > color #1 #9cd6ffff > color #1 #9bd1ffff > color #1 #9bcfffff > color #1 #9acdffff > color #1 #9acbffff > color #1 #9acaffff > color #1 #9ac8ffff > color #1 #9ac7ffff > color #1 #99c6ffff > color #1 #99c5ffff > color #1 #99c4ffff > color #1 #98c3ffff > color #1 #98c2ffff > color #1 #97c0ffff > color #1 #97bfffff > color #1 #97beffff > color #1 #96bdffff > color #1 #96bcffff > color #1 #96bbffff > color #1 #95bcffff > color #1 #95beffff > color #1 #93c8ffff > color #1 #92ccffff > color #1 #8fd1ffff > color #1 #8dd3ffff > color #1 #8bd4ffff > color #1 #89d5ffff > color #1 #86d6ffff > color #1 #81d7ffff > color #1 #7fd7ffff > color #1 #7dd7ffff > color #1 #7dd8ffff > color #1 #7cd8ffff > color #1 #7cd9ffff > color #1 #78dfffff > color #1 #76e2ffff > color #1 #73e4ffff > color #1 #71e7ffff > color #1 #6eeaffff > color #1 #6decffff > color #1 #6aefffff > color #1 #69f1ffff > color #1 #68f2ffff > color #1 #68f1ffff > color #1 #69f1ffff > color #1 #6aeeffff > color #1 #6aedffff > color #1 #6beaffff > color #1 #6ce9ffff > color #1 #6ee6ffff > color #1 #6fe4ffff > color #1 #70e4ffff > color #1 #70e3ffff > color #1 #71e3ffff > color #1 #70e1ffff > color #1 #70deffff > color #1 #70dcffff > color #1 #6fdaffff > color #1 #6fd7ffff > color #1 #6fd6ffff > color #1 #6ed4ffff > color #1 #6ed3ffff > color #1 #6ed4ffff > color #1 #6dd4ffff > color #1 #6bd5ffff > color #1 #6ad6ffff > color #1 #69d6ffff > color #1 #69d7ffff > color #1 #68d8ffff > color #1 #68d9ffff > color #1 #67daffff > color #1 #67dbffff > color #1 #67dcffff > color #1 #66dcffff > color #1 #67dcffff > color #1 #66ddffff > color #1 #66deffff > color #1 #65dfffff > color #1 #65e0ffff > color #1 #65e1ffff > color #1 #64e2ffff > color #1 #64e4ffff > color #1 #64e6ffff > color #1 #63e8ffff > color #1 #61ecffff > color #1 #62edffff > color #1 #61eeffff > color #1 #61efffff > color #1 #62f4ffff > color #1 #62f7ffff > color #1 #63fbffff > color #1 #63fdffff > color #1 #64fdffff > color #1 #63fdffff > color #1 #63feffff > color #1 #5fffffff > color #1 #5cfffeff > color #1 #55fffbff > color #1 #4cfff8ff > color #1 #4afff7ff > color #1 #45fff6ff > color #1 #43fff6ff > color #1 #40fff5ff > color #1 #3efff5ff > color #1 #3cfff5ff > color #1 #3bfff5ff > color #1 #37fff5ff > color #1 #35fff5ff > color #1 #33fff5ff > color #1 #31fff5ff > color #1 #2ffff5ff > color #1 #2efff5ff > color #1 #2dfff5ff > color #1 #2cfff5ff > color #1 #2afff5ff > color #1 #29fff4ff > color #1 #28fff4ff > color #1 #27fff3ff > color #1 #26fff1ff > color #1 #26fff0ff > color #1 #26ffefff > color #1 #25ffeeff > color #1 #25ffedff > color #1 #25ffecff > color #1 #26ffebff > color #1 #26ffeaff > color #1 #2affe1ff > color #1 #34ffcbff > color #1 #3dffb5ff > color #1 #3fffb2ff > color #1 #41ffaeff > color #1 #42ffaeff > color #1 #43ffaeff > color #1 #47ffb0ff > color #1 #49ffb2ff > color #1 #4fffb6ff > color #1 #54ffbbff > color #1 #56ffbcff > color #1 #5cffbfff > color #1 #64ffc0ff > color #1 #68ffc1ff > color #1 #75ffc2ff > color #1 #7affc3ff > color #1 #80ffc3ff > color #1 #83ffc3ff > color #1 #85ffc3ff > color #1 #85ffc1ff > color #1 #86ffc1ff > color #1 #87ffc1ff > color #1 #89ffbeff > color #1 #8bffbdff > color #1 #8bffbcff > color #1 #8bffbbff > color #1 #8affb9ff > color #1 #88ffb7ff > color #1 #88ffb5ff > color #1 #86ffb4ff > color #1 #86ffb2ff > color #1 #85ffb1ff > color #1 #84ffb0ff > color #1 #83ffb0ff > color #1 #83ffafff > color #1 #82ffaeff > color #1 #81ffaeff > color #1 #82ffafff > color #1 #82ffb0ff > color #1 #83ffb1ff > color #1 #83ffb3ff > color #1 #84ffb4ff > color #1 #84ffb5ff > color #1 #84ffb6ff > color #1 #84ffb7ff > color #1 #84ffb8ff > color #1 #85ffb8ff > color #1 #85ffb9ff > color #1 #85ffbaff > color #1 #86ffbaff > color #1 #86ffbbff > color #1 #86ffbcff > color #1 #86ffbdff > color #1 #87ffbdff > color #1 #87ffbeff > color #1 #87ffbfff > color #1 #88ffbfff > color #1 #88ffc0ff > color #1 #89ffc1ff > color #1 #8affc3ff > color #1 #8affc4ff > color #1 #8bffc7ff > color #1 #8cffc9ff > color #1 #8dffcaff > color #1 #8dffc9ff > color #1 #8cffc5ff > color #1 #8bffc1ff > color #1 #8bffc0ff > color #1 #8affbfff > color #1 #8affbeff > color #1 #8affbdff > color #1 #8bffbdff > color #1 #8bffbcff > color #1 #8bffbaff ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 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 Metal - 83 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple 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: MacBookPro18,3 Model Number: MKGQ3LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8419.60.44 OS Loader Version: 8419.60.44 Software: System Software Overview: System Version: macOS 13.1 (22C65) Kernel Version: Darwin 22.2.0 Time since boot: 22 days, 18 hours, 18 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2518D: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes 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-Clipper: 0.22.4 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