id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14937 Crash in python_instances_of_class chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6.3-x86_64-i386-64bit ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000116ec000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700007e06000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff85fb85780 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 44 in python_instances_of_class File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 149 in combine File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py"", line 522 in bind File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py"", line 376 in cn_peptide_bond File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/cmd.py"", line 205 in cmd_join_peptide File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2904 in run File ""/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py"", line 774 in _jm_apply_cb File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py"", line 1193 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 280 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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\nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 1440K 8 \nCG image 192K 35 \nColorSync 264K 30 \nCoreAnimation 172K 23 \nCoreGraphics 32K 5 \nCoreServices 624K 2 \nCoreUI image data 1992K 30 \nFoundation 40K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 449.8M 668 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 168K 42 \nStack 202.8M 43 \nStack Guard 56.0M 1 \nVM_ALLOCATE 222.1M 271 \nVM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 42.2M 788 \n__DATA_CONST 62.2M 453 \n__DATA_DIRTY 1850K 236 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 202.5M 157 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 992.0M 796 \ndyld private memory 292K 4 \nmapped file 519.9M 83 \nshared memory 3504K 28 \n=========== ======= ======= \nTOTAL 3.2G 3737 \nTOTAL, minus reserved VM space 2.8G 3737 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""3da9e29b85ea84ba98020a51ab4e357a6a596e69"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000368 } ], ""experiments"" : [ { ""treatmentId"" : ""130776ea-444f-4cb4-8def-f71b4f47391b"", ""experimentId"" : ""66105e203b960674f9490906"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/yingyingjin/Box Sync/Alpha-S/NAC PDB > build/NAC_rebuild/102723_tutorial/NAC_cylindrin.pdb"" Chain information for NAC_cylindrin.pdb --- Chain | Description 1.1/? 1.2/? 1.3/? 1.4/? 1.5/? 1.6/? | No description available > open ""/Users/yingyingjin/Box Sync/Alpha-S/NAC PDB > build/NAC_rebuild/102723_tutorial/preNAC_cylindrin.pdb"" Chain information for preNAC_cylindrin.pdb --- Chain | Description 2.1/? 2.2/? 2.3/? 2.4/? 2.5/? 2.6/? | No description available > show cartoons > hide atoms > hide #2.1 models > hide #2.3 models > hide #2.5 models > show #2.5 models > hide #2.4 models > show #2.4 models > hide #2.6 models > show #2.6 models > hide #2.5 models > show #2.5 models > hide #2.6 models > show #2.6 models > hide #2.2 models > hide #1.1 models > show #1.1 models > hide #1.1 models > hide #1.3 models > show #1.3 models > hide #1.3 models > hide #1.5 models > show #1.5 models > hide #1.4 models > show #1.4 models > hide #1.6 models > show #1.6 models > show #1.1 models > hide #1.1 models > hide #1.2 models > select clear Drag select of 63 residues > save ""/Users/yingyingjin/Desktop/NAC_paper/structure PDB/NACpreNACmodel.pdb"" > displayedOnly true Drag select of 63 residues > select clear > save ""/Users/yingyingjin/Desktop/NAC_paper/structure PDB/NACpreNACmodel.pdb"" > selectedOnly true > ui tool show ""Change Chain IDs"" > select add #1.1 139 atoms, 138 bonds, 11 residues, 1 model selected > select subtract #1.1 Nothing selected > save ""/Users/yingyingjin/Desktop/NAC_paper/structure > PDB/NACpreNACmodel.mol2"" > select add #1.1 139 atoms, 138 bonds, 11 residues, 1 model selected > select add #1.2 278 atoms, 276 bonds, 22 residues, 2 models selected > select add #1.3 417 atoms, 414 bonds, 33 residues, 3 models selected > select add #2.1 551 atoms, 548 bonds, 43 residues, 4 models selected > select add #2.2 685 atoms, 682 bonds, 53 residues, 5 models selected > select subtract #2.2 551 atoms, 548 bonds, 43 residues, 4 models selected > select add #2.2 685 atoms, 682 bonds, 53 residues, 5 models selected > select add #2.3 819 atoms, 816 bonds, 63 residues, 6 models selected > hide #1.4 models > hide #1.5 models > hide #1.6 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > delete atoms #!1-2 > delete bonds #!1-2 > show #2.1 models > show #2.2 models > show #2.3 models > show #1.1 models > show #1.2 models > show #1.3 models > delete atoms sel > delete bonds sel > show #1.4 models > show #1.5 models > show #1.6 models > show #2.4 models > show #2.5 models > show #2.6 models > save ""/Users/yingyingjin/Desktop/NAC_paper/structure > PDB/NACpreNACmodel.mol2"" > save ""/Users/yingyingjin/Desktop/NAC_paper/structure PDB/nacprenac.cxs"" > ui tool show ""Change Chain IDs"" > changechains A Chain IDs of 63 residues changed > changechains A Chain IDs of 0 residues changed > changechains #* B Chain IDs of 63 residues changed > select add #1.4 139 atoms, 138 bonds, 11 residues, 1 model selected > changechains sel A Chain IDs of 11 residues changed > select subtract #1.4 Nothing selected > select add #1.5 139 atoms, 138 bonds, 11 residues, 1 model selected > changechains sel B Chain IDs of 0 residues changed > changechains sel B Chain IDs of 0 residues changed > select subtract #1.5 Nothing selected > select add #1.4 139 atoms, 138 bonds, 11 residues, 1 model selected > select add #1.5 278 atoms, 276 bonds, 22 residues, 2 models selected > select subtract #1.5 139 atoms, 138 bonds, 11 residues, 1 model selected > select add #2.4 273 atoms, 272 bonds, 21 residues, 2 models selected > select subtract #2.4 139 atoms, 138 bonds, 11 residues, 1 model selected > select add #2.5 273 atoms, 272 bonds, 21 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel A Chain IDs of 10 residues changed > select subtract #1.4 134 atoms, 134 bonds, 10 residues, 1 model selected > select subtract #2.5 Nothing selected > select add #1.5 139 atoms, 138 bonds, 11 residues, 1 model selected > select add #2.4 273 atoms, 272 bonds, 21 residues, 2 models selected > select subtract #2.4 139 atoms, 138 bonds, 11 residues, 1 model selected > select add #2.6 273 atoms, 272 bonds, 21 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel B Chain IDs of 0 residues changed > select add #2.5 407 atoms, 406 bonds, 31 residues, 3 models selected > select subtract #2.5 273 atoms, 272 bonds, 21 residues, 2 models selected > select add #2.4 407 atoms, 406 bonds, 31 residues, 3 models selected > select subtract #2.6 273 atoms, 272 bonds, 21 residues, 2 models selected > select subtract #1.5 134 atoms, 134 bonds, 10 residues, 1 model selected > select add #1.6 273 atoms, 272 bonds, 21 residues, 2 models selected > ui tool show ""Change Chain IDs"" > changechains sel C Chain IDs of 21 residues changed > changechains sel C Chain IDs of 0 residues changed > ui tool show ""Build Structure"" > build start peptide ""custom built"" EKTKEQVTNVG -57.0,-47.0 -57.0,-47.0 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 > -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack Chain information for custom built #3 --- Chain | Description A | No description available > select add #3 359 atoms, 357 bonds, 32 residues, 3 models selected > select add #1 637 atoms, 633 bonds, 54 residues, 6 models selected > select subtract #1 220 atoms, 219 bonds, 21 residues, 2 models selected > select add #2 488 atoms, 487 bonds, 41 residues, 5 models selected > select subtract #2.4 354 atoms, 353 bonds, 31 residues, 4 models selected > select subtract #2.5 220 atoms, 219 bonds, 21 residues, 3 models selected > select subtract #2.6 86 atoms, 85 bonds, 11 residues, 2 models selected > select add #2 488 atoms, 487 bonds, 41 residues, 5 models selected > select subtract #2 86 atoms, 85 bonds, 11 residues, 1 model selected > ui mousemode right select > ui mousemode right translate > select clear > select add #3 86 atoms, 85 bonds, 11 residues, 1 model selected > ui mousemode right translate > hide #!1 models > hide #!2 models > select clear Drag select of 11 residues > show #!2 models > hide #!2 models > show #!2 models Drag select of 1 residues Alignment identifier is 3/A > show #!1 models Drag select of 1 residues Alignment identifier is 1.6/C Drag select of 3 residues > select #1.6/C:2-3 26 atoms, 25 bonds, 2 residues, 1 model selected Drag select of 2 residues > ui tool show ""Build Structure"" > build join peptide sel length 1.33 omega 180 phi -120 move small > build start peptide ""custom built"" EKTKEQVTNVG -57.0,-70.0 -57.0,-70.0 > -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 > -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 rotLib Dunbrack Chain information for custom built #3 --- Chain | Description A | No description available Drag select of 2 residues Alignment identifier is 1.4/A Alignment identifier is 3/A > ui tool show ""Build Structure"" > build join peptide sel length 1.33 omega 180 phi -120 move small > build start peptide ""custom built"" EKTKEQVTNVG -57.0,-70.0 -57.0,-70.0 > -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 > -57.0,-70.0 -57.0,-70.0 -57.0,-70.0 rotLib Dunbrack Chain information for custom built #3 --- Chain | Description A | No description available Drag select of 5 residues Drag select of 3 residues > select add #3 114 atoms, 85 bonds, 13 residues, 2 models selected > select subtract #3 28 atoms, 2 residues, 1 model selected > select add #3 114 atoms, 85 bonds, 13 residues, 2 models selected > hide #3 models > select subtract #3 28 atoms, 2 residues, 1 model selected > hide #!1 models > show #!1 models > build start peptide ""custom built"" EKTKEQVTNVG -119.0,113.0 -119.0,113.0 > -119.0,113.0 -119.0,113.0 -119.0,113.0 -119.0,113.0 -119.0,113.0 > -119.0,113.0 -119.0,113.0 -119.0,113.0 -119.0,113.0 rotLib Dunbrack Chain information for custom built #4 --- Chain | Description A | No description available Drag select of 2 residues Alignment identifier is 1.5/B Alignment identifier is 4/A > build join peptide sel length 1.33 omega 180 phi -120 move small ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0) OS Loader Version: 577.140.2~22 Software: System Software Overview: System Version: macOS 13.6.3 (22G436) Kernel Version: Darwin 22.6.0 Time since boot: 20 days, 5 hours, 54 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: 27GL650F: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 72.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 909NTZN6Y069 Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI LG FULL HD: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Installed Packages: alabaster: 0.7.16 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: 1.1.1 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: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.2 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: 2.12.1 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.dev202403210048 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: 2.1.3 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: 2.14 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: 1.13.3 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 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: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.3 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: 2.5 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: 1.37.1 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: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 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: 5.7.2 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: 3.8.3 matplotlib-inline: 0.1.6 msgpack: 1.0.8 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: 1.10.0 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: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 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: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 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 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX