id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18881 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.7.dev202309272145 (2023-09-27 21:45:56 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003682c7000 (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 0x000000034619b000 (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 0x000000020b659f00 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 1602 in remove_deleted_pointers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 123 in __init__ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 796 in __init__ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 86 in _atoms_pair File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 198 in get_prop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 2211 in _bond_intercept File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/pbgroup.py"", line 281 in first_intercept File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 725 in _position_intercepts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 692 in first_intercept File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1075 in first_intercept_children File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1058 in first_intercept File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 131 in first_intercept File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 852 in picked_object_on_segment File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 820 in picked_object File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 801 in _front_center_point File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 792 in _front_center_cofr File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 724 in _compute_center_of_rotation File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 697 in _get_cofr File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 1016 in rotate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py"", line 392 in _rotate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py"", line 354 in touchpad_two_finger_trans File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 599 in _dispatch_touch_event File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/trackpad.py"", line 130 in _collapse_touch_events File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/trackpad.py"", line 63 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 138 in invoke File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 237 in _activate File 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swapped_out=58.5M(2%) unallocated=3.1G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 2112K 32 \nColorSync 720K 37 \nCoreAnimation 2160K 115 \nCoreGraphics 64K 4 \nCoreUI image data 5120K 40 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 106 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 592K 37 \nStack 193.4M 38 \nStack Guard 56.0M 1 \nVM_ALLOCATE 248.0M 204 \nVM_ALLOCATE (reserved) 224.0M 6 reserved VM address space (unallocated)\n__AUTH 5927K 715 \n__AUTH_CONST 79.4M 963 \n__CTF 824 1 \n__DATA 36.9M 1091 \n__DATA_CONST 36.5M 1113 \n__DATA_DIRTY 2778K 343 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 646.3M 144 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.2G 1112 \n__TEXT (graphics) 150.1M 21 \n__TPRO_CONST 128K 2 \ndyld private memory 2320K 20 \nmapped file 571.2M 88 \npage table in kernel 1847K 1 \nshared memory 3232K 27 \n=========== ======= ======= \nTOTAL 5.9G 6295 \nTOTAL, minus reserved VM space 5.7G 6295 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""bf349f30d2e5c2d48a4c9d5c5af753c95604cad2"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""670ea6eb7a111748a97092a4"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""68cb4f17689c1273c25a4e6c"" }, ""deploymentId"" : 240000180 }, { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : { }, ""deploymentId"" : 240000013 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Registration file '/Users/svearikeoeverdieck/Library/Application Support/ChimeraX/registration' has expired UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9mia 9mia title: 206-3G08 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab [more info...] Chain information for 9mia #1 --- Chain | Description | UniProt A C E | GT1.1 v4.1 SOSIP gp120 | B D F | Envelope glycoprotein gp160 | Q2N0S6_9HIV1 512-664 G J O | RM20A3 heavy chain Fv | H K P | 206-3G08 heavy chain Fv | I M Q | RM20A3 light chain Fv | L N R | 206-3G08 lambda chain Fv | Non-standard residues in 9mia #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > show cartoons > hide atoms Drag select of 98 residues > select up 1095 atoms, 1116 bonds, 145 residues, 1 model selected > select up 1712 atoms, 1759 bonds, 224 residues, 1 model selected > hide sel atoms > hide sel cartoons Drag select of 99 residues > select up 2762 atoms, 2834 bonds, 360 residues, 1 model selected > select up 3424 atoms, 3518 bonds, 448 residues, 1 model selected > hide sel cartoons Drag select of 187 residues > select up 5468 atoms, 5600 bonds, 720 residues, 1 model selected > select up 6904 atoms, 7080 bonds, 910 residues, 1 model selected > hide sel cartoons Drag select of 123 residues > select up 8122 atoms, 8320 bonds, 1075 residues, 1 model selected > select up 8644 atoms, 8861 bonds, 1141 residues, 1 model selected > hide sel cartoons > color #1 #aaaca5ff > ui tool show ""Show Sequence Viewer"" > sequence chain /A /C /E Alignment identifier is 1 > select /A,C,E:69 42 atoms, 45 bonds, 3 residues, 1 model selected > select /A,C,E:69-70 57 atoms, 60 bonds, 6 residues, 1 model selected > select /A,C,E:69 42 atoms, 45 bonds, 3 residues, 1 model selected > select /A,C,E:69 42 atoms, 45 bonds, 3 residues, 1 model selected > color sel purple > show sel atoms > style sel stick Changed 42 atom styles > select sel @ select up 351 atoms, 348 bonds, 42 residues, 1 model selected > show sel atoms > style sel stick Changed 351 atom styles > color sel byhetero > select clear > open 9mia 9mia title: 206-3G08 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab [more info...] Chain information for 9mia #2 --- Chain | Description | UniProt A C E | GT1.1 v4.1 SOSIP gp120 | B D F | Envelope glycoprotein gp160 | Q2N0S6_9HIV1 512-664 G J O | RM20A3 heavy chain Fv | H K P | 206-3G08 heavy chain Fv | I M Q | RM20A3 light chain Fv | L N R | 206-3G08 lambda chain Fv | Non-standard residues in 9mia #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide #!2 models > select #1/C:253 7 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Rotamers Populating font family aliases took 149 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > swapaa interactive sel TRP rotLib Richardson.mode 9mia #1/C PRO 253: phi -77.8, psi 71.1 trans Changed 91 bond radii > select #1/C:67 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel TRP rotLib Richardson.mode 9mia #1/C ASN 67: phi -125.2, psi 149.6 trans Changed 91 bond radii > select #1/C:69 14 atoms, 15 bonds, 1 residue, 1 model selected > select sel @ select #1/A,C,E:249 30 atoms, 30 bonds, 3 residues, 1 model selected > select #1/A,C,E:249 30 atoms, 30 bonds, 3 residues, 1 model selected > select #1/A,C,E:100 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:100 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:99 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:99 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > select #1/A,C,E:185 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:185-186 51 atoms, 48 bonds, 6 residues, 1 model selected > select #1/A,C,E:186 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A,C,E:186-186A 51 atoms, 48 bonds, 6 residues, 1 model selected > select #1/A,C,E:186 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A,C,E:186 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A,C,E:234 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:234 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > color sel light sea green > select sel @ show sel & #!1 atoms > style sel & #!1 stick Changed 156 atom styles > select clear > select #1/A,C,E:267 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A,C,E:267-268 54 atoms, 51 bonds, 6 residues, 1 model selected > select #1/A,C,E:267 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A,C,E:267 27 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 27 atom styles > color sel forest green > select sel @ show sel & #!1 atoms > style sel & #!1 stick Changed 108 atom styles > color (#!1 & sel) byhetero > select up 516 atoms, 498 bonds, 60 residues, 2 models selected > show sel & #!1 atoms > style sel & #!1 stick Changed 258 atom styles > select clear > select #1/A,C,E:283 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:283 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > color sel cornflower blue > select sel @ show sel & #!1 atoms > style sel & #!1 stick Changed 165 atom styles > color (#!1 & sel) byhetero > select up 786 atoms, 762 bonds, 96 residues, 2 models selected > show sel & #!1 atoms > style sel & #!1 stick Changed 393 atom styles > select clear > select #1/P:33@OH 1 atom, 1 residue, 1 model selected > select add #1/E:283@ND2 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #1/P:33@OH #1/E:283@ND2 Distance between 9mia #1/P TYR 33 OH and /E ASN 283 ND2: 4.915Å > select #1/E:283@OD1 1 atom, 1 residue, 1 model selected > select add #1/E:477@OD2 2 atoms, 2 residues, 1 model selected > distance #1/E:283@OD1 #1/E:477@OD2 Distance between 9mia #1/E ASN 283 OD1 and ASP 477 OD2: 3.368Å > select #1/A,C,E:283 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:283 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:324 12 atoms, 9 bonds, 3 residues, 1 model selected > select #1/A,C,E:324-330 165 atoms, 165 bonds, 21 residues, 1 model selected > select #1/A,C,E:325 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:325 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > color sel purple > select sel @ show sel & #!1 atoms > select up 378 atoms, 360 bonds, 48 residues, 2 models selected > show sel & #!1 atoms > style sel & #!1 stick Changed 189 atom styles > select up 1476 atoms, 1476 bonds, 186 residues, 2 models selected > select down 378 atoms, 360 bonds, 48 residues, 2 models selected > select #1/A,C,E:329 15 atoms, 12 bonds, 3 residues, 1 model selected > select #1/A,C,E:329 15 atoms, 12 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 15 atom styles > select #1/A,C,E:397 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A,C,E:397 18 atoms, 15 bonds, 3 residues, 1 model selected > style sel stick Changed 18 atom styles > show sel atoms > select #1/A,C,E:426 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A,C,E:426 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > color sel magenta > select sel @ show sel & #!1 atoms > select up 540 atoms, 546 bonds, 54 residues, 2 models selected > select up 2334 atoms, 2370 bonds, 282 residues, 2 models selected > select down 540 atoms, 546 bonds, 54 residues, 2 models selected > show sel & #!1 atoms > style sel & #!1 stick Changed 270 atom styles > color (#!1 & sel) byhetero > select #1/A,C,E:463-464 39 atoms, 36 bonds, 6 residues, 1 model selected > select #1/A,C,E:463-464 39 atoms, 36 bonds, 6 residues, 1 model selected > select #1/A,C,E:463 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A,C,E:463 18 atoms, 15 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #1/D #1/F #2/B #2/D #2/F Alignment identifier is 1 > close #2 > ui tool show ""Show Sequence Viewer"" > sequence chain /B /D /F Alignment identifier is 1 > select /B,D,F:543-544 48 atoms, 45 bonds, 6 residues, 1 model selected > select /B,D,F:543-545 72 atoms, 69 bonds, 9 residues, 1 model selected > select /B,D,F:546 18 atoms, 15 bonds, 3 residues, 1 model selected > select /B,D,F:546 18 atoms, 15 bonds, 3 residues, 1 model selected > select /B,D,F:545 24 atoms, 21 bonds, 3 residues, 1 model selected > select /B,D,F:545 24 atoms, 21 bonds, 3 residues, 1 model selected > select /B,D,F:598 18 atoms, 15 bonds, 3 residues, 1 model selected > select /B,D,F:598 18 atoms, 15 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Registration file '/Users/svearikeoeverdieck/Library/Application Support/ChimeraX/registration' has expired UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: en_US.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: Mac14,9 Model Number: Z17G002THN/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 8 days, 21 hours, 1 minute Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 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 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.0 Babel: 2.12.1 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: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.11.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.48 ChimeraX-AtomicLibrary: 10.1 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: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309272145 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: 1.1.2 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: 1.2.1 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 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: 1.5.12 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: 1.11 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.10 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: 1.12.2 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: 1.32.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 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: 5.3.2 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 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: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 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: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.5 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX