id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17410 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.7.2-arm64-arm-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 0x000000035d05f000 (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 0x0000000204854f80 (most recent call first): Garbage-collecting File 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""/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/core/updateloop.py"", line 69 in draw_new_frame File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File 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\n__DATA 25.3M 772 \n__DATA_CONST 42.6M 786 \n__DATA_DIRTY 1880K 228 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 555.1M 147 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 963.6M 803 \ndyld private memory 464K 4 \nmapped file 230.4M 57 \nshared memory 3200K 25 \n=========== ======= ======= \nTOTAL 4.7G 4421 \nTOTAL, minus reserved VM space 4.5G 4421 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""18281ce59e3c19da021e54f6a3e38836c2a0abaa"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final- > files/M_PRO-120538_.pdb Chain information for M_PRO-120538_.pdb #1 --- Chain | Description H | No description available L | No description available M | No description available > save /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/M_PRO-120538.cif relModel #1 Not saving entity_poly_seq for non-authoritative sequences > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final- > files/M_PRO-120538.cif Summary of feedback from opening /Users/pfeliciano/Library/CloudStorage/OneDrive- GenerateBiomedicines/Documents/Projects/Outer- Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final- files/M_PRO-120538.cif --- warnings | Unknown polymer entity '1' near line 124 Unknown polymer entity '2' near line 1624 Unknown polymer entity '3' near line 3177 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for M_PRO-120538.cif #2 --- Chain | Description H | No description available L | No description available M | No description available > hide #!1 models > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final- > files/M_PRO-120538.mrc Opened M_PRO-120538.mrc as #3, grid size 300,300,300, pixel 0.81, shown at level 0.0735, step 2, values float32 > volume #3 step 1 > volume #3 level 0.22 > surface dust #3 size 8.1 > transparency 50 > close > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final- > files/M_PRO-120549_.pdb Chain information for M_PRO-120549_.pdb #1 --- Chain | Description H | No description available L | No description available M | No description available > save /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/M_PRO-120549.cif relModel #1 Not saving entity_poly_seq for non-authoritative sequences > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final- > files/M_PRO-120549.cif Summary of feedback from opening /Users/pfeliciano/Library/CloudStorage/OneDrive- GenerateBiomedicines/Documents/Projects/Outer- Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final- files/M_PRO-120549.cif --- warnings | Unknown polymer entity '1' near line 124 Unknown polymer entity '2' near line 1683 Unknown polymer entity '3' near line 3209 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for M_PRO-120549.cif #2 --- Chain | Description H | No description available L | No description available M | No description available > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final- > files/M_PRO-120549.mrc Opened M_PRO-120549.mrc as #3, grid size 288,288,288, pixel 0.888, shown at level 0.0764, step 2, values float32 > volume #3 step 1 > volume #3 level 0.3047 > surface dust #3 size 8.88 > transparency 50 > hide #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.1763 > close #1 > close > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120446/cryosparc- > maps/cryosparc_P651_J24_006_volume_map.mrc Opened cryosparc_P651_J24_006_volume_map.mrc as #1, grid size 240,240,240, pixel 1.01, shown at level 0.0244, step 1, values float32 > volume #1 level 0.1073 > volume #1 level 0.1768 > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120446/docking/M.pdb Chain information for M.pdb #2 --- Chain | Description M | No description available > transparency 50 > ui mousemode right select > select /M:453 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,14.681,0,1,0,27.996,0,0,1,27.878 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.86738,-0.33462,-0.36834,123.44,-0.019404,-0.76236,0.64687,169.61,-0.49726,-0.55393,-0.66775,384.29 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.86738,-0.33462,-0.36834,129.78,-0.019404,-0.76236,0.64687,139.8,-0.49726,-0.55393,-0.66775,379.39 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.71314,-0.18001,-0.67751,339.2,-0.25638,-0.83254,0.49107,198.06,-0.65245,0.5239,0.54757,94.201 > view matrix models > #2,-0.98061,-0.028674,0.19385,233.29,0.15835,-0.69869,0.69768,103.63,0.11544,0.71485,0.68969,-40.717 > view matrix models > #2,0.65813,0.66719,0.34888,-71.68,0.23386,-0.62161,0.7476,77.982,0.71566,-0.41043,-0.56513,203.17 > view matrix models > #2,0.85394,0.042596,-0.51862,103.16,0.43109,-0.61613,0.65921,65.871,-0.29146,-0.78649,-0.5445,368.23 > view matrix models > #2,0.97954,-0.07836,-0.18539,58.671,0.18431,-0.020785,0.98265,-25.4,-0.080853,-0.99671,-0.0059165,297.33 > view matrix models > #2,0.91322,-0.15335,-0.37751,102.24,0.31436,-0.32432,0.89219,10.54,-0.25925,-0.93344,-0.24796,343.14 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.91322,-0.15335,-0.37751,111.53,0.31436,-0.32432,0.89219,46.276,-0.25925,-0.93344,-0.24796,370.37 > view matrix models > #2,0.91322,-0.15335,-0.37751,119.27,0.31436,-0.32432,0.89219,37.968,-0.25925,-0.93344,-0.24796,349.02 > view matrix models > #2,0.91322,-0.15335,-0.37751,88.281,0.31436,-0.32432,0.89219,2.2807,-0.25925,-0.93344,-0.24796,335.71 > view matrix models > #2,0.91322,-0.15335,-0.37751,84.428,0.31436,-0.32432,0.89219,0.26385,-0.25925,-0.93344,-0.24796,328.92 > view matrix models > #2,0.91322,-0.15335,-0.37751,82.348,0.31436,-0.32432,0.89219,-2.0106,-0.25925,-0.93344,-0.24796,327.22 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.63338,-0.77195,0.054041,286.92,0.64554,-0.48857,0.587,21.249,-0.42673,0.40668,0.80778,31.332 > view matrix models > #2,-0.81837,0.25488,0.51508,114.09,0.3214,-0.54002,0.77787,40.437,0.47642,0.80213,0.36002,-65.999 > view matrix models > #2,-0.70139,-0.29119,-0.65059,328.58,-0.053967,0.93182,-0.35888,49.465,0.71074,-0.21661,-0.66928,176.98 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.70139,-0.29119,-0.65059,335.3,-0.053967,0.93182,-0.35888,49.905,0.71074,-0.21661,-0.66928,170.74 > view matrix models > #2,-0.70139,-0.29119,-0.65059,336.26,-0.053967,0.93182,-0.35888,49.008,0.71074,-0.21661,-0.66928,169.38 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.97251,0.21204,-0.096276,-2.198,-0.18938,0.47955,-0.85684,190.83,-0.13552,0.85151,0.50652,-27.252 > view matrix models > #2,0.65446,0.7485,0.10691,-61.13,-0.31718,0.40014,-0.85982,216.62,-0.68636,0.5288,0.49928,80.615 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.65446,0.7485,0.10691,-67.21,-0.31718,0.40014,-0.85982,218.17,-0.68636,0.5288,0.49928,87.272 > view matrix models > #2,0.65446,0.7485,0.10691,-67.795,-0.31718,0.40014,-0.85982,218.58,-0.68636,0.5288,0.49928,88.135 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.98875,0.031142,-0.14633,253.79,0.091881,0.8983,-0.42966,47.595,0.11807,-0.43827,-0.89105,305.8 > view matrix models > #2,-0.73128,-0.28844,-0.61809,328.38,-0.034634,0.92072,-0.38869,54.156,0.6812,-0.26283,-0.68329,188.26 > view matrix models > #2,-0.62632,0.073332,0.77611,80.327,0.29153,-0.9013,0.32043,154.04,0.723,0.42695,0.54312,-71.81 > view matrix models > #2,0.98588,-0.093341,0.13902,-3.0098,-0.16728,-0.51228,0.84237,87.58,-0.0074124,-0.85373,-0.52066,323.98 > view matrix models > #2,0.96203,-0.066266,-0.26479,51.074,0.21115,-0.43408,0.87578,28.104,-0.17298,-0.89843,-0.40361,333.5 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.96203,-0.066266,-0.26479,54.178,0.21115,-0.43408,0.87578,29.177,-0.17298,-0.89843,-0.40361,330.9 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.95353,0.11359,0.27907,184.43,0.030514,-0.88505,0.4645,164.44,0.29975,0.45143,0.84045,-67.683 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.95353,0.11359,0.27907,187.6,0.030514,-0.88505,0.4645,165.96,0.29975,0.45143,0.84045,-70.5 > fitmap #2 inMap #1 Fit molecule M.pdb (#2) to map cryosparc_P651_J24_006_volume_map.mrc (#1) using 2869 atoms average map value = 0.2367, steps = 88 shifted from previous position = 1.96 rotated from previous position = 16.4 degrees atoms outside contour = 1032, contour level = 0.1768 Position of M.pdb (#2) relative to cryosparc_P651_J24_006_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.99487046 -0.01208539 0.10043247 232.52816565 0.04133776 -0.95472591 0.29460073 197.17801270 0.09232512 0.29724122 0.95032820 -41.09388798 Axis 0.04880821 0.14986057 0.98750168 Axis point 115.92943955 103.29969258 0.00000000 Rotation angle (degrees) 178.44998031 Shift along axis 0.31820898 > ui mousemode right select > select clear > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-1-107.pdb Summary of feedback from opening /Users/pfeliciano/Library/CloudStorage/OneDrive- GenerateBiomedicines/Documents/Projects/Outer- Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-1-107.pdb --- warnings | Ignored bad PDB record found on line 818 Ignored bad PDB record found on line 819 Chain information for PRO-120446-LC-1-107.pdb #3 --- Chain | Description B | No description available Drag select of 107 residues > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,120.07,0,1,0,195.59,0,0,1,91.346 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.14032,0.72388,-0.67551,133.59,0.22901,-0.64003,-0.73342,186.47,-0.96326,-0.25761,-0.075972,99.05 > view matrix models > #3,0.32037,-0.90251,0.28781,100.62,-0.34471,-0.39407,-0.85199,188.46,0.88235,0.17374,-0.43735,119.52 > view matrix models > #3,-0.73363,0.42935,-0.52673,124.51,0.30011,-0.49073,-0.818,190.03,-0.60969,-0.75819,0.23116,89.836 > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > select #3/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.27261,0.87117,-0.40835,130.84,-0.96188,-0.23726,0.13598,172.61,0.021575,0.42985,0.90264,98.461 > view matrix models > #3,-0.86765,0.48419,-0.11289,118.38,-0.45783,-0.68959,0.56113,163.04,0.19384,0.53854,0.82,101.98 > view matrix models > #3,0.81376,-0.37534,0.44376,107.66,-0.21651,0.5128,0.83076,175.82,-0.53937,-0.77211,0.33603,88.459 > view matrix models > #3,0.64278,-0.75398,0.13542,106.47,-0.038665,0.14462,0.98873,169.63,-0.76507,-0.64078,0.063809,93.041 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.64278,-0.75398,0.13542,120.72,-0.038665,0.14462,0.98873,122.83,-0.76507,-0.64078,0.063809,109.45 > view matrix models > #3,0.64278,-0.75398,0.13542,125,-0.038665,0.14462,0.98873,126.01,-0.76507,-0.64078,0.063809,110.11 > fitmap #3 inMap #1 Fit molecule PRO-120446-LC-1-107.pdb (#3) to map cryosparc_P651_J24_006_volume_map.mrc (#1) using 817 atoms average map value = 0.2922, steps = 76 shifted from previous position = 4.82 rotated from previous position = 21.9 degrees atoms outside contour = 220, contour level = 0.1768 Position of PRO-120446-LC-1-107.pdb (#3) relative to cryosparc_P651_J24_006_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.43655222 -0.80127769 0.40911637 119.05741592 -0.32884853 0.28115519 0.90155998 124.25784465 -0.83742509 -0.52811533 -0.14076007 110.94223559 Axis -0.73138727 0.63770043 0.24168332 Axis point 0.00000000 172.68837722 13.28666144 Rotation angle (degrees) 102.21181425 Shift along axis 18.97509006 > ui mousemode right select > select clear > open /Users/pfeliciano/Library/CloudStorage/OneDrive- > GenerateBiomedicines/Documents/Projects/Outer- > Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-108.pdb Summary of feedback from opening /Users/pfeliciano/Library/CloudStorage/OneDrive- GenerateBiomedicines/Documents/Projects/Outer- Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-108.pdb --- warning | Ignored bad PDB record found on line 871 Chain information for PRO-120446-LC-108.pdb #4 --- Chain | Description B | No description available Drag select of 112 residues > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-7.7056,0,1,0,93.523,0,0,1,102.08 > view matrix models #4,1,0,0,129.28,0,1,0,39.027,0,0,1,101.98 > view matrix models #4,1,0,0,137.39,0,1,0,102.27,0,0,1,106.39 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.90704,-0.35953,0.21913,141.8,0.17649,0.79717,0.57739,106.57,-0.38227,-0.48504,0.78652,110.31 > ui mousemode right select > select clear > select #4/B:108 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" ===== 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 Metal - 88.1 OpenGL renderer: Apple M2 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: Mac14,9 Model Number: Z17G002HSLL/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.61.3 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.2 (23H311) Kernel Version: Darwin 23.6.0 Time since boot: 7 days, 23 hours, 40 minutes 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: 0.7.16 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