id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15280 Crash in garbage collection hchou01@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-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 0x0000000376b73000 (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 0x00000001e43b9c40 (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 576 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 807 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py"", line 31 in atoms File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 177 in get_prop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 782 in get_selected File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py"", line 41 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py"", line 41 in models File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py"", line 45 in items File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/select.py"", line 167 in report_selection File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/select.py"", line 120 in select_add 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 2908 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/model_panel/tool.py"", line 366 in _tree_change_cb File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, 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""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000023 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet 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/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/Chimera_session/20240513_TNFR2-2Fabs_20-22.cxs > format session Opened cryosparc_P128_J917_map_sharp_flip.mrc as #3, grid size 256,256,256, pixel 0.813, shown at level 0.497, step 1, values float32 Opened deepemhancer_cryosparc_P128_J333_005_flip.mrc as #5, grid size 256,256,256, pixel 0.813, shown at level 0.201, step 1, values float32 Opened cryosparc_P128_cryosparc_P128_J594_005_volume_map.mrc as #6, grid size 480,480,480, pixel 0.813, shown at level 0.0456, step 1, values float32 opened ChimeraX session > hide #!5 models > hide #10 models > show #11 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > close session > open > /Users/hchou01@amgen.com/Downloads/cryosparc_P140_J492_003_volume_map_sharp.mrc Opened cryosparc_P140_J492_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.917, shown at level 0.0753, step 2, values float32 > volume #1 level 0.1169 > close session > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/Chimera_session/20240513_TNFR2-2Fabs_20-22.cxs > format session Opened cryosparc_P128_J917_map_sharp_flip.mrc as #3, grid size 256,256,256, pixel 0.813, shown at level 0.497, step 1, values float32 Opened deepemhancer_cryosparc_P128_J333_005_flip.mrc as #5, grid size 256,256,256, pixel 0.813, shown at level 0.201, step 1, values float32 Opened cryosparc_P128_cryosparc_P128_J594_005_volume_map.mrc as #6, grid size 480,480,480, pixel 0.813, shown at level 0.0456, step 1, values float32 opened ChimeraX session > open > /Users/hchou01@amgen.com/Downloads/cryosparc_P140_J500_class_01_final_volume.mrc Opened cryosparc_P140_J500_class_01_final_volume.mrc as #12, grid size 128,128,128, pixel 2.87, shown at level 0.0231, step 1, values float32 > open > /Users/hchou01@amgen.com/Downloads/cryosparc_P140_J500_class_00_final_volume.mrc Opened cryosparc_P140_J500_class_00_final_volume.mrc as #13, grid size 128,128,128, pixel 2.87, shown at level 0.0263, step 1, values float32 > close session > open > /Users/hchou01@amgen.com/Downloads/cryosparc_P140_J500_class_01_final_volume.mrc Opened cryosparc_P140_J500_class_01_final_volume.mrc as #1, grid size 128,128,128, pixel 2.87, shown at level 0.0231, step 1, values float32 > open > /Users/hchou01@amgen.com/Downloads/cryosparc_P140_J500_class_00_final_volume.mrc Opened cryosparc_P140_J500_class_00_final_volume.mrc as #2, grid size 128,128,128, pixel 2.87, shown at level 0.0263, step 1, values float32 > tile 2 models tiled > volume #2 level 0.09663 > volume #1 level 0.08246 > close session > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/Chimera_session/20240513_TNFR2-2Fabs_20-22.cxs > format session Opened cryosparc_P128_J917_map_sharp_flip.mrc as #3, grid size 256,256,256, pixel 0.813, shown at level 0.497, step 1, values float32 Opened deepemhancer_cryosparc_P128_J333_005_flip.mrc as #5, grid size 256,256,256, pixel 0.813, shown at level 0.201, step 1, values float32 Opened cryosparc_P128_cryosparc_P128_J594_005_volume_map.mrc as #6, grid size 480,480,480, pixel 0.813, shown at level 0.0456, step 1, values float32 opened ChimeraX session > hide #1 models > hide #!5 models > show #!5 models > hide #10 models > show #10 models > volume #5 level 0.304 > ui tool show ""Show Sequence Viewer"" > sequence chain #4/H #1/H Alignment identifier is 1 > select #4/H:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select #4/H 928 atoms, 954 bonds, 120 residues, 1 model selected > select #4/H:1 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/H 928 atoms, 954 bonds, 120 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #7/L #2/L #11/L #10/H Alignment identifier is 1 > select #7/L:123 #2/L:123 #11/L:123 #10/H:3 52 atoms, 48 bonds, 4 residues, 4 models selected > select #7/L:123-192 #2/L:123-192 #11/L:123-192 #10/H:3-72 2692 atoms, 2760 bonds, 280 residues, 4 models selected 1 [ID: 1] region 4 chains [3-72] RMSD: 0.378 > select add #10 10947 atoms, 11161 bonds, 1183 residues, 4 models selected > select subtract #10 2019 atoms, 2070 bonds, 210 residues, 3 models selected > select #7/L:121 #2/L:121 #11/L:121 #10/H:1 44 atoms, 40 bonds, 4 residues, 4 models selected > select #7/L:121-139 #2/L:121-139 #11/L:121-139 #10/H:1-19 648 atoms, 648 bonds, 76 residues, 4 models selected 1 [ID: 1] region 4 chains [1-19] RMSD: 0.368 > select add #11 9399 atoms, 9560 bonds, 1030 residues, 4 models selected > select subtract #11 486 atoms, 486 bonds, 57 residues, 3 models selected > select add #11 9399 atoms, 9560 bonds, 1030 residues, 4 models selected > select add #10 18165 atoms, 18489 bonds, 1984 residues, 4 models selected > select subtract #10 9237 atoms, 9398 bonds, 1011 residues, 3 models selected > select #7/L:121 #2/L:121 #11/L:121 #10/H:1 44 atoms, 40 bonds, 4 residues, 4 models selected > select #7/L:121-125 #2/L:121-125 #11/L:121-125 #10/H:1-5 188 atoms, 188 bonds, 20 residues, 4 models selected 1 [ID: 1] region 4 chains [1-5] RMSD: 0.412 > select #7/L:226 #2/L:226 #11/L:226 #10/H:106 20 atoms, 16 bonds, 4 residues, 4 models selected > select #7/L:226-230 #2/L:226-230 #11/L:226-230 #10/H:106-110 164 atoms, 160 bonds, 20 residues, 4 models selected 1 [ID: 1] region 4 chains [106-110] RMSD: 0.332 > select #7/L:121 #2/L:121 #11/L:121 #10/H:1 44 atoms, 40 bonds, 4 residues, 4 models selected > select #7/L:121-128 #2/L:121-128 #11/L:121-128 #10/H:1-8 308 atoms, 308 bonds, 32 residues, 4 models selected 1 [ID: 1] region 4 chains [1-8] RMSD: 0.411 > hide #!5 models > hide #10 models > hide #!3 models > show #!3 models > hide #!3 models > show #!5 models > show #10 models > select #7/L:128 #2/L:128 #11/L:128 #10/H:8 36 atoms, 32 bonds, 4 residues, 4 models selected > select #7/L:121-128 #2/L:121-128 #11/L:121-128 #10/H:1-8 308 atoms, 308 bonds, 32 residues, 4 models selected 1 [ID: 1] region 4 chains [1-8] RMSD: 0.411 > select #7/L:121 #2/L:121 #11/L:121 #10/H:1 44 atoms, 40 bonds, 4 residues, 4 models selected > select #7/L:121-127 #2/L:121-127 #11/L:121-127 #10/H:1-7 272 atoms, 272 bonds, 28 residues, 4 models selected 1 [ID: 1] region 4 chains [1-7] RMSD: 0.413 > hide #10 models > show #10 models > hide #10 models > show #10 models > volume #5 level 0.3871 > volume #5 level 0.1932 > volume #5 level 0.1759 > volume #6 level -0.1251 > volume #6 level -0.02565 > volume #6 level 0.02614 > volume #5 level 0.2555 > close session > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1_ranked_0_C.pdb Chain information for anti-TNFR2_Fab69720-1_ranked_0_C.pdb #1 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1_ranked_0_V.pdb Chain information for anti-TNFR2_Fab69720-1_ranked_0_V.pdb #2 --- Chain | Description B | No description available C | No description available > close session > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69722-1_ranked_0_C.pdb Chain information for anti-TNFR2_Fab69722-1_ranked_0_C.pdb #1 --- Chain | Description I | No description available J | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69722-1_ranked_0_V.pdb Chain information for anti-TNFR2_Fab69722-1_ranked_0_V.pdb #2 --- Chain | Description B | No description available C | No description available > close session > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1_ranked_0_C.pdb Chain information for anti-TNFR2_Fab69720-1_ranked_0_C.pdb #1 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1_ranked_0_V.pdb Chain information for anti-TNFR2_Fab69720-1_ranked_0_V.pdb #2 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_4.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_4.pdb #3 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_0.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_0.pdb #4 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_1.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_1.pdb #5 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_2.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_2.pdb #6 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_3.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_3.pdb #7 --- Chain | Description B | No description available C | No description available > hide #1 models > hide #2 models > select add #3 3297 atoms, 3371 bonds, 438 residues, 1 model selected > select add #4 6594 atoms, 6742 bonds, 876 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,1,0,0,-81.823,0,1,0,54.418,0,0,1,0,#4,1,0,0,-81.823,0,1,0,54.418,0,0,1,0 > select subtract #3 3297 atoms, 3371 bonds, 438 residues, 1 model selected > select add #5 6594 atoms, 6742 bonds, 876 residues, 2 models selected > close session > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1_ranked_0_C.pdb Chain information for anti-TNFR2_Fab69720-1_ranked_0_C.pdb #1 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1_ranked_0_V.pdb Chain information for anti-TNFR2_Fab69720-1_ranked_0_V.pdb #2 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69722-1_ranked_0_C.pdb Chain information for anti-TNFR2_Fab69722-1_ranked_0_C.pdb #3 --- Chain | Description I | No description available J | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69722-1_ranked_0_V.pdb Chain information for anti-TNFR2_Fab69722-1_ranked_0_V.pdb #4 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_0.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_0.pdb #5 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_1.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_1.pdb #6 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_2.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_2.pdb #7 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_3.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_3.pdb #8 --- Chain | Description B | No description available C | No description available > open /Users/hchou01@amgen.com/Library/CloudStorage/OneDrive- > Amgen/Documents_Mac/Projects/TNFR2/AmgenFold/anti-TNFR2_Fab69720-1/anti- > TNFR2_Fab69720-1-ranked_4.pdb Chain information for anti-TNFR2_Fab69720-1-ranked_4.pdb #9 --- Chain | Description B | No description available C | No description available > select add #1 1557 atoms, 1591 bonds, 209 residues, 1 model selected > select add #2 3304 atoms, 3376 bonds, 439 residues, 2 models selected > view matrix models > #1,1,0,0,-66.772,0,1,0,50.569,0,0,1,0,#2,1,0,0,-66.772,0,1,0,50.569,0,0,1,0 > view matrix models > #1,1,0,0,-91.453,0,1,0,65.867,0,0,1,0,#2,1,0,0,-91.453,0,1,0,65.867,0,0,1,0 > select subtract #2 1557 atoms, 1591 bonds, 209 residues, 1 model selected > select subtract #1 Nothing selected > select add #3 1557 atoms, 1591 bonds, 209 residues, 1 model selected > select add #4 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet 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 OpenGL renderer: Apple M3 Max 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: Mac15,9 Model Number: Z1AJ0019DLL/A Chip: Apple M3 Max Total Number of Cores: 16 (12 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 12 days, 3 hours, 19 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: P27h-20: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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-ISOLDE: 1.7.1 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 Tom Goddard all ChimeraX