id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16240 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8rc202406102315 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000031248f000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000311483000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000310477000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f46b000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030e45f000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030d453000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030c447000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030b43b000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030a42f000 (most recent call first): File 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""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000308417000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ec9b0f40 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, 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Bytes after previous region: 72529331986873 Bytes before following region: 32542747942472\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV "", ""exception"" : {""codes"":""0x0000000000000001, 0x000042670d11a1b8"",""rawCodes"":[1,73010368324024],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x000042670d11a1b8""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":17275}, ""vmregioninfo"" : ""0x42670d11a1b8 is not in any region. 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""ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=3.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 304K 16 \nColorSync 656K 31 \nCoreAnimation 1120K 58 \nCoreGraphics 48K 3 \nCoreUI image data 3392K 24 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 2.8G 95 \nMALLOC guard page 192K 12 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 736K 46 \nStack 330.2M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 370.7M 219 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 1864K 374 \n__AUTH_CONST 29.6M 586 \n__CTF 824 1 \n__DATA 21.1M 727 \n__DATA_CONST 39.9M 738 \n__DATA_DIRTY 1873K 223 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 553.7M 147 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 896.7M 755 \ndyld private memory 544K 4 \nmapped file 220.5M 58 \nshared memory 3840K 30 \n=========== ======= ======= \nTOTAL 5.4G 4213 \nTOTAL, minus reserved VM space 5.3G 4213 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6adeb57a55f13df3622dee06b3c3cc10cf749019"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645197bf528fbf3c3af54105"", ""factorPackIds"" : { ""SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION"" : ""663e65b4a1526e1ca0e288a1"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/jenniferherman/Downloads/fold_2024_11_03_3xkdv_bsub168/fold_2024_11_03_3xkdv_bsub168_model_0.cif Chain information for fold_2024_11_03_3xkdv_bsub168_model_0.cif #1 --- Chain | Description A B C | . > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C Alignment identifier is 1 > select /A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A-C:687 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A-C:687 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > open > /Users/jenniferherman/Downloads/fold_3gp146_phagek/fold_3gp146_phagek_model_0.cif Chain information for fold_3gp146_phagek_model_0.cif #2 --- Chain | Description A B C | . > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #1 models > show #1 models > select add #1 16338 atoms, 16713 bonds, 2061 residues, 1 model selected > hide #2 models > hide #1 models > select subtract #1 Nothing selected > show #2 models > show #1 models > select add #2 15375 atoms, 15753 bonds, 1920 residues, 1 model selected > select add #1 31713 atoms, 32466 bonds, 3981 residues, 2 models selected > select subtract #1 15375 atoms, 15753 bonds, 1920 residues, 1 model selected > select subtract #2 Nothing selected > hide #2 models > select add #1 16338 atoms, 16713 bonds, 2061 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > show #2 models > hide #2 models > show #1 models > show #2 models > hide #2 models > hide target m > show #2 models > show #1 models > open > /Users/jenniferherman/Downloads/fold_2024_11_03_3xkdv_bsub168/fold_2024_11_03_3xkdv_bsub168_model_0.cif > format mmcif Chain information for fold_2024_11_03_3xkdv_bsub168_model_0.cif #3 --- Chain | Description A B C | . > hide #3 models > hide #2 models > open > /Users/jenniferherman/Downloads/fold_2024_11_03_3xkdv_bsub168/fold_2024_11_03_3xkdv_bsub168_model_0.cif > format mmcif Chain information for fold_2024_11_03_3xkdv_bsub168_model_0.cif #4 --- Chain | Description A B C | . > open > /Users/jenniferherman/Downloads/fold_3gp146_phagek/fold_3gp146_phagek_model_0.cif > format mmcif Chain information for fold_3gp146_phagek_model_0.cif #5 --- Chain | Description A B C | . > select add #1 16338 atoms, 16713 bonds, 2061 residues, 1 model selected > view orient > ui tool show ""Side View"" > view sel > view > view orient > ui mousemode right rotate > ui mousemode right select > show #2 models > hide #2 models > show #3 models > hide #3 models > hide #5 models > hide #4 models > show #2 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > hide #2 models > select #1/A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A-C:1-416 9825 atoms, 10032 bonds, 1248 residues, 1 model selected > select #1/A-C:409 36 atoms, 36 bonds, 3 residues, 1 model selected > select #1/A-C:1-409 9669 atoms, 9876 bonds, 1227 residues, 1 model selected > hide sel surfaces > hide sel cartoons > show #2 models > view matrix models > #1,-0.34633,0.78836,-0.50846,-31.357,0.93563,0.32965,-0.12617,35.191,0.068152,-0.51943,-0.85179,54.053 > view matrix models > #1,-0.10491,0.99306,-0.053169,-34.059,0.98466,0.096226,-0.14555,35.966,-0.13943,-0.067623,-0.98792,53.353 > view matrix models > #1,-0.10491,0.99306,-0.053169,-85.71,0.98466,0.096226,-0.14555,77.475,-0.13943,-0.067623,-0.98792,86.237 > view matrix models #2,1,0,0,-1.1955,0,1,0,17.417,0,0,1,9.9186 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B #2/C #5/A #5/B #5/C Alignment identifier is 2 > select #2/A-C:1 #5/A-C:1 48 atoms, 42 bonds, 6 residues, 2 models selected > select #2/A-C:1-10 #5/A-C:1-10 492 atoms, 504 bonds, 60 residues, 2 models selected . [ID: 2] region 6 chains [1-10] RMSD: 20.079 > select #2/A-C:11 #5/A-C:11 42 atoms, 36 bonds, 6 residues, 2 models selected > select #2/A-C:9-11 #5/A-C:9-11 138 atoms, 132 bonds, 18 residues, 2 models selected . [ID: 2] region 6 chains [9-11] RMSD: 20.079 > select #2/A-C:12 #5/A-C:12 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:12 #5/A-C:12 54 atoms, 48 bonds, 6 residues, 2 models selected . [ID: 2] region 6 chains [12] RMSD: 20.079 > select add #5 15402 atoms, 15777 bonds, 1923 residues, 2 models selected > select subtract #5 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A-C:1-5 129 atoms, 129 bonds, 15 residues, 1 model selected > select #1/A-C:685-686 54 atoms, 54 bonds, 6 residues, 1 model selected > select #1/A-C:686-687 57 atoms, 54 bonds, 6 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B #2/C #5/A #5/B #5/C Alignment identifier is 3 > select > #1/A-C:17-39,65-72,81-89,93-115,142-149,158-166,188-190,200-202,246-248,265-273,300-321,348-353,355-360,379-381,414-435,438-442,446-448,457-459 3936 atoms, 3954 bonds, 504 residues, 1 model selected > select #2/A-C:12 #5/A-C:12 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:1-12 #5/A-C:1-12 588 atoms, 600 bonds, 72 residues, 2 models selected . [ID: 3] region 6 chains [1-12] RMSD: 20.079 > select #2/A-C:12 #5/A-C:12 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:11-12 #5/A-C:11-12 96 atoms, 90 bonds, 12 residues, 2 models selected . [ID: 3] region 6 chains [11-12] RMSD: 20.079 > select #2/A-C:13 #5/A-C:13 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:11-13 #5/A-C:11-13 150 atoms, 144 bonds, 18 residues, 2 models selected . [ID: 3] region 6 chains [11-13] RMSD: 20.079 > select #1/A-C:687 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A-C:375-687 7536 atoms, 7734 bonds, 939 residues, 1 model selected > select #1/A-C:687 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A-C:255-687 10368 atoms, 10614 bonds, 1299 residues, 1 model selected > select #1/A-C:283 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:283-287 123 atoms, 120 bonds, 15 residues, 1 model selected > select #1/A-C:283-284 48 atoms, 45 bonds, 6 residues, 1 model selected > select #1/A-C:283-687 9687 atoms, 9921 bonds, 1215 residues, 1 model selected > show sel cartoons > view matrix models > #2,0.98068,-0.16891,0.098713,-0.20084,0.14972,0.97275,0.17706,17.9,-0.12593,-0.15886,0.97924,10.627 > select #2/A-C:11 #5/A-C:11 42 atoms, 36 bonds, 6 residues, 2 models selected > select #2/A-C:11-13 #5/A-C:11-13 150 atoms, 144 bonds, 18 residues, 2 models selected . [ID: 3] region 6 chains [11-13] RMSD: 28.057 > select #2/A-C:1 #5/A-C:1 48 atoms, 42 bonds, 6 residues, 2 models selected > select #2/A-C:1-13 #5/A-C:1-13 642 atoms, 654 bonds, 78 residues, 2 models selected . [ID: 3] region 6 chains [1-13] RMSD: 26.339 > select #1/A-C:282 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:281-282 39 atoms, 36 bonds, 6 residues, 1 model selected > select #1/A-C:283 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:283-287 123 atoms, 120 bonds, 15 residues, 1 model selected > select #1/A-C:283 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:283-299 390 atoms, 387 bonds, 51 residues, 1 model selected > select #1/A-C:300 21 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A-C:283-300 411 atoms, 411 bonds, 54 residues, 1 model selected > select #2/A-C:19 #5/A-C:19 42 atoms, 42 bonds, 6 residues, 2 models selected > select #2/A-C:18 #5/A-C:18 72 atoms, 72 bonds, 6 residues, 2 models selected > select #2/A-C:18 #5/A-C:18 72 atoms, 72 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [18] RMSD: 27.284 > select #2/A-C:17 #5/A-C:17 48 atoms, 42 bonds, 6 residues, 2 models selected > select #2/A-C:17 #5/A-C:17 48 atoms, 42 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [17] RMSD: 27.361 > select #2/A-C:16 #5/A-C:16 48 atoms, 42 bonds, 6 residues, 2 models selected > select #2/A-C:16 #5/A-C:16 48 atoms, 42 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [16] RMSD: 27.104 > select #2/A-C:15 #5/A-C:15 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:15 #5/A-C:15 54 atoms, 48 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [15] RMSD: 27.591 > select #2/A-C:14 #5/A-C:14 48 atoms, 42 bonds, 6 residues, 2 models selected > select #2/A-C:14 #5/A-C:14 48 atoms, 42 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [14] RMSD: 28.249 > select #2/A-C:13 #5/A-C:13 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:13 #5/A-C:13 54 atoms, 48 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [13] RMSD: 28.193 > select #1/A-C:283 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:283-284 48 atoms, 45 bonds, 6 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296-297 54 atoms, 51 bonds, 6 residues, 1 model selected > select #2/A-C:12 #5/A-C:12 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:12 #5/A-C:12 54 atoms, 48 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [12] RMSD: 27.782 > select #2/A-C:13 #5/A-C:13 54 atoms, 48 bonds, 6 residues, 2 models selected > select #2/A-C:13 #5/A-C:13 54 atoms, 48 bonds, 6 residues, 2 models selected . [ID: 3] region 6 chains [13] RMSD: 28.193 > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296-297 54 atoms, 51 bonds, 6 residues, 1 model selected > select #1/A-C:295 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:71-295 5259 atoms, 5361 bonds, 675 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296-687 9399 atoms, 9633 bonds, 1176 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296-297 54 atoms, 51 bonds, 6 residues, 1 model selected > select #1/A-C:296-338 987 atoms, 996 bonds, 129 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A-C:296 27 atoms, 24 bonds, 3 residues, 1 model selected > view matrix models > #2,0.98068,-0.16891,0.098713,-0.30571,0.14972,0.97275,0.17706,66.373,-0.12593,-0.15886,0.97924,13.701 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MXCU3LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 33 days, 10 hours, 25 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202406102315 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: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 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: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 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: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 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: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX