id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16285 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6.4-arm64-arm-64bit ChimeraX Version: 1.7rc202311070653 (2023-11-07 06:53:13 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002aa1ff000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a91f3000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a81e7000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a71db000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a272f000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a1723000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a0717000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029f70b000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029e6ff000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029d6f3000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029c6e7000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029b6db000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000299e07000 (most recent call first): File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ddda2100 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 907 in atomspec_atoms File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 627 in _add_model_parts File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 476 in _check File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 470 in find_matches File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 612 in find_matches File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 455 in find_matches File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1004 in find_matches File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1001 in evaluate File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1091 in evaluate File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 36 in parse File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 71 in parse File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2499 in _parse_arg File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2640 in _process_positional_arguments File ""/Applications/ChimeraX-1.7-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2864 in run File ""/Applications/ChimeraX-1.7-rc2023.11.07.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-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 303 in run_matchmaker File ""/Applications/ChimeraX-1.7-rc2023.11.07.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-rc2023.11.07.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-rc2023.11.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2024-11-11 14:27:26.00 +0900"",""app_version"":""1.7.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.6.4 (22G513)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""5044628F-73DF-42FC-A079-AB05E688C5EF""} { ""uptime"" : 880000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 1013, ""deployVersion"" : 210, ""modelCode"" : ""Mac13,1"", ""coalitionID"" : 49338, ""osVersion"" : { ""train"" : ""macOS 13.6.4"", ""build"" : ""22G513"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-11-11 14:27:23.0108 +0900"", ""incident"" : ""5044628F-73DF-42FC-A079-AB05E688C5EF"", ""pid"" : 62467, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-11-11 14:22:38.7507 +0900"", ""procStartAbsTime"" : 21152170695327, ""procExitAbsTime"" : 21158992343105, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7-rc2023.11.07.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""04F891C2-8826-5B0C-940C-6823948F03E2"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""DEA9930E-687B-B74B-D89A-885FB24CB4A5"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 105554592661335\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600058000000-600060000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":62467}, ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 105554592661335\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600058000000-600060000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0}, ""faultingThread"" : 0, ""threads"" : 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""experiments"" : [ ] } } ===== 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: 1.7rc202311070653 (2023-11-07) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/DmMyo1D-1IQ_5actins.cif Chain information for DmMyo1D-1IQ_5actins.cif #1 --- Chain | Description A | . B C D E F | . > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/DrMyo1D-1IQ_5actins.cif Chain information for DrMyo1D-1IQ_5actins.cif #2 --- Chain | Description A | . B C D E F | . > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/Dr- > DmMyo1D_UL50k-1IQ_3actins.cif Chain information for Dr-DmMyo1D_UL50k-1IQ_3actins.cif #3 --- Chain | Description A | . B C D | . > hide #1 models > show #1 models > hide #1 models > hide #2 models > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/Dr- > DmMyo1D_UL50k-1IQ.cif Chain information for Dr-DmMyo1D_UL50k-1IQ.cif #4 --- Chain | Description A | . > hide #3 models > hide #4 models > show #3 models > hide #3 models > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/Dr- > DmMyo1D_UL50k-1IQ_5actins.cif Chain information for Dr-DmMyo1D_UL50k-1IQ_5actins.cif #5 --- Chain | Description A | . B C D E F | . > show #2 models > hide #2 models > show #1 models > hide #1 models > ui tool show Matchmaker > matchmaker #2,5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker DmMyo1D-1IQ_5actins.cif, chain A (#1) with DrMyo1D-1IQ_5actins.cif, chain A (#2), sequence alignment score = 2703.5 RMSD between 621 pruned atom pairs is 0.777 angstroms; (across all 719 pairs: 3.064) Matchmaker DmMyo1D-1IQ_5actins.cif, chain A (#1) with Dr- DmMyo1D_UL50k-1IQ_5actins.cif, chain A (#5), sequence alignment score = 3370.2 RMSD between 446 pruned atom pairs is 0.588 angstroms; (across all 719 pairs: 12.892) > show #1 models > hide #1 models > show #1 models > show #2 models > hide #5 models > show #5 models > hide #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > show #1 models > select add #1 20760 atoms, 21189 bonds, 2615 residues, 1 model selected > select add #2 41535 atoms, 42401 bonds, 5235 residues, 2 models selected > select add #3 56356 atoms, 57527 bonds, 7094 residues, 3 models selected > select add #4 62252 atoms, 63536 bonds, 7816 residues, 4 models selected > select add #5 83023 atoms, 84740 bonds, 10433 residues, 5 models selected > select subtract #4 77127 atoms, 78731 bonds, 9711 residues, 4 models selected > select subtract #3 62306 atoms, 63605 bonds, 7852 residues, 3 models selected > select subtract #1 41546 atoms, 42416 bonds, 5237 residues, 2 models selected > select subtract #2 20771 atoms, 21204 bonds, 2617 residues, 1 model selected > select subtract #5 Nothing selected > select add #3 14821 atoms, 15126 bonds, 1859 residues, 1 model selected > select add #4 20717 atoms, 21135 bonds, 2581 residues, 2 models selected > close > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/DrMyo1D-1IQ_3actins.cif Chain information for DrMyo1D-1IQ_3actins.cif #1 --- Chain | Description A | . B C D | . > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/DmMyo1D-1IQ_3actins.cif Chain information for DmMyo1D-1IQ_3actins.cif #2 --- Chain | Description A | . B C D | . > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/Dr- > DmMyo1D_UL50k-1IQ_3actins.cif Chain information for Dr-DmMyo1D_UL50k-1IQ_3actins.cif #3 --- Chain | Description A | . B C D | . > ui tool show Matchmaker ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7rc202311070653 (2023-11-07) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/DrMyo1D-1IQ_3actins.cif Chain information for DrMyo1D-1IQ_3actins.cif #1 --- Chain | Description A | . B C D | . > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/DmMyo1D-1IQ_3actins.cif Chain information for DmMyo1D-1IQ_3actins.cif #2 --- Chain | Description A | . B C D | . > open > /Users/toshi/Library/CloudStorage/Dropbox/05_Kyushu/project_actomyosin_Ito/20241105_Dr_Dm/Dr- > DmMyo1D_UL50k-1IQ_3actins.cif Chain information for Dr-DmMyo1D_UL50k-1IQ_3actins.cif #3 --- Chain | Description A | . B C D | . OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 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: Mac Studio Model Identifier: Mac13,1 Model Number: Z14J000L8J/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 10151.81.1 OS Loader Version: 8422.141.2.700.1 Software: System Software Overview: System Version: macOS 13.6.4 (22G513) Kernel Version: Darwin 22.6.0 Time since boot: 10日 4時間 54分 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: EV3285: Resolution: 6720 x 3780 UI Looks like: 3360 x 1890 @ 30.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported EV3285: Resolution: 6720 x 3780 UI Looks like: 3360 x 1890 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.13.1 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: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 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 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: 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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: 1.13 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: 2.0.2 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: 1.12.2 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: 1.33.2 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-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: 0.2.0 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: 4.44.0 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.4 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: 5.5.0 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: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.11.0 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: 2.4.1 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: 1.0.7 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: 0.6.3 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: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.7 wcwidth: 0.2.9 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX