id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15202 Crash in garbage collection genfren@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-x86_64-i386-64bit 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 0x0000000318807000 (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 0x00000002044c6240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 15 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 90 in copy File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 642 in _try File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 665 in _option File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 334 in _chain_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 323 in block0 File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 325 in _model_parts_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 200 in _model_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 157 in block0 File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 159 in _model_list_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 136 in _as_term_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 89 in _atom_specifier_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 206 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 192 in _parse_unquoted File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 121 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py"", line 180 in defattr File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 81 in add_standard_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 34 in add_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 110 in assign_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic 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/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in 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 ""/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, 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, lxml._elementpath, lxml.etree, 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.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 58) {""app_name"":""ChimeraX"",""timestamp"":""2024-05-14 14:05:40.00 -0400"",""app_version"":""1.7.1"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.4.1 (23E224)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""3D60ECD6-0EAE-42D1-B8C1-AA89985FFC93""} { ""uptime"" : 65000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir10,1"", ""coalitionID"" : 993, ""osVersion"" : { ""train"" : ""macOS 14.4.1"", ""build"" : ""23E224"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-05-14 14:05:38.9804 -0400"", ""codeSigningMonitor"" : 1, ""incident"" : ""3D60ECD6-0EAE-42D1-B8C1-AA89985FFC93"", ""pid"" : 28475, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-05-14 13:26:50.2469 -0400"", ""procStartAbsTime"" : 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""32bbae1b2b96c0f978f07cdb4c59aa6d2194a637"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000119 }, { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000550 } ], ""experiments"" : [ { ""treatmentId"" : ""a34d22a1-a1a5-4126-a477-0c499e502c6a"", ""experimentId"" : ""65835bc103dc58766bab2d27"", ""deploymentId"" : 400000011 }, { ""treatmentId"" : ""5d85d104-adc7-4ebf-8b7c-96d84fdad9cc"", ""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000032 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF8981E2A78)"" ] } ===== 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/genya/moreAlphaFold/AF3/fold_opa3_3/fold_opa3_3_model_0.cif Chain information for fold_opa3_3_model_0.cif #1 --- Chain | Description A B C | . > close > open > /Users/genya/moreAlphaFold/AF3/fold_opa3_3_iars2/fold_opa3_3_iars2_model_0.cif Chain information for fold_opa3_3_iars2_model_0.cif #1 --- Chain | Description A B C | . D | . > open > /Users/genya/moreAlphaFold/AF3/fold_opa3_4_iars2nomts/fold_opa3_4_iars2nomts_model_0.cif Chain information for fold_opa3_4_iars2nomts_model_0.cif #2 --- Chain | Description A B C D | . E | . > hide #1 models > select #2 13308 atoms, 13610 bonds, 1685 residues, 1 model selected > show sel cartoons > hide sel atoms > select #2/e 7684 atoms, 7874 bonds, 969 residues, 1 model selected > color sel dark grey > select #2/e:1-60 484 atoms, 494 bonds, 60 residues, 1 model selected > hide sel cartoons > select #2/a-d 5624 atoms, 5736 bonds, 716 residues, 1 model selected > color sel goldenrod > select #2/a-d:1-30 924 atoms, 936 bonds, 120 residues, 1 model selected > color sel dark salmon > select #2/a-d:80-100 572 atoms, 572 bonds, 84 residues, 1 model selected > color sel saddle brown > select #2/a-d:152-159,115-140 1072 atoms, 1076 bonds, 136 residues, 1 model selected > color sel cornflower blue > select clear > lighting simple > open > /Users/genya/moreAlphaFold/AF3/fold_opa3_3_iars2/fold_opa3_3_iars2_model_0.cif Chain information for fold_opa3_3_iars2_model_0.cif #3 --- Chain | Description A B C | . D | . > hide #2 models > hide #3 models > open /Users/genya/moreAlphaFold/AF3/fold_opa3_3/fold_opa3_3_model_0.cif Chain information for fold_opa3_3_model_0.cif #4 --- Chain | Description A B C | . > select #4 4218 atoms, 4302 bonds, 537 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_opa3_3_model_0.cif_A SES surface #4.1: minimum, -13.06, mean 0.11, maximum 11.89 Coulombic values for fold_opa3_3_model_0.cif_B SES surface #4.2: minimum, -13.01, mean 0.12, maximum 11.43 Coulombic values for fold_opa3_3_model_0.cif_C SES surface #4.3: minimum, -14.06, mean 0.11, maximum 14.45 To also show corresponding color key, enter the above coulombic command and add key true > set bgColor white > select #4\ Expected an objects specifier or a keyword > select #4 4218 atoms, 4302 bonds, 537 residues, 1 model selected > hide sel surfaces > show #3 models > hide #!4 models > select #3 12230 atoms, 12515 bonds, 1549 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_opa3_3_iars2_model_0.cif_A SES surface #3.1: minimum, -15.75, mean 0.06, maximum 20.02 Coulombic values for fold_opa3_3_iars2_model_0.cif_B SES surface #3.2: minimum, -13.84, mean 0.07, maximum 14.14 Coulombic values for fold_opa3_3_iars2_model_0.cif_C SES surface #3.3: minimum, -13.32, mean 0.03, maximum 13.51 Coulombic values for fold_opa3_3_iars2_model_0.cif_D SES surface #3.4: minimum, -19.42, mean -1.03, maximum 11.58 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_opa3_3_iars2_model_0.cif_A SES surface"": minimum -25.65, mean -2.179, maximum 22.94 Map values for surface ""fold_opa3_3_iars2_model_0.cif_B SES surface"": minimum -25.96, mean -2.146, maximum 23.05 Map values for surface ""fold_opa3_3_iars2_model_0.cif_C SES surface"": minimum -25.65, mean -2.134, maximum 23.06 Map values for surface ""fold_opa3_3_iars2_model_0.cif_D SES surface"": minimum -29.98, mean -5.067, maximum 23.24 To also show corresponding color key, enter the above mlp command and add key true > show #!4 models > hide #!3 models > select #4/a-c:10,17,21,86,82,32,29,28,100 255 atoms, 231 bonds, 27 residues, 1 model selected > show sel atoms > style sel sphere Changed 255 atom styles > coulombic sel Coulombic values for fold_opa3_3_model_0.cif_A SES surface #4.1: minimum, -13.06, mean 0.11, maximum 11.89 Coulombic values for fold_opa3_3_model_0.cif_B SES surface #4.2: minimum, -13.01, mean 0.12, maximum 11.43 Coulombic values for fold_opa3_3_model_0.cif_C SES surface #4.3: minimum, -14.06, mean 0.11, maximum 14.45 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #2/A #2/B #2/C #2/D #3/A #3/B #3/C #4/A #4/B > #4/C Alignment identifier is 1 > select #1/A-C:2-33,35-60,73-142,146-164,168-173 > #2/A-D:2-33,35-60,73-142,146-164,168-173 > #3/A-C:2-33,35-60,73-142,146-164,168-173 > #4/A-C:2-33,35-60,73-142,146-164,168-173 15834 atoms, 16068 bonds, 1989 residues, 4 models selected > select #4/a-c:10,17,21,86,82,32,29,28,100,101 291 atoms, 270 bonds, 30 residues, 1 model selected > show sel atoms > select #4/a-c:10,17,21,86,82,32,29,28,100 255 atoms, 231 bonds, 27 residues, 1 model selected > ui mousemode right clip > ui mousemode right translate > ui mousemode right clip > ui mousemode right ""clip rotate"" > ui mousemode right clip > clip off > select 4/c Expected an objects specifier or a keyword > select #4/c 1406 atoms, 1434 bonds, 179 residues, 1 model selected > transparency #4/c 50 > transparency #4/c 50 All > transparency #4/c 20 All > transparency #4/c 75 All > transparency #4/c 0 All > clip off > ui mousemode right translate > select #4/c 1406 atoms, 1434 bonds, 179 residues, 1 model selected > transparency #4/c 75 > transparency #4/c 75 All > transparency #4/c 100 All > graphics selection color black width 5 > transparency #3/c 90 All > select clear > transparency #3/c 60 All > transparency #3/c 0 All > select #3/c 1406 atoms, 1434 bonds, 179 residues, 1 model selected > show #!4 cartoons > close #1-2#3-4 > open /Users/genya/moreAlphaFold/AF3/fold_opa3_3/fold_opa3_3_model_0.cif Chain information for fold_opa3_3_model_0.cif #1 --- Chain | Description A B C | . > open > /Users/genya/moreAlphaFold/AF3/fold_opa3_3_iars2/fold_opa3_3_iars2_model_0.cif Chain information for fold_opa3_3_iars2_model_0.cif #2 --- Chain | Description A B C | . D | . > select #2 12230 atoms, 12515 bonds, 1549 residues, 1 model selected > show sel cartoons > hide sel atoms > select #2/d 8012 atoms, 8213 bonds, 1012 residues, 1 model selected > color sel dark grey > select #2/d:1-60 451 atoms, 464 bonds, 60 residues, 1 model selected > hide sel cartoons > select #2/a-c 4218 atoms, 4302 bonds, 537 residues, 1 model selected > color sel goldenrod > select #2/a-c:1-30 693 atoms, 702 bonds, 90 residues, 1 model selected > color sel dark salmon > select #2/a-c:80-100 429 atoms, 429 bonds, 63 residues, 1 model selected > color sel saddle brown > select #2/a-c:152-159,115-140 804 atoms, 807 bonds, 102 residues, 1 model selected > color sel cornflower blue > select clear > lighting simple > hide #1 models > select #1 4218 atoms, 4302 bonds, 537 residues, 1 model selected > show sel cartoons > hide sel atoms > select #1/a-c 4218 atoms, 4302 bonds, 537 residues, 1 model selected > color sel goldenrod > select #1/a-c:1-30 693 atoms, 702 bonds, 90 residues, 1 model selected > color sel dark salmon > select #1/a-c:80-100 429 atoms, 429 bonds, 63 residues, 1 model selected > color sel saddle brown > select #1/a-c:152-159,115-140 804 atoms, 807 bonds, 102 residues, 1 model selected > color sel cornflower blue > select clear > lighting simple > show #1 models > hide #2 models > select #2/a-d:10,17,21,86,82,32,29,28,100 320 atoms, 290 bonds, 36 residues, 1 model selected > select #1:10,17,21,86,82,32,29,28,100 255 atoms, 231 bonds, 27 residues, 1 model selected > show sel atoms > style sel sphere Changed 255 atom styles > color sel byhetero > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > select #2/a-c:10,17,21,86,82,32,29,28,100 255 atoms, 231 bonds, 27 residues, 1 model selected > show sel atoms > style sel sphere Changed 255 atom styles > color sel byhetero > select #2/a-c:10,17,21,86,82,32,29,28,100,29,26 288 atoms, 261 bonds, 30 residues, 1 model selected > show sel atoms > style sel sphere Changed 288 atom styles > color sel byhetero > show #1 models > hide #2 models > select #1 4218 atoms, 4302 bonds, 537 residues, 1 model selected > coulombic sel ===== 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 OpenGL renderer: Apple M1 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 Air Model Identifier: MacBookAir10,1 Model Number: MGQN3LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 1 day, 8 hours, 36 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal MNN: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes 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 Tom Goddard all ChimeraX