id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15145 Crash in garbage collection carlton.petermark.3v@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.7.1-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 0x00007000148f1000 (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 0x0000000112a8e600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py"", line 576 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 1613 in remove_deleted_pointers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 134 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 807 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 171 in check_residues 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 41 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.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.surface._surface, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 56) {""app_name"":""ChimeraX"",""timestamp"":""2024-05-09 11:34:59.00 +0900"",""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"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.7.1 (21G920)"",""incident_id"":""04FD0313-88DE-4BAE-8E2F-B1CB372C74B0"",""name"":""ChimeraX""} { ""uptime"" : 760000, ""procLaunch"" : ""2024-05-09 10:56:56.1785 +0900"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""iMac17,1"", ""procStartAbsTime"" : 764162361979334, ""coalitionID"" : 10384, ""osVersion"" : { ""train"" : ""macOS 12.7.1"", ""build"" : ""21G920"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-05-09 11:34:58.6971 +0900"", ""incident"" : ""04FD0313-88DE-4BAE-8E2F-B1CB372C74B0"", ""bug_type"" : ""309"", ""pid"" : 35154, ""procExitAbsTime"" : 766444873871212, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.1"",""CFBundleVersion"":""1.7.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D41E3EDD-7FA9-56A0-9281-5F0E9725ED09"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""B9141A2B-BB6A-AD8E-3FB5-46A0DD310398"", ""sip"" : ""disabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 140737486774103\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe7e000-7fffffe7f000 [ 4K] r-x\/r-x SM=ALI "", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 140737486774103\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe7e000-7fffffe7f000 [ 4K] r-x\/r-x SM=ALI "", ""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"" : [{""queue"":""com.apple.main-thread"",""instructionState"":{""instructionStream"":{""bytes"":[255,255,255,255,72,137,216,72,139,0,72,255,194,72,57,195,117,245,72,141,61,197,18,22,0,72,141,181,112,255,255,255,49,192,232,191,131,254,255,72,139,5,104,231,22,0,72,139,0,72,59,69,216,117,13,72,131,196,112,91,65,92,65,94,65,95,93,195,232,205,174,14,0,102,46,15,31,132,0,0,0,0,0,15,31,0,85,72,137,229,83,80,72,139,71,8,246,128,169,0,0,0,64,117,9,49,192,72,131,196,8,91,93,195,72,137,251,72,139,128,72,1,0,0,72,133,192,117,18,72,139,67,248,168,2,116,224,72,131,192,252,72,137,67,248,235,214,72,137,223,255,208,133,192,117,229,235,203,15,31,132,0,0,0,0,0,85,72,137,229,65,86,83,72,139,71,8,246,128,169,0,0,0,64,117,7,49,192,91,65,94,93],""offset"":96}},""frames"":[{""imageOffset"":32766,""symbol"":""__pthread_kill"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":25087,""symbol"":""pthread_kill"",""symbolLocation"":263,""imageIndex"":1},{""imageOffset"":279240,""symbol"":""raise"",""symbolLocation"":26,""imageIndex"":2},{""imageOffset"":2590164,""symbol"":""faulthandler_fatal_error"",""symbolLocation"":388,""imageIndex"":3},{""imageOffset"":15869,""symbol"":""_sigtramp"",""symbolLocation"":29,""imageIndex"":4},{""imageOffset"":0,""imageIndex"":5},{""imageOffset"":995827,""symbol"":""dict_traverse"",""symbolLocation"":195,""imageIndex"":3},{""imageOffset"":2574472,""symbol"":""gc_collect_main"",""symbolLocation"":2568,""imageIndex"":3},{""imageOffset"":2580738,""symbol"":""_PyObject_GC_Link"",""symbolLocation"":306,""imageIndex"":3},{""imageOffset"":1289213,""symbol"":""_PyType_AllocNoTrack"",""symbolLocation"":125,""imageIndex"":3},{""imageOffset"":1237630,""symbol"":""PyType_GenericAlloc"",""symbolLocation"":14,""imageIndex"":3},{""imageOffset"":1575370,""symbol"":""weakref___new__"",""symbolLocation"":218,""imageIndex"":3},{""imageOffset"":1223445,""symbol"":""type_call"",""symbolLocation"":69,""imageIndex"":3},{""imageOffset"":680881,""symbol"":""_PyObject_MakeTpCall"",""symbolLocation"":129,""imageIndex"":3},{""imageOffset"":1917927,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60455,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":681584,""symbol"":""_PyObject_FastCallDictTstate"",""symbolLocation"":96,""imageIndex"":3},{""imageOffset"":1264021,""symbol"":""slot_tp_init"",""symbolLocation"":181,""imageIndex"":3},{""imageOffset"":1223498,""symbol"":""type_call"",""symbolLocation"":122,""imageIndex"":3},{""imageOffset"":680881,""symbol"":""_PyObject_MakeTpCall"",""symbolLocation"":129,""imageIndex"":3},{""imageOffset"":1917927,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60455,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":681584,""symbol"":""_PyObject_FastCallDictTstate"",""symbolLocation"":96,""imageIndex"":3},{""imageOffset"":1264021,""symbol"":""slot_tp_init"",""symbolLocation"":181,""imageIndex"":3},{""imageOffset"":1223498,""symbol"":""type_call"",""symbolLocation"":122,""imageIndex"":3},{""imageOffset"":50967,""symbol"":""__Pyx_PyObject_CallOneArg(_object*, _object*)"",""symbolLocation"":199,""imageIndex"":6},{""imageOffset"":261486,""symbol"":""__pyx_getprop_8chimerax_6atomic_5cymol_9CyResidue_atoms(_object*, void*)"",""symbolLocation"":1230,""imageIndex"":6},{""imageOffset"":1122116,""symbol"":""_PyObject_GenericGetAttrWithDict"",""symbolLocation"":420,""imageIndex"":3},{""imageOffset"":1888802,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":31330,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":683896,""symbol"":""_PyVectorcall_Call"",""symbolLocation"":120,""imageIndex"":3},{""imageOffset"":1930570,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":73098,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":1930570,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":73098,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":683896,""symbol"":""_PyVectorcall_Call"",""symbolLocation"":120,""imageIndex"":3},{""imageOffset"":1930570,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":73098,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":698270,""symbol"":""method_vectorcall"",""symbolLocation"":334,""imageIndex"":3},{""imageOffset"":683896,""symbol"":""_PyVectorcall_Call"",""symbolLocation"":120,""imageIndex"":3},{""imageOffset"":1930570,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":73098,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":1257453,""symbol"":""PyQtSlot::call(_object*, _object*) const"",""symbolLocation"":125,""imageIndex"":7},{""imageOffset"":1257114,""symbol"":""PyQtSlot::invoke(void**, _object*, void*, bool) const"",""symbolLocation"":362,""imageIndex"":7},{""imageOffset"":1261029,""symbol"":""PyQtSlotProxy::unislot(void**)"",""symbolLocation"":85,""imageIndex"":7},{""imageOffset"":1260890,""symbol"":""PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**)"",""symbolLocation"":58,""imageIndex"":7},{""imageOffset"":777575,""imageIndex"":8},{""imageOffset"":3947277,""symbol"":""QAction::activate(QAction::ActionEvent)"",""symbolLocation"":397,""imageIndex"":9},{""imageOffset"":186197,""symbol"":""sipQToolButton::nextCheckState()"",""symbolLocation"":101,""imageIndex"":10},{""imageOffset"":1254275,""imageIndex"":11},{""imageOffset"":1258649,""symbol"":""QAbstractButton::mouseReleaseEvent(QMouseEvent*)"",""symbolLocation"":185,""imageIndex"":11},{""imageOffset"":2368399,""symbol"":""QToolButton::mouseReleaseEvent(QMouseEvent*)"",""symbolLocation"":15,""imageIndex"":11},{""imageOffset"":182329,""symbol"":""sipQToolButton::mouseReleaseEvent(QMouseEvent*)"",""symbolLocation"":121,""imageIndex"":10},{""imageOffset"":389077,""symbol"":""QWidget::event(QEvent*)"",""symbolLocation"":389,""imageIndex"":11},{""imageOffset"":2370442,""symbol"":""QToolButton::event(QEvent*)"",""symbolLocation"":218,""imageIndex"":11},{""imageOffset"":184655,""symbol"":""sipQToolButton::event(QEvent*)"",""symbolLocation"":191,""imageIndex"":10},{""imageOffset"":51847,""symbol"":""QApplicationPrivate::notify_helper(QObject*, QEvent*)"",""symbolLocation"":247,""imageIndex"":11},{""imageOffset"":61378,""symbol"":""QApplication::notify(QObject*, QEvent*)"",""symbolLocation"":6002,""imageIndex"":11},{""imageOffset"":1282534,""symbol"":""sipQApplication::notify(QObject*, QEvent*)"",""symbolLocation"":230,""imageIndex"":10},{""imageOffset"":449594,""symbol"":""QCoreApplication::notifyInternal2(QObject*, QEvent*)"",""symbolLocation"":170,""imageIndex"":8},{""imageOffset"":53655,""symbol"":""QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool)"",""symbolLocation"":935,""imageIndex"":11},{""imageOffset"":481294,""imageIndex"":11},{""imageOffset"":476809,""imageIndex"":11},{""imageOffset"":51847,""symbol"":""QApplicationPrivate::notify_helper(QObject*, QEvent*)"",""symbolLocation"":247,""imageIndex"":11},{""imageOffset"":55875,""symbol"":""QApplication::notify(QObject*, QEvent*)"",""symbolLocation"":499,""imageIndex"":11},{""imageOffset"":1282534,""symbol"":""sipQApplication::notify(QObject*, QEvent*)"",""symbolLocation"":230,""imageIndex"":10},{""imageOffset"":449594,""symbol"":""QCoreApplication::notifyInternal2(QObject*, QEvent*)"",""symbolLocation"":170,""imageIndex"":8},{""imageOffset"":542428,""symbol"":""QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*)"",""symbolLocation"":2332,""imageIndex"":9},{""imageOffset"":901788,""symbol"":""QWindowSystemInterface::sendWindowSystemEvents(QFlags)"",""symbolLocation"":444,""imageIndex"":9},{""imageOffset"":107163,""imageIndex"":12},{""imageOffset"":524459,""symbol"":""__CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__"",""symbolLocation"":17,""imageIndex"":13},{""imageOffset"":524307,""symbol"":""__CFRunLoopDoSource0"",""symbolLocation"":180,""imageIndex"":13},{""imageOffset"":523661,""symbol"":""__CFRunLoopDoSources0"",""symbolLocation"":242,""imageIndex"":13},{""imageOffset"":518056,""symbol"":""__CFRunLoopRun"",""symbolLocation"":892,""imageIndex"":13},{""imageOffset"":515436,""symbol"":""CFRunLoopRunSpecific"",""symbolLocation"":562,""imageIndex"":13},{""imageOffset"":189926,""symbol"":""RunCurrentEventLoopInMode"",""symbolLocation"":292,""imageIndex"":14},{""imageOffset"":188947,""symbol"":""ReceiveNextEventCommon"",""symbolLocation"":283,""imageIndex"":14},{""imageOffset"":188645,""symbol"":""_BlockUntilNextEventMatchingListInModeWithFilter"",""symbolLocation"":70,""imageIndex"":14},{""imageOffset"":257901,""symbol"":""_DPSNextEvent"",""symbolLocation"":927,""imageIndex"":15},{""imageOffset"":251434,""symbol"":""-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]"",""symbolLocation"":1394,""imageIndex"":15},{""imageOffset"":195801,""symbol"":""-[NSApplication run]"",""symbolLocation"":586,""imageIndex"":15},{""imageOffset"":102572,""imageIndex"":12},{""imageOffset"":488230,""symbol"":""QEventLoop::exec(QFlags)"",""symbolLocation"":486,""imageIndex"":8},{""imageOffset"":451125,""symbol"":""QCoreApplication::exec()"",""symbolLocation"":133,""imageIndex"":8},{""imageOffset"":2252186,""symbol"":""meth_QApplication_exec(_object*, _object*)"",""symbolLocation"":90,""imageIndex"":10},{""imageOffset"":1095658,""symbol"":""cfunction_call"",""symbolLocation"":90,""imageIndex"":3},{""imageOffset"":680881,""symbol"":""_PyObject_MakeTpCall"",""symbolLocation"":129,""imageIndex"":3},{""imageOffset"":1917927,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60455,""imageIndex"":3},{""imageOffset"":1852538,""symbol"":""PyEval_EvalCode"",""symbolLocation"":282,""imageIndex"":3},{""imageOffset"":1830115,""symbol"":""builtin_exec"",""symbolLocation"":483,""imageIndex"":3},{""imageOffset"":1098052,""symbol"":""cfunction_vectorcall_FASTCALL_KEYWORDS"",""symbolLocation"":68,""imageIndex"":3},{""imageOffset"":1917679,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60207,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":2561789,""symbol"":""pymain_run_module"",""symbolLocation"":253,""imageIndex"":3},{""imageOffset"":2560449,""symbol"":""Py_RunMain"",""symbolLocation"":2225,""imageIndex"":3},{""imageOffset"":2564475,""symbol"":""pymain_main"",""symbolLocation"":43,""imageIndex"":3},{""imageOffset"":2564426,""symbol"":""Py_Main"",""symbolLocation"":42,""imageIndex"":3},{""imageOffset"":15770,""symbol"":""main"",""symbolLocation"":122,""imageIndex"":16},{""imageOffset"":21806,""symbol"":""start"",""symbolLocation"":462,""imageIndex"":17}],""id"":5722128,""triggered"":true,""threadState"":{""r13"":{""value"":4432951297,""symbolLocation"":17,""symbol"":""show_stats_each_generations""},""rax"":{""value"":0},""rflags"":{""value"":582},""cpu"":{""value"":0},""r14"":{""value"":11},""rsi"":{""value"":11},""r8"":{""value"":2},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":4608026112,""symbolLocation"":0,""symbol"":""_main_thread""},""r9"":{""value"":14757395258967641293},""r15"":{""value"":22},""rbx"":{""value"":4608026112,""symbolLocation"":0,""symbol"":""_main_thread""},""trap"":{""value"":133},""err"":{""value"":33554760},""r11"":{""value"":582},""rip"":{""value"":140703560241150,""matchesCrashFrame"":1},""rbp"":{""value"":140525424638480},""rsp"":{""value"":140525424638440},""r12"":{""value"":259},""rcx"":{""value"":140525424638440},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":259}},""name"":""CrBrowserMain""},{""id"":5722251,""name"":""ThreadPoolServiceThread"",""frames"":[{""imageOffset"":43194,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":66456106,""imageIndex"":18},{""imageOffset"":66455847,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":65958573,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722254,""name"":""Chrome_IOThread"",""frames"":[{""imageOffset"":43194,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":66456106,""imageIndex"":18},{""imageOffset"":66455847,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":48386978,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722255,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722259,""name"":""CompositorTileWorker1"",""frames"":[{""imageOffset"":17370,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":27247,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1249,""imageIndex"":1},{""imageOffset"":66219291,""imageIndex"":18},{""imageOffset"":100616493,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722260,""name"":""Chrome_InProcGpuThread"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722261,""name"":""Chrome_ChildIOThread"",""frames"":[{""imageOffset"":43194,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":66456106,""imageIndex"":18},{""imageOffset"":66455847,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722263,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722264,""name"":""VizCompositorThread"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722273,""name"":""NetworkService"",""frames"":[{""imageOffset"":43194,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":66456106,""imageIndex"":18},{""imageOffset"":66455847,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722274,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722275,""name"":""ThreadPoolSingleThreadForegroundBlocking0"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66009023,""imageIndex"":18},{""imageOffset"":66011756,""imageIndex"":18},{""imageOffset"":66010829,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722300,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722333,""name"":""com.apple.NSEventThread"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":524957,""symbol"":""__CFRunLoopServiceMachPort"",""symbolLocation"":319,""imageIndex"":13},{""imageOffset"":518440,""symbol"":""__CFRunLoopRun"",""symbolLocation"":1276,""imageIndex"":13},{""imageOffset"":515436,""symbol"":""CFRunLoopRunSpecific"",""symbolLocation"":562,""imageIndex"":13},{""imageOffset"":1755534,""symbol"":""_NSEventThread"",""symbolLocation"":132,""imageIndex"":15},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722344,""name"":""MemoryInfra"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66251759,""imageIndex"":18},{""imageOffset"":65421769,""imageIndex"":18},{""imageOffset"":65919580,""imageIndex"":18},{""imageOffset"":65624472,""imageIndex"":18},{""imageOffset"":66059960,""imageIndex"":18},{""imageOffset"":66060362,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5722345,""name"":""ThreadPoolSingleThreadSharedBackgroundBlocking1"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66009023,""imageIndex"":18},{""imageOffset"":66011034,""imageIndex"":18},{""imageOffset"":66010637,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5731208,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66009023,""imageIndex"":18},{""imageOffset"":66011756,""imageIndex"":18},{""imageOffset"":66010589,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5731209,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66009023,""imageIndex"":18},{""imageOffset"":66011756,""imageIndex"":18},{""imageOffset"":66010733,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5731310,""frames"":[{""imageOffset"":17370,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":27247,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1249,""imageIndex"":1},{""imageOffset"":3466879,""symbol"":""blas_thread_server"",""symbolLocation"":207,""imageIndex"":19},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5731311,""frames"":[{""imageOffset"":17370,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":27247,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1249,""imageIndex"":1},{""imageOffset"":3466879,""symbol"":""blas_thread_server"",""symbolLocation"":207,""imageIndex"":19},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5731312,""frames"":[{""imageOffset"":17370,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":27247,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1249,""imageIndex"":1},{""imageOffset"":3466879,""symbol"":""blas_thread_server"",""symbolLocation"":207,""imageIndex"":19},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5739041,""frames"":[{""imageOffset"":8008,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":5740118,""frames"":[{""imageOffset"":8008,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":5740135,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66009023,""imageIndex"":18},{""imageOffset"":66011034,""imageIndex"":18},{""imageOffset"":66010733,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5740136,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":6506,""symbol"":""mach_msg_trap"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":7384,""symbol"":""mach_msg"",""symbolLocation"":56,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":18},{""imageOffset"":66009023,""imageIndex"":18},{""imageOffset"":66011034,""imageIndex"":18},{""imageOffset"":66010589,""imageIndex"":18},{""imageOffset"":66222344,""imageIndex"":18},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]},{""id"":5740220,""frames"":[{""imageOffset"":8008,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":5740252,""frames"":[{""imageOffset"":17370,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":27247,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1249,""imageIndex"":1},{""imageOffset"":2482708,""symbol"":""PyThread_acquire_lock_timed"",""symbolLocation"":340,""imageIndex"":3},{""imageOffset"":3022238,""symbol"":""acquire_timed"",""symbolLocation"":318,""imageIndex"":3},{""imageOffset"":3022812,""symbol"":""lock_PyThread_acquire_lock"",""symbolLocation"":44,""imageIndex"":3},{""imageOffset"":752391,""symbol"":""method_vectorcall_VARARGS_KEYWORDS"",""symbolLocation"":167,""imageIndex"":3},{""imageOffset"":1917679,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60207,""imageIndex"":3},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":3},{""imageOffset"":698390,""symbol"":""method_vectorcall"",""symbolLocation"":454,""imageIndex"":3},{""imageOffset"":3025702,""symbol"":""thread_run"",""symbolLocation"":230,""imageIndex"":3},{""imageOffset"":2481828,""symbol"":""pythread_wrapper"",""symbolLocation"":36,""imageIndex"":3},{""imageOffset"":25825,""symbol"":""_pthread_start"",""symbolLocation"":125,""imageIndex"":1},{""imageOffset"":8043,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":1}]}], ""usedImages"" : [ { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703560208384, ""size"" : 229376, ""uuid"" : ""5bbc2e64-012e-34dd-8c02-41294a3d66e9"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703560437760, ""size"" : 49152, ""uuid"" : ""e097f78f-fcfb-30f3-9164-dbc9709ba134"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703559192576, ""size"" : 561152, ""uuid"" : ""4ecd1661-9d96-3669-bb31-4c6d5c685d4c"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4430372864, ""CFBundleShortVersionString"" : ""3.11.2, (c) 2001-2023 Python Software Foundation."", ""CFBundleIdentifier"" : ""org.python.python"", ""size"" : 4079616, ""uuid"" : ""24670b23-d78a-3eaa-bca8-22faf877f190"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python"", ""name"" : ""Python"", ""CFBundleVersion"" : ""3.11.2"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703560536064, ""size"" : 40960, ""uuid"" : ""92c1278d-2673-3513-8239-3da30ea67648"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4811034624, ""size"" : 360448, ""uuid"" : ""618ec769-18aa-37be-b55b-7e22658dae7d"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/cymol.cpython-311-darwin.so"", ""name"" : ""cymol.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4509290496, ""size"" : 1589248, ""uuid"" : ""2be8100b-aa99-3117-95ff-0200ddc4032f"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so"", ""name"" : ""QtCore.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4584534016, ""size"" : 5259264, ""uuid"" : ""35b47b1c-6952-3d39-a5e7-711f3ca228f2"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore"", ""name"" : ""QtCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4747493376, ""size"" : 6979584, ""uuid"" : ""49d915f7-1c6d-3bbd-b96f-064260e7d998"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui"", ""name"" : ""QtGui"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4501753856, ""size"" : 2801664, ""uuid"" : ""babd94e3-ec19-3110-ab5b-11c39432d8c5"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so"", ""name"" : ""QtWidgets.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4596965376, ""size"" : 4964352, ""uuid"" : ""f36760e5-d1e7-3a93-ae8c-1c3e55e3fc35"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets"", ""name"" : ""QtWidgets"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4740366336, ""size"" : 655360, ""uuid"" : ""4bf756eb-ff87-3f7f-8c98-b1eda6463b81"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib"", ""name"" : ""libqcocoa.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64h"", ""base"" : 140703560753152, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5255168, ""uuid"" : ""fb79a14a-fda9-3a3b-bc97-6eb525b794a6"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""1866"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703708590080, ""CFBundleShortVersionString"" : ""2.1.1"", ""CFBundleIdentifier"" : ""com.apple.HIToolbox"", ""size"" : 3096576, ""uuid"" : ""913d3d2e-4e4c-3907-98fe-8f4abd551297"", ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703605293056, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 15269888, ""uuid"" : ""461a4d7c-b3e3-3cbc-92b7-a2a419007281"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2113.60.148"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4414951424, ""CFBundleShortVersionString"" : ""1.7.1"", ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"", ""size"" : 16384, ""uuid"" : ""194a3167-3db5-3029-8d22-1d742b826bb9"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""name"" : ""ChimeraX"", ""CFBundleVersion"" : ""1.7.1.0"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4607500288, ""size"" : 442368, ""uuid"" : ""771e1916-3a62-34cd-8488-c1021053c7fa"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4930666496, ""size"" : 165052416, ""uuid"" : ""4aa1de3e-464c-340c-ab61-bcd39bfc7658"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4517556224, ""size"" : 64094208, ""uuid"" : ""9d768904-ac4b-327d-8126-cec11a08b966"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" } ], ""sharedCache"" : { ""base"" : 140703557177344, ""size"" : 19331678208, ""uuid"" : ""172bd7f4-7e24-3286-a975-45e4e44c23c1"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 4256K 8 \nCG image 272K 21 \nColorSync 236K 28 \nCoreAnimation 160K 14 \nCoreGraphics 16K 3 \nCoreServices 932K 4 \nCoreUI image data 4276K 32 \nFoundation 68K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.5G 271 \nMALLOC guard page 48K 9 \nMALLOC_MEDIUM (reserved) 240.0M 4 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 104K 26 \nStack 171.7M 27 \nStack Guard 56.0M 1 \nVM_ALLOCATE 334.8M 283 \n__CTF 756 1 \n__DATA 59.0M 679 \n__DATA_CONST 31.1M 342 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.6M 155 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 809.3M 681 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 191.0M 47 \nshared memory 3500K 26 \n=========== ======= ======= \nTOTAL 4.3G 2900 \nTOTAL, minus reserved VM space 3.9G 2900 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000614 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/pcarlton/Downloads/fold_2024_05_09_10_36phosdsb_1_wdna/fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif Chain information for fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif #1 --- Chain | Description A B | . C D | . E F | . G H | . > hide atoms > show cartoons > lighting shadows false > lighting simple > set bgColor white > set bgColor black > select /F:110 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 455 atoms, 455 bonds, 55 residues, 1 model selected > select add /E:111 464 atoms, 463 bonds, 56 residues, 1 model selected > select up 910 atoms, 910 bonds, 110 residues, 1 model selected Alignment identifier is 1 > select clear > select /E:118 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /F:107 20 atoms, 18 bonds, 2 residues, 1 model selected > select up 910 atoms, 910 bonds, 110 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #f500e7 radius 0.2 dashes 0 interModel false intraRes false > select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif 137 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A TYR 307 OH /F GLU 93 OE1 no hydrogen 2.053 N/A /B TYR 307 OH /E GLU 93 OE1 no hydrogen 2.028 N/A /B ARG 311 NH2 /E GLU 93 OE1 no hydrogen 2.849 N/A /E CYS 83 SG /F GLY 234 O no hydrogen 3.632 N/A /E SER 84 OG /F ASP 9 OD1 no hydrogen 2.613 N/A /E SER 84 OG /F ASP 9 OD2 no hydrogen 3.450 N/A /E ARG 86 NE /B ASP 304 OD1 no hydrogen 3.226 N/A /E ARG 86 NH2 /B SEP 199 O no hydrogen 2.486 N/A /E LEU 87 N /E CYS 83 O no hydrogen 2.947 N/A /E ALA 88 N /E SER 84 O no hydrogen 3.023 N/A /E VAL 89 N /E MET 85 O no hydrogen 3.084 N/A /E LEU 90 N /E ARG 86 O no hydrogen 3.039 N/A /E GLU 91 N /E LEU 87 O no hydrogen 2.923 N/A /E ILE 92 N /E ALA 88 O no hydrogen 3.051 N/A /E GLU 93 N /E VAL 89 O no hydrogen 3.095 N/A /E ARG 94 N /E LEU 90 O no hydrogen 2.920 N/A /E ARG 94 NH1 /B SEP 204 O3P no hydrogen 3.097 N/A /E ARG 94 NH2 /B SEP 204 O3P no hydrogen 2.521 N/A /E ARG 94 NH2 /B SEP 209 O2P no hydrogen 3.374 N/A /E GLN 95 N /E GLU 91 O no hydrogen 2.887 N/A /E GLU 96 N /E ILE 92 O no hydrogen 2.920 N/A /E THR 97 N /E GLU 93 O no hydrogen 2.907 N/A /E THR 97 OG1 /E GLU 93 O no hydrogen 2.672 N/A /E ALA 98 N /E ARG 94 O no hydrogen 2.825 N/A /E MET 99 N /E GLN 95 O no hydrogen 2.809 N/A /E LYS 100 N /E GLU 96 O no hydrogen 2.968 N/A /E LYS 101 N /E THR 97 O no hydrogen 3.008 N/A /E LYS 102 N /E ALA 98 O no hydrogen 2.788 N/A /E GLU 103 N /E MET 99 O no hydrogen 2.958 N/A /E GLU 104 N /E LYS 100 O no hydrogen 2.989 N/A /E SER 105 N /E LYS 101 O no hydrogen 2.814 N/A /E LYS 106 N /E LYS 102 O no hydrogen 2.751 N/A /E ARG 107 N /E GLU 103 O no hydrogen 2.934 N/A /E GLN 108 N /E GLU 104 O no hydrogen 2.779 N/A /E LYS 109 N /E SER 105 O no hydrogen 2.646 N/A /E ILE 110 N /E LYS 106 O no hydrogen 3.171 N/A /E LYS 111 N /E ARG 107 O no hydrogen 3.385 N/A /E LYS 112 N /E GLN 108 O no hydrogen 2.721 N/A /E LYS 112 NZ /E GLN 108 OE1 no hydrogen 2.774 N/A /E THR 113 N /E LYS 109 O no hydrogen 2.763 N/A /E THR 113 N /E ILE 110 O no hydrogen 3.292 N/A /E THR 113 OG1 /E LYS 109 O no hydrogen 2.528 N/A /E GLU 115 N /E LYS 111 O no hydrogen 3.151 N/A /E ARG 116 N /E LYS 112 O no hydrogen 2.711 N/A /E LYS 117 N /E THR 113 O no hydrogen 3.112 N/A /E LYS 118 N /E LYS 114 O no hydrogen 3.262 N/A /E HIS 119 N /E GLU 115 O no hydrogen 2.812 N/A /E ALA 120 N /E ARG 116 O no hydrogen 2.701 N/A /E ILE 121 N /E LYS 117 O no hydrogen 3.050 N/A /E GLN 122 N /E LYS 118 O no hydrogen 3.036 N/A /E ALA 123 N /E HIS 119 O no hydrogen 2.752 N/A /E ALA 124 N /E ALA 120 O no hydrogen 2.859 N/A /E LYS 125 N /E ILE 121 O no hydrogen 3.058 N/A /E THR 126 N /E GLN 122 O no hydrogen 2.888 N/A /E THR 126 OG1 /E GLN 122 O no hydrogen 2.973 N/A /E ARG 127 N /E ALA 123 O no hydrogen 2.813 N/A /E LYS 128 N /E ALA 124 O no hydrogen 2.890 N/A /E GLN 129 N /E LYS 125 O no hydrogen 2.916 N/A /E ARG 130 N /E THR 126 O no hydrogen 2.823 N/A /E ASN 131 N /E ARG 127 O no hydrogen 2.905 N/A /E ASN 131 ND2 /H DC 10 OP2 no hydrogen 2.719 N/A /E GLU 132 N /E LYS 128 O no hydrogen 2.908 N/A /E ILE 133 N /E GLN 129 O no hydrogen 2.853 N/A /E GLU 134 N /E ARG 130 O no hydrogen 2.786 N/A /E GLU 135 N /E ASN 131 O no hydrogen 2.782 N/A /E ALA 136 N /E GLU 132 O no hydrogen 2.933 N/A /E SER 137 N /E ILE 133 O no hydrogen 2.757 N/A /E SER 137 OG /E ILE 133 O no hydrogen 2.576 N/A /E GLN 138 N /E GLU 134 O no hydrogen 3.023 N/A /E ARG 142 NH1 /E GLU 135 OE1 no hydrogen 3.551 N/A /E ARG 145 NH2 /E GLU 134 OE1 no hydrogen 2.611 N/A /F CYS 83 SG /E GLY 234 O no hydrogen 3.414 N/A /F SER 84 OG /E ASP 9 OD1 no hydrogen 2.290 N/A /F SER 84 OG /E ASP 9 OD2 no hydrogen 3.183 N/A /F ARG 86 NE /A ASP 304 OD1 no hydrogen 2.876 N/A /F ARG 86 NH2 /A VAL 203 O no hydrogen 2.419 N/A /F LEU 87 N /F CYS 83 O no hydrogen 2.943 N/A /F ALA 88 N /F SER 84 O no hydrogen 3.021 N/A /F VAL 89 N /F MET 85 O no hydrogen 3.103 N/A /F LEU 90 N /F ARG 86 O no hydrogen 3.025 N/A /F GLU 91 N /F LEU 87 O no hydrogen 2.924 N/A /F ILE 92 N /F ALA 88 O no hydrogen 3.059 N/A /F GLU 93 N /F VAL 89 O no hydrogen 3.126 N/A /F ARG 94 N /F LEU 90 O no hydrogen 2.937 N/A /F ARG 94 NH1 /A SEP 204 O3P no hydrogen 3.195 N/A /F ARG 94 NH2 /A SEP 204 O3P no hydrogen 2.483 N/A /F GLN 95 N /F GLU 91 O no hydrogen 2.889 N/A /F GLU 96 N /F ILE 92 O no hydrogen 2.939 N/A /F THR 97 N /F GLU 93 O no hydrogen 2.936 N/A /F THR 97 OG1 /F GLU 93 O no hydrogen 2.687 N/A /F ALA 98 N /F ARG 94 O no hydrogen 2.816 N/A /F MET 99 N /F GLN 95 O no hydrogen 2.801 N/A /F LYS 100 N /F GLU 96 O no hydrogen 2.991 N/A /F LYS 101 N /F THR 97 O no hydrogen 3.040 N/A /F LYS 102 N /F ALA 98 O no hydrogen 2.794 N/A /F GLU 103 N /F MET 99 O no hydrogen 2.974 N/A /F GLU 104 N /F LYS 100 O no hydrogen 3.007 N/A /F SER 105 N /F LYS 101 O no hydrogen 2.826 N/A /F LYS 106 N /F LYS 102 O no hydrogen 2.789 N/A /F ARG 107 N /F GLU 103 O no hydrogen 2.981 N/A /F GLN 108 N /F GLU 104 O no hydrogen 2.803 N/A /F LYS 109 N /F SER 105 O no hydrogen 2.664 N/A /F ILE 110 N /F LYS 106 O no hydrogen 3.237 N/A /F LYS 111 N /F ARG 107 O no hydrogen 3.425 N/A /F LYS 112 N /F GLN 108 O no hydrogen 2.747 N/A /F LYS 112 NZ /F GLN 108 OE1 no hydrogen 2.801 N/A /F THR 113 N /F LYS 109 O no hydrogen 2.807 N/A /F THR 113 N /F ILE 110 O no hydrogen 3.293 N/A /F THR 113 OG1 /F LYS 109 O no hydrogen 2.572 N/A /F GLU 115 N /F LYS 111 O no hydrogen 3.171 N/A /F ARG 116 N /F LYS 112 O no hydrogen 2.732 N/A /F LYS 117 N /F THR 113 O no hydrogen 3.163 N/A /F LYS 118 N /F LYS 114 O no hydrogen 3.291 N/A /F HIS 119 N /F GLU 115 O no hydrogen 2.829 N/A /F ALA 120 N /F ARG 116 O no hydrogen 2.736 N/A /F ILE 121 N /F LYS 117 O no hydrogen 3.078 N/A /F GLN 122 N /F LYS 118 O no hydrogen 3.064 N/A /F ALA 123 N /F HIS 119 O no hydrogen 2.770 N/A /F ALA 124 N /F ALA 120 O no hydrogen 2.881 N/A /F LYS 125 N /F ILE 121 O no hydrogen 3.083 N/A /F THR 126 N /F GLN 122 O no hydrogen 2.918 N/A /F THR 126 OG1 /F GLN 122 O no hydrogen 3.002 N/A /F ARG 127 N /F ALA 123 O no hydrogen 2.832 N/A /F LYS 128 N /F ALA 124 O no hydrogen 2.918 N/A /F GLN 129 N /F LYS 125 O no hydrogen 2.956 N/A /F ARG 130 N /F THR 126 O no hydrogen 2.852 N/A /F ASN 131 N /F ARG 127 O no hydrogen 2.936 N/A /F ASN 131 ND2 /G DC 10 OP2 no hydrogen 3.191 N/A /F GLU 132 N /F LYS 128 O no hydrogen 2.950 N/A /F ILE 133 N /F GLN 129 O no hydrogen 2.875 N/A /F GLU 134 N /F ARG 130 O no hydrogen 2.813 N/A /F GLU 135 N /F ASN 131 O no hydrogen 2.813 N/A /F ALA 136 N /F GLU 132 O no hydrogen 2.970 N/A /F SER 137 N /F ILE 133 O no hydrogen 2.807 N/A /F SER 137 OG /F ILE 133 O no hydrogen 2.626 N/A /F GLN 138 N /F GLU 134 O no hydrogen 3.062 N/A /F ARG 145 NH2 /F GLU 134 OE1 no hydrogen 2.688 N/A 137 hydrogen bonds found > style sel ball Changed 258 atom styles > select up 1121 atoms, 1109 bonds, 131 residues, 1 model selected > style sel ball Changed 1121 atom styles > select clear Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 > select clear > select /G-H:1-2 86 atoms, 94 bonds, 4 residues, 1 model selected > select /G-H:1-43 1766 atoms, 1976 bonds, 86 residues, 1 model selected > select clear > select /A-B:186 20 atoms, 18 bonds, 2 residues, 1 model selected > select /A-B:186 20 atoms, 18 bonds, 2 residues, 1 model selected > close #1.1 > show sel atoms > style sel sphere Changed 20 atom styles > color sel byhetero > select clear Drag select of 7 residues Drag select of 15 residues > select up 846 atoms, 851 bonds, 112 residues, 1 model selected > select up 7523 atoms, 7683 bonds, 945 residues, 1 model selected > hide sel cartoons Drag select of 14 residues > select up 482 atoms, 490 bonds, 64 residues, 1 model selected > select up 3055 atoms, 3127 bonds, 385 residues, 1 model selected > hide sel cartoons > select clear Drag select of 2 residues > select up 75 atoms, 75 bonds, 10 residues, 1 model selected > select up 2817 atoms, 2865 bonds, 345 residues, 1 model selected > rainbow sel Drag select of 4 residues > select up 216 atoms, 220 bonds, 26 residues, 1 model selected > select up 2817 atoms, 2865 bonds, 345 residues, 1 model selected > rainbow sel > select clear Drag select of 21 residues > select up 380 atoms, 382 bonds, 45 residues, 1 model selected > select up 5634 atoms, 5730 bonds, 690 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif_E SES surface #1.1: minimum, -19.54, mean -0.18, maximum 15.79 Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif_F SES surface #1.2: minimum, -18.71, mean -0.20, maximum 15.51 To also show corresponding color key, enter the above coulombic command and add key true > show sel cartoons > select clear > select /A-B:285-286 30 atoms, 30 bonds, 4 residues, 1 model selected > select /A-B:285-385 1632 atoms, 1662 bonds, 202 residues, 1 model selected > show sel cartoons > select /C-D:201 14 atoms, 12 bonds, 2 residues, 1 model selected > select /C-D:201-280 1298 atoms, 1324 bonds, 160 residues, 1 model selected > show sel cartoons > select clear > show cartoons > select clear Drag select of fold_2024_05_09_10_36phosdsb_1_wdna_model_0.cif_F SES surface, 35405 of 414852 triangles, 16 atoms, 43 residues, 13 bonds > select clear > select /E-F:100 18 atoms, 16 bonds, 2 residues, 1 model selected > select /E-F:100-119 358 atoms, 358 bonds, 40 residues, 1 model selected > set bgColor white > movie record > turn y 2 180 > wait 180 > movie encode /Users/pcarlton/Desktop/movie3.mp4 Movie saved to /Users/pcarlton/Desktop/movie3.mp4 > close > open > /Users/pcarlton/Downloads/fold_2024_05_09_10_36phosdsb_1_wdna/fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif Chain information for fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif #1 --- Chain | Description A B | . C D | . E F | . G H | . > hide atoms > show cartoons Drag select of 3 residues > select up 438 atoms, 438 bonds, 52 residues, 1 model selected > select up 2817 atoms, 2865 bonds, 345 residues, 1 model selected > select up 18062 atoms, 18610 bonds, 2110 residues, 1 model selected > select down 2817 atoms, 2865 bonds, 345 residues, 1 model selected > select add /F:110 2825 atoms, 2872 bonds, 346 residues, 1 model selected > select up 3249 atoms, 3297 bonds, 396 residues, 1 model selected > select up 5634 atoms, 5730 bonds, 690 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif_E SES surface #1.1: minimum, -17.65, mean -0.16, maximum 19.29 Coulombic values for fold_2024_05_09_10_36phosdsb_1_wdna_model_1.cif_F SES surface #1.2: minimum, -17.58, mean -0.16, maximum 18.76 To also show corresponding color key, enter the above coulombic command and add key true > open > /Users/pcarlton/Downloads/fold_2024_05_09_10_36dsb_123_wdna/fold_2024_05_09_10_36dsb_123_wdna_model_0.cif Chain information for fold_2024_05_09_10_36dsb_123_wdna_model_0.cif #2 --- Chain | Description A B | . C D | . E F | . G H | . > hide #!1 models > close #1 > hide atoms > show cartoons > select /F:88 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /E:135 14 atoms, 12 bonds, 2 residues, 1 model selected > select up 874 atoms, 874 bonds, 104 residues, 1 model selected > select up 5634 atoms, 5730 bonds, 690 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 > open > /Users/pcarlton/Downloads/fold_2024_05_09_11_32_scerec114x4_mei4x2_dna/fold_2024_05_09_11_32_scerec114x4_mei4x2_dna_model_0.cif Chain information for fold_2024_05_09_11_32_scerec114x4_mei4x2_dna_model_0.cif #1 --- Chain | Description A B C D | . E F | . G H | . OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: iMac Model Identifier: iMac17,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 32 GB System Firmware Version: 522.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.33f12 Software: System Software Overview: System Version: macOS 12.7.1 (21G920) Kernel Version: Darwin 21.6.0 Time since boot: 8 days 21:10 Graphics/Displays: AMD Radeon R9 M380: Chipset Model: AMD Radeon R9 M380 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x6640 Revision ID: 0x0080 ROM Revision: 113-C6005R-800 VBIOS Version: 113-C6005T-009 EFI Driver Version: 01.00.800 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal EV2336W: Resolution: 1080 x 1920 UI Looks like: 1080 x 1920 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 80101073 Mirror: Off Online: Yes Rotation: 90 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