id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7339 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000144d0000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1284 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070002758c000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700026589000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700025586000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700024583000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700023580000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070002257d000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070002157a000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700020577000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001f574000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001e571000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001d56e000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001c56b000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001b568000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001a565000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700019562000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001855f000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001755c000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700016559000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700015556000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000011165fdc0 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main Process: ChimeraX [604] Path: /Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.3.0 (1.3.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [604] User ID: 573055 Date/Time: 2022-07-28 15:04:14.834 +0200 OS Version: Mac OS X 10.15.7 (19H1615) Report Version: 12 Bridge OS Version: 6.1 (19P647) Anonymous UUID: BF10E68F-7EB4-A7BF-BFD0-67ED6F3CDCA0 Time Awake Since Boot: 270000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff711fc33a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff712b8e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff7111393e raise + 26 3 libsystem_platform.dylib 0x00007fff712ad5fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 org.python.python 0x000000010be6c06d cfunction_call + 125 6 org.python.python 0x000000010be2d6cc _PyObject_Call + 140 7 QtCore.abi3.so 0x00000001111e9957 PyQtSlot::call(_object*, _object*) const + 39 8 QtCore.abi3.so 0x00000001111e9866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374 9 QtCore.abi3.so 0x00000001111ea455 PyQtSlotProxy::unislot(void**) + 85 10 QtCore.abi3.so 0x00000001111ea3ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58 11 QtCore 0x00000001218bdb9f QObject::event(QEvent*) + 943 12 QtWidgets 0x0000000123e3f9ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266 13 QtWidgets 0x0000000123e40e11 QApplication::notify(QObject*, QEvent*) + 497 14 QtWidgets.abi3.so 0x00000001239f2db9 sipQApplication::notify(QObject*, QEvent*) + 233 15 QtCore 0x0000000121892a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 16 QtCore 0x0000000121893d79 QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 809 17 libqcocoa.dylib 0x000000013209d259 QCocoaEventDispatcherPrivate::processPostedEvents() + 313 18 libqcocoa.dylib 0x000000013209d9c8 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void*) + 40 19 com.apple.CoreFoundation 0x00007fff37317682 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 20 com.apple.CoreFoundation 0x00007fff37317621 __CFRunLoopDoSource0 + 103 21 com.apple.CoreFoundation 0x00007fff3731743b __CFRunLoopDoSources0 + 209 22 com.apple.CoreFoundation 0x00007fff3731616a __CFRunLoopRun + 927 23 com.apple.CoreFoundation 0x00007fff3731576e CFRunLoopRunSpecific + 462 24 com.apple.HIToolbox 0x00007fff35f41aad RunCurrentEventLoopInMode + 292 25 com.apple.HIToolbox 0x00007fff35f416e4 ReceiveNextEventCommon + 359 26 com.apple.HIToolbox 0x00007fff35f41569 _BlockUntilNextEventMatchingListInModeWithFilter + 64 27 com.apple.AppKit 0x00007fff3458a659 _DPSNextEvent + 883 28 com.apple.AppKit 0x00007fff34588ea0 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352 29 com.apple.AppKit 0x00007fff3457abae -[NSApplication run] + 658 30 libqcocoa.dylib 0x000000013209c62f QCocoaEventDispatcher::processEvents(QFlags) + 2495 31 QtCore 0x000000012188eacf QEventLoop::exec(QFlags) + 431 32 QtCore 0x0000000121893042 QCoreApplication::exec() + 130 33 QtWidgets.abi3.so 0x0000000123ae4702 meth_QApplication_exec_(_object*, _object*) + 82 34 org.python.python 0x000000010be6c06d cfunction_call + 125 35 org.python.python 0x000000010be2d17d _PyObject_MakeTpCall + 365 36 org.python.python 0x000000010bf0561c call_function + 876 37 org.python.python 0x000000010bf02ab3 _PyEval_EvalFrameDefault + 25219 38 org.python.python 0x000000010be2d948 function_code_fastcall + 104 39 org.python.python 0x000000010be2f98a method_vectorcall + 202 40 org.python.python 0x000000010bf0558c call_function + 732 41 org.python.python 0x000000010bf02ab3 _PyEval_EvalFrameDefault + 25219 42 org.python.python 0x000000010bf06283 _PyEval_EvalCode + 2611 43 org.python.python 0x000000010be2d8d1 _PyFunction_Vectorcall + 289 44 org.python.python 0x000000010bf0558c call_function + 732 45 org.python.python 0x000000010bf02b4b _PyEval_EvalFrameDefault + 25371 46 org.python.python 0x000000010bf06283 _PyEval_EvalCode + 2611 47 org.python.python 0x000000010befc70b PyEval_EvalCode + 139 48 org.python.python 0x000000010bef9592 builtin_exec + 626 49 org.python.python 0x000000010be6b86a cfunction_vectorcall_FASTCALL + 218 50 org.python.python 0x000000010bf0558c call_function + 732 51 org.python.python 0x000000010bf02b4b _PyEval_EvalFrameDefault + 25371 52 org.python.python 0x000000010bf06283 _PyEval_EvalCode + 2611 53 org.python.python 0x000000010be2d8d1 _PyFunction_Vectorcall + 289 54 org.python.python 0x000000010bf0558c call_function + 732 55 org.python.python 0x000000010bf02b4b _PyEval_EvalFrameDefault + 25371 56 org.python.python 0x000000010bf06283 _PyEval_EvalCode + 2611 57 org.python.python 0x000000010be2d8d1 _PyFunction_Vectorcall + 289 58 org.python.python 0x000000010bf6be20 pymain_run_module + 208 59 org.python.python 0x000000010bf6b537 Py_RunMain + 1431 60 org.python.python 0x000000010bf6bb3f pymain_main + 223 61 org.python.python 0x000000010bf6ba4b Py_Main + 43 62 edu.ucsf.cgl.ChimeraX 0x000000010bdeadc8 main + 120 63 libdyld.dylib 0x00007fff710b4cc9 start + 1 Thread 1:: ThreadPoolServiceThread 0 libsystem_kernel.dylib 0x00007fff711feb96 kevent64 + 10 1 QtWebEngineCore 0x0000000127950e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x0000000127950cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x00000001278d962b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x000000012789d7cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x00000001278e4a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20 6 QtWebEngineCore 0x00000001278f8a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x0000000127941e07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15 Thread 2:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60 2 QtWebEngineCore 0x0000000127946492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001278ee778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x00000001278ef150 base::internal::WorkerThread::RunWorker() + 1024 5 QtWebEngineCore 0x00000001278eec44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20 6 QtWebEngineCore 0x0000000127941e07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15 Thread 3:: Chrome_IOThread 0 libsystem_kernel.dylib 0x00007fff711feb96 kevent64 + 10 1 QtWebEngineCore 0x0000000127950e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x0000000127950cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x00000001278d962b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x000000012789d7cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x000000012b81df06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102 6 QtWebEngineCore 0x00000001278f8a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x0000000127941e07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15 Thread 4:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff711f5dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff711f6170 mach_msg + 60 2 QtWebEngineCore 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base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001278ee778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x00000001278eee3d base::internal::WorkerThread::RunWorker() + 237 5 QtWebEngineCore 0x00000001278eecd4 base::internal::WorkerThread::RunPooledWorker() + 20 6 QtWebEngineCore 0x0000000127941e07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15 Thread 59: 0 libsystem_kernel.dylib 0x00007fff711f8882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff712b9425 _pthread_cond_wait + 698 2 org.python.python 0x000000010bf5bd6c PyThread_acquire_lock_timed + 700 3 org.python.python 0x000000010bfaaa1f acquire_timed + 111 4 org.python.python 0x000000010bfaab30 lock_PyThread_acquire_lock + 48 5 org.python.python 0x000000010be35e54 method_vectorcall_VARARGS_KEYWORDS + 388 6 org.python.python 0x000000010bf0558c call_function + 732 7 org.python.python 0x000000010bf02a92 _PyEval_EvalFrameDefault + 25186 8 org.python.python 0x000000010bf06283 _PyEval_EvalCode + 2611 9 org.python.python 0x000000010be2d8d1 _PyFunction_Vectorcall + 289 10 org.python.python 0x000000010bf0558c call_function + 732 11 org.python.python 0x000000010bf02a92 _PyEval_EvalFrameDefault + 25186 12 org.python.python 0x000000010bf06283 _PyEval_EvalCode + 2611 13 org.python.python 0x000000010be2d8d1 _PyFunction_Vectorcall + 289 14 org.python.python 0x000000010bf0558c call_function + 732 15 org.python.python 0x000000010bf02a92 _PyEval_EvalFrameDefault + 25186 16 org.python.python 0x000000010be2d948 function_code_fastcall + 104 17 org.python.python 0x000000010bf0558c call_function + 732 18 org.python.python 0x000000010bf02a92 _PyEval_EvalFrameDefault + 25186 19 org.python.python 0x000000010be2d948 function_code_fastcall + 104 20 org.python.python 0x000000010bf0558c call_function + 732 21 org.python.python 0x000000010bf02a92 _PyEval_EvalFrameDefault + 25186 22 org.python.python 0x000000010be2d948 function_code_fastcall + 104 23 org.python.python 0x000000010be2f9d2 method_vectorcall + 274 24 org.python.python 0x000000010bfaa3c6 t_bootstrap + 70 25 org.python.python 0x000000010bf5b8c9 pythread_wrapper + 25 26 libsystem_pthread.dylib 0x00007fff712b9109 _pthread_start + 148 27 libsystem_pthread.dylib 0x00007fff712b4b8b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000011165fdc0 rcx: 0x00007fe418047a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fe418047a80 rsp: 0x00007fe418047a58 r8: 0x00007fe418047f48 r9: 0x8a2f902ab8232aec r10: 0x000000011165fdc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x0000600002513540 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff711fc33a rfl: 0x0000000000000246 cr2: 0x00007fe418046f00 Logical CPU: 0 Error Code: 0x02000148 Trap 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0x7fff710e5ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff710e6000 - 0x7fff710e8ff3 libquarantine.dylib (110.40.5) /usr/lib/system/libquarantine.dylib 0x7fff710e9000 - 0x7fff710eaff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff710eb000 - 0x7fff71102ff3 libsystem_asl.dylib (377.60.3) /usr/lib/system/libsystem_asl.dylib 0x7fff71103000 - 0x7fff71103ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff71104000 - 0x7fff7118bfff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib 0x7fff7118c000 - 0x7fff7118fffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib 0x7fff71190000 - 0x7fff71193fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib 0x7fff71194000 - 0x7fff7119cfff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib 0x7fff7119d000 - 0x7fff711a4fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff711a5000 - 0x7fff711a6ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff711a7000 - 0x7fff711f4ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff711f5000 - 0x7fff71221ff7 libsystem_kernel.dylib (6153.141.50) /usr/lib/system/libsystem_kernel.dylib 0x7fff71222000 - 0x7fff71269fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff7126a000 - 0x7fff71291fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff71292000 - 0x7fff7129fffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff712a0000 - 0x7fff712a9ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff712aa000 - 0x7fff712b2fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff712b3000 - 0x7fff712bdfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff712be000 - 0x7fff712c2ff3 libsystem_sandbox.dylib (1217.141.7) /usr/lib/system/libsystem_sandbox.dylib 0x7fff712c3000 - 0x7fff712c5fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff712c6000 - 0x7fff712cdffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib 0x7fff712ce000 - 0x7fff712e4ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib 0x7fff712e6000 - 0x7fff712ebff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff712ec000 - 0x7fff71321ffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 55823 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 24668467 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%) Writable regions: Total=13.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=13.3G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 768K 6 Activity Tracing 256K 1 CG backing stores 2096K 4 CG image 572K 42 CoreAnimation 4724K 84 CoreGraphics 8K 1 CoreImage 48K 6 CoreUI image data 4140K 36 Foundation 28K 2 Kernel Alloc Once 8K 1 MALLOC 10.8G 686 MALLOC guard page 48K 10 MALLOC_MEDIUM (reserved) 1.3G 16 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) Mach message 24K 4 OpenGL GLSL 384K 5 STACK GUARD 236K 59 Stack 468.0M 60 Stack Guard 56.0M 1 VM_ALLOCATE 207.8M 288 VM_ALLOCATE (reserved) 352.0M 2 reserved VM address space (unallocated) __DATA 66.4M 651 __DATA_CONST 136K 7 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 494.8M 218 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 643.5M 591 __UNICODE 564K 1 mapped file 425.5M 95 shared memory 2992K 34 =========== ======= ======= TOTAL 15.0G 2917 TOTAL, minus reserved VM space 13.1G 2917 ===== Log before crash start ===== > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC- > AdML18W_1_Fr16/processing/Frankenmaps/PIC-NCP- > CAK_comp/composite/composite_half1.mrc Opened composite_half1.mrc as #1, grid size 400,400,400, pixel 1.05, shown at level 0.00929, step 2, values float32 > volume #1 step 1 > volume #1 level 0.006359 > volume #1 level 0.005137 > volume #1 level 0.01247 > volume #1 level 0.01076 > volume #1 level 0.00868 > open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC- > AdML18W_1_Fr16/processing/Relion/MaskCreate/job349/mask.mrc Opened mask.mrc as #2, grid size 400,400,400, pixel 1.05, shown at level 1, step 2, values float32 > volume #2 step 1 > volume #2 level 1 > volume #2 level 0.9533 > volume #2 level 1 > volume #2 level 0.2513 > open /Volumes/EM11600_2/DATA/jabrilg/20220405_33_hPIC- > AdML18W_1_Fr16/processing/Relion/LocalRes/job641/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #3, grid size 400,400,400, pixel 1.05, shown at level 0.0181, step 2, values float32 > hide #!2 models > hide #!1 models > volume #3 step 1 > volume #3 level 0.01452 > volume #3 level 0.02931 > volume #3 level 0.01715 > hide #!3 models > open ""/Users/jabrilg/Desktop/Lab meetings/Lab meeting > 6/Images/Scripting/PIC-NCP_plusRPB6-plusCAK_REFINED.pdb"" Chain information for PIC-NCP_plusRPB6-plusCAK_REFINED.pdb #4 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available Q | No description available R | No description available T | No description available U | No description available V | No description available W | No description available X | No description available a | No description available b f | No description available c | No description available d | No description available e | No description available g | No description available h | No description available > show cartoons > hide atoms > dssp > close #4 > open /Users/jabrilg/Desktop/10W_processing/Ref/j29/run_ct22_class001.mrc Opened run_ct22_class001.mrc as #4, grid size 400,400,400, pixel 1.05, shown at level 0.0167, step 2, values float32 > volume #4 step 1 > volume #4 level 0.008012 > volume #4 level 0.00496 > volume #4 level 0.003193 > volume #4 level 0.007369 > volume #4 level 0.003996 > open /Users/jabrilg/Desktop/10W_processing/CAK_gauss_mask-j29.mrc Opened CAK_gauss_mask-j29.mrc as #5, grid size 400,400,400, pixel 1.05, shown at level 1, step 2, values float32 > volume #5 level 0.9982 > volume #5 color #ffb2ff69 > volume #5 color #ffb2ff68 > close #4-5 > open /Users/jabrilg/Desktop/18W_processing/Ref/j364/PIC-NCP- > CAK_comp/composite/PIC-NCP-CAK_lres_comp_sharpened_map.ccp4 Opened PIC-NCP-CAK_lres_comp_sharpened_map.ccp4 as #4, grid size 400,400,400, pixel 1.05, shown at level 4.29, step 2, values float32 > volume #4 step 1 > volume #4 level 6.471 > volume #4 level 3.258 > volume #4 level 3.643 > open /Volumes/EM11600/DATA/jabrilg/maps_Julio_PIC-NCP_18W/Modelling/PIC-NCP- > CAK/PIC-NCP-CAK_lres_comp_sharpened_map.ccp4 Opened PIC-NCP-CAK_lres_comp_sharpened_map.ccp4 as #5, grid size 400,400,400, pixel 1.05, shown at level 4.29, step 2, values float32 > hide #!4 models > volume #5 step 1 > volume #5 level 3.386 > volume #5 level 5.443 > volume #5 level 4.286 > volume #5 level 3.9 > close #5 > show #!4 models > open /Users/jabrilg/Desktop/18W_processing/Ref/j364/PIC-NCP- > CAK_comp/composite/composite_half1.mrc Opened composite_half1.mrc as #5, grid size 400,400,400, pixel 1.05, shown at level 0.00929, step 2, values float32 > volume #5 step 1 > volume #5 level 0.008285 > volume #5 level 0.008033 > volume #4 level 2.487 > volume #5 level 0.007027 > close #1-5 > open /Volumes/EM11600/DATA/jabrilg/maps_Julio_PIC-NCP_18W/Modelling/PIC-NCP- > CAK/PIC-NCP-CAK_lres_comp_sharpened_map.ccp4 Opened PIC-NCP-CAK_lres_comp_sharpened_map.ccp4 as #1, grid size 400,400,400, pixel 1.05, shown at level 4.29, step 2, values float32 > open /Volumes/EM11600/DATA/jabrilg/maps_Julio_PIC-NCP_18W/Modelling/PIC-NCP- > CAK/j364_PIC-NCP-CAK_lres-sharpened_map.ccp4 Opened j364_PIC-NCP-CAK_lres-sharpened_map.ccp4 as #2, grid size 400,400,400, pixel 1.05, shown at level 4.44, step 2, values float32 > open /Volumes/EM11600/DATA/jabrilg/maps_Julio_PIC-NCP_18W/Refinements/PIC- > NCP-CAK_ref/6cycles/PIC-NCP18W_refined-final.pdb Chain information for PIC-NCP18W_refined-final.pdb #3 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available Q | No description available R | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available > show cartoons > hide atoms > dssp > volume #1 step 1 > volume #1 level 3.287 > volume #2 step 1 > volume #2 level 1.931 > volume #1 level 3.162 > volume #2 level 1.248 > volume #2 level 1.59 > volume #2 level 1.704 > volume #2 level 1.248 > volume #2 level 1.59 > volume #2 level 2.045 > open /Volumes/EM11600/DATA/jabrilg/20210727_27_hPIC- > AdML10W_2/processing/Relion/LocalRes/job906/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #4, grid size 200,200,200, pixel 1.05, shown at level 0.0262, step 1, values float32 > open /Volumes/EM11600/DATA/jabrilg/20210727_27_hPIC- > AdML10W_2/processing/Relion/LocalRes/job907/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #5, grid size 200,200,200, pixel 1.05, shown at level 0.0307, step 1, values float32 > hide #!4 models > hide #!3 models > hide #!2 models > show #!4 models > hide #!5 models > volume #4 level 0.01807 > show #!5 models > hide #!4 models > volume #5 level 0.01959 > open ""/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for > figures/chimera_lres.cxs"" Opened run_class001.mrc as #10, grid size 400,400,400, pixel 1.05, shown at level 0.00637, step 1, values float32 Opened run_class001.mrc as #12, grid size 400,400,400, pixel 1.05, shown at level 0.00654, step 1, values float32 Opened Gauss_Mask.mrc as #11, grid size 400,400,400, pixel 1.05, shown at level 0.791, step 1, values float32 Opened run_it060_class001.mrc copy as #7, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class002.mrc copy as #13, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class003.mrc copy as #14, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class004.mrc copy as #15, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class001.mrc copy as #19, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class002.mrc copy as #20, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class003.mrc copy as #21, grid size 400,400,400, pixel 1.05, shown at level 0.0095, step 1, values float32 Opened run_it060_class001.mrc as #2, grid size 400,400,400, pixel 1.05, shown at level 0.01, step 1, values float32 Opened run_it060_class003.mrc as #4, grid size 400,400,400, pixel 1.05, shown at level 0.01, step 1, values float32 Opened run_it060_class001.mrc as #3, grid size 400,400,400, pixel 1.05, shown at level 0.008, step 1, values float32 Opened run_it060_class002.mrc as #5, grid size 400,400,400, pixel 1.05, shown at level 0.008, step 1, values float32 Opened run_it060_class003.mrc as #16, grid size 400,400,400, pixel 1.05, shown at level 0.008, step 1, values float32 Opened run_it060_class004.mrc as #17, grid size 400,400,400, pixel 1.05, shown at level 0.008, step 1, values float32 Opened run_it060_class001.mrc as #18, grid size 400,400,400, pixel 1.05, shown at level 0.012, step 1, values float32 Opened run_it060_class002.mrc as #22, grid size 400,400,400, pixel 1.05, shown at level 0.012, step 1, values float32 Opened run_it060_class003.mrc as #23, grid size 400,400,400, pixel 1.05, shown at level 0.012, step 1, values float32 Opened run_it060_class004.mrc as #24, grid size 400,400,400, pixel 1.05, shown at level 0.012, step 1, values float32 Opened postprocess.mrc as #25, grid size 250,250,250, pixel 1.05, shown at level 0.015, step 1, values float32 Opened run_class001.mrc as #26, grid size 400,400,400, pixel 1.05, shown at level 0.0083, step 1, values float32 Opened j662_cPIC_rec_lres_sharpened_map.ccp4 copy as #28, grid size 300,300,300, pixel 1.05, shown at level 3.5, step 1, values float32 Opened postprocess_masked.mrc as #27, grid size 200,200,200, pixel 1.05, shown at level 0.021, step 1, values float32 Opened NCP_postprocess.mrc as #29, grid size 200,200,200, pixel 1.05, shown at level 0.025, step 1, values float32 Opened j665_cPIC-high_rec_lres_sharpened_map.ccp4 copy as #31, grid size 300,300,300, pixel 1.05, shown at level 2.8, step 1, values float32 Opened j803_cPIC-NCP_lres_sharpened.ccp4 as #30, grid size 400,400,400, pixel 1.05, shown at level 4.13, step 1, values float32 Opened postprocess.mrc as #32, grid size 300,300,300, pixel 1.05, shown at level 0.016, step 1, values float32 Opened postprocess.mrc as #33, grid size 300,300,300, pixel 1.05, shown at level 0.01, step 1, values float32 Opened run_half1_class001_unfil.mrc as #34, grid size 300,300,300, pixel 1.05, shown at level 0.0145, step 1, values float32 Opened upstr_post.mrc as #35, grid size 300,300,300, pixel 1.05, shown at level 0.018, step 2, values float32 Opened run_class001.mrc as #36, grid size 400,400,400, pixel 1.05, shown at level 0.0203, step 1, values float32 Opened relion_locres_filtered.mrc as #6, grid size 300,300,300, pixel 1.05, shown at level 0.0181, step 1, values float32 Opened relion_locres.mrc as #37, grid size 300,300,300, pixel 1.05, shown at level 23.5, step 2, values float32 Opened relion_locres_filtered.mrc as #39, grid size 400,400,400, pixel 1.05, shown at level 0.0135, step 1, values float32 Opened relion_locres.mrc as #40, grid size 400,400,400, pixel 1.05, shown at level 24.7, step 2, values float32 Opened relion_locres_filtered.mrc as #41, grid size 300,300,300, pixel 1.05, shown at level 0.0184, step 1, values float32 Opened relion_locres.mrc as #42, grid size 300,300,300, pixel 1.05, shown at level 24.2, step 2, values float32 Opened relion_locres_filtered.mrc copy as #44, grid size 300,300,300, pixel 1.05, shown at level 0.0184, step 1, values float32 Opened relion_locres_filtered.mrc as #43, grid size 200,200,200, pixel 1.05, shown at level 0.0213, step 1, values float32 Opened relion_locres.mrc as #45, grid size 200,200,200, pixel 1.05, shown at level 34.5, step 1, values float32 Opened relion_locres_filtered.mrc as #46, grid size 250,250,250, pixel 1.05, shown at level 0.0263, step 1, values float32 Opened relion_locres.mrc as #47, grid size 250,250,250, pixel 1.05, shown at level 43.8, step 1, values float32 Opened relion_locres_filtered.mrc as #48, grid size 400,400,400, pixel 1.05, shown at level 0.0152, step 1, values float32 Opened relion_locres.mrc as #49, grid size 400,400,400, pixel 1.05, shown at level 24.7, step 2, values float32 Opened relion_locres_filtered.mrc as #50, grid size 200,200,200, pixel 1.05, shown at level 0.0196, step 1, values float32 Opened relion_locres.mrc as #51, grid size 200,200,200, pixel 1.05, shown at level 22, step 1, values float32 opened ChimeraX session > hide #!50 models > hide #38 models > show #38 models > open ""/Users/jabrilg/Desktop/10W_processing/fRef/w: > sub/j897/relion_locres_filtered.mrc"" Opened relion_locres_filtered.mrc as #52, grid size 200,200,200, pixel 1.05, shown at level 0.0307, step 1, values float32 > open ""/Users/jabrilg/Desktop/10W_processing/fRef/w: > sub/j897/relion_locres.mrc"" Opened relion_locres.mrc as #53, grid size 200,200,200, pixel 1.05, shown at level 26.3, step 1, values float32 > hide #!53 models > open /Volumes/EM11600/DATA/jabrilg/maps_Julio_PIC- > NCP_18W/Modelling/cPIC/10W_PIC-NCP_plusRPB6-plusCAK_REFINED.pdb Chain information for 10W_PIC-NCP_plusRPB6-plusCAK_REFINED.pdb #54 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available Q | No description available R | No description available T | No description available U | No description available V | No description available W | No description available X | No description available a | No description available b f | No description available c | No description available d | No description available e | No description available g | No description available h | No description available > select #54 168354 atoms, 170769 bonds, 35 pseudobonds, 10265 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #54,1,0,0,-63.658,0,1,0,-21.787,0,0,1,-73.258 > view matrix models #54,1,0,0,-79.579,0,1,0,-55.978,0,0,1,-56.834 > view matrix models #54,1,0,0,-91.706,0,1,0,-59.399,0,0,1,-51.755 > fitmap #54 inMap #52 Fit molecule 10W_PIC-NCP_plusRPB6-plusCAK_REFINED.pdb (#54) to map relion_locres_filtered.mrc (#52) using 168354 atoms average map value = 0.01215, steps = 808 shifted from previous position = 11.8 rotated from previous position = 6.27 degrees atoms outside contour = 153634, contour level = 0.030652 Position of 10W_PIC-NCP_plusRPB6-plusCAK_REFINED.pdb (#54) relative to relion_locres_filtered.mrc (#52) coordinates: Matrix rotation and translation 0.99791878 -0.02670145 -0.05869537 -79.84595055 0.03177997 0.99566917 0.08736673 -74.47510020 0.05610835 -0.08905024 0.99444553 -47.48358220 Axis -0.80756385 -0.52552388 0.26770373 Axis point 0.00000000 -823.02788813 264.82139190 Rotation angle (degrees) 6.27080825 Shift along axis 90.90761461 > ~select #54 Nothing selected > hide #!54 models > view matrix camera > -0.73766,0.50707,-0.44578,-179.57,0.60783,0.21133,-0.76543,-448.78,-0.29392,-0.8356,-0.46411,-196.55 > surface dust #52 size 10.5 > volume #52 level 0.02143 > ui tool show ""Surface Color"" > key red:0.00 white:0.25 blue:0.50 grey:0.75 grey:1.00 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > hide #38 models > show #38 models > key rainbow :0.00 :0.25 :0.50 :0.75 :1.00 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > color sample #52.1 map #53 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000 Map values for surface ""surface"": minimum 3.333, mean 4.059, maximum 7.756 > key rainbow :3.33 :4.44 :5.54 :6.65 :7.76 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > save ""/Users/jabrilg/Desktop/PhD projects/Papers/hPIC-NCP/Images for > figures/Ex.Fig2/CAK_lres_color.png"" width 1984 height 1134 supersample 3 > transparentBackground true > key rainbow :3.33 :4.44 :5.54 :6.65 :7.76 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > hide #!52 models > open ""/Users/jabrilg/Desktop/10W_processing/fRef/w: sub/j897/Validation/CAK- > fitted_real_space_refined_000.cif"" Summary of feedback from opening /Users/jabrilg/Desktop/10W_processing/fRef/w: sub/j897/Validation/CAK-fitted_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 132 Missing entity information. Treating each chain as a separate entity. Invalid residue range for struct_conf ""1"": invalid chain ""0"", near line 93 Invalid residue range for struct_conf ""2"": invalid chain ""0"", near line 94 Invalid residue range for struct_conf ""3"": invalid chain ""0"", near line 95 Invalid residue range for struct_conf ""4"": invalid chain ""8"", near line 96 Invalid residue range for struct_conf ""5"": invalid chain ""8"", near line 97 33 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for CAK-fitted_real_space_refined_000.cif #55 --- Chain | Description 0 | No description available 8 | No description available 9 | No description available > open ""/Users/jabrilg/Desktop/10W_processing/fRef/w: > sub/j897/j897_CAK_lres_sharp.ccp4"" Opened j897_CAK_lres_sharp.ccp4 as #56, grid size 200,200,200, pixel 1.05, shown at level 4.56, step 1, values float32 > close #56 > open ""/Users/jabrilg/Desktop/10W_processing/fRef/w: sub/j897/CAK.mrc"" Opened CAK.mrc as #56, grid size 200,200,200, pixel 1.05, shown at level 1.54, step 1, values float32 > volume #53 level 27.91 > volume #53 level 27.64 > volume #56 level 3.516 > close #56 > open ""/Users/jabrilg/Desktop/Lab meetings/Lab meeting 6/Images/PIC- > NCP18W_toHaibo_colored_withdensities3.cxs"" Opened run_it025_class003.mrc as #3, grid size 400,400,400, pixel 1.05, shown at level 0.00472, step 1, values float32 Opened postprocess.mrc as #61, grid size 200,200,200, pixel 1.05, shown at level 0.0109, step 1, values float32 Opened postprocess.mrc as #64, grid size 250,250,250, pixel 1.05, shown at level 0.0226, step 1, values float32 Opened postprocess.mrc as #65, grid size 250,250,250, pixel 1.05, shown at level 0.011, step 1, values float32 opened ChimeraX session ===== Log before crash end ===== Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-3.10.23 OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,2 Processor Name: 8-Core Intel Core i7 Processor Speed: 3,8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H1615) Kernel Version: Darwin 19.6.0 Time since boot: 3 days 4:48 Graphics/Displays: AMD Radeon Pro 5700: Chipset Model: AMD Radeon Pro 5700 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x731b Revision ID: 0x0040 ROM Revision: 113-D1820Q-231 VBIOS Version: 113-D182A2XG-013 Option ROM Version: 113-D182A2XG-013 EFI Driver Version: 01.01.231 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: iMac: Display Type: LCD Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 0FFXD46G3GLS Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: Thunderbolt/DisplayPort Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX