id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5146 Mac graphics crash, macOS 10.14.6, Geforce GT 750M apadavannil@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.14.6-x86_64-i386-64bit ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00000001094245c0 (most recent call first): File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/opengl.py"", line 2692 in draw_elements File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 1695 in draw File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 823 in _draw_geometry File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 762 in draw_self File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 751 in draw File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 1511 in _draw_multiple File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 1505 in File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/opengl.py"", line 1228 in draw_transparent File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/drawing.py"", line 1503 in draw_transparent File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/view.py"", line 240 in _draw_scene File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/view.py"", line 165 in draw File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/sideview/tool.py"", line 276 in render File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/sideview/tool.py"", line 112 in _redraw File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 213 in _activate File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 182 in activate File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/triggerset.py"", line 350 in activate_trigger File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/updateloop.py"", line 88 in draw_new_frame File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/updateloop.py"", line 138 in _redraw_timer_callback File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 293 in event_loop File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 866 in init File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 1015 in File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py"", line 87 in _run_code File ""/Users/apadavan/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py"", line 194 in _run_module_as_main Process: ChimeraX [293] Path: /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.2.3 (1.2.3.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [293] User ID: 479104604 Date/Time: 2021-09-01 11:43:20.460 -0700 OS Version: Mac OS X 10.14.6 (18G87) Report Version: 12 Anonymous UUID: 122A6F6A-D537-C9DF-0F9A-C6FAB78E30CD Time Awake Since Boot: 1300000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Application Specific Information: abort() called Application Specific Signatures: Graphics hardware encountered an error and was reset: 0x0000002b Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff703a62c6 __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff70461bf1 pthread_kill + 284 2 libsystem_c.dylib 0x00007fff702c3d8a raise + 26 3 libsystem_platform.dylib 0x00007fff70456b5d _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 libsystem_c.dylib 0x00007fff703106a6 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com.apple.HIToolbox 0x00007fff43574ee5 ReceiveNextEventCommon + 603 117 com.apple.HIToolbox 0x00007fff43574c76 _BlockUntilNextEventMatchingListInModeWithFilter + 64 118 com.apple.AppKit 0x00007fff4190d79d _DPSNextEvent + 1135 119 com.apple.AppKit 0x00007fff4190c48b -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1361 120 com.apple.AppKit 0x00007fff419065a8 -[NSApplication run] + 699 121 libqcocoa.dylib 0x00000001252ad62f QCocoaEventDispatcher::processEvents(QFlags) + 2495 122 QtCore 0x00000001088c3acf QEventLoop::exec(QFlags) + 431 123 QtCore 0x00000001088c8042 QCoreApplication::exec() + 130 124 QtWidgets.abi3.so 0x00000001153d5702 meth_QApplication_exec_(_object*, _object*) + 82 125 org.python.python 0x0000000105eba0c2 cfunction_call_varargs + 290 126 org.python.python 0x0000000105eb9a85 _PyObject_MakeTpCall + 373 127 org.python.python 0x0000000105f88665 call_function + 533 128 org.python.python 0x0000000105f8546e _PyEval_EvalFrameDefault + 25678 129 org.python.python 0x0000000105eba3d0 function_code_fastcall + 128 130 org.python.python 0x0000000105ebca9a method_vectorcall + 170 131 org.python.python 0x0000000105f8860c call_function + 444 132 org.python.python 0x0000000105f8546e _PyEval_EvalFrameDefault + 25678 133 org.python.python 0x0000000105f89454 _PyEval_EvalCodeWithName + 2804 134 org.python.python 0x0000000105eba56e _PyFunction_Vectorcall + 270 135 org.python.python 0x0000000105f8860c call_function + 444 136 org.python.python 0x0000000105f85505 _PyEval_EvalFrameDefault + 25829 137 org.python.python 0x0000000105f89454 _PyEval_EvalCodeWithName + 2804 138 org.python.python 0x0000000105f7ef44 PyEval_EvalCode + 100 139 org.python.python 0x0000000105f7c332 builtin_exec + 626 140 org.python.python 0x0000000105ef65ff cfunction_vectorcall_FASTCALL + 175 141 org.python.python 0x0000000105f8860c call_function + 444 142 org.python.python 0x0000000105f85505 _PyEval_EvalFrameDefault + 25829 143 org.python.python 0x0000000105f89454 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libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 2: 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 libopenblas.0.dylib 0x000000010978627b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 3: 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 libopenblas.0.dylib 0x000000010978627b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 4:: ThreadPoolServiceThread 0 libsystem_kernel.dylib 0x00007fff703a80a6 kevent64 + 10 1 QtWebEngineCore 0x0000000119059e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x0000000119059cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x0000000118feda94 base::internal::ServiceThread::Run(base::RunLoop*) + 20 6 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 5:: 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mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118f771db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 8:: CompositorTileWorker1 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 QtWebEngineCore 0x0000000119046e18 base::ConditionVariable::Wait() + 104 3 QtWebEngineCore 0x000000011a2fe5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56 4 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 5 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 6 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 7 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 9:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x0000000118f7720f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223 4 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 5 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 6 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 10:: Chrome_ChildIOThread 0 libsystem_kernel.dylib 0x00007fff703a80a6 kevent64 + 10 1 QtWebEngineCore 0x0000000119059e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x0000000119059cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 6 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 8 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 9 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 11:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118f771db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 12:: VizCompositorThread 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118f771db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 13:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118f771db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 14:: ThreadPoolSingleThreadForegroundBlocking0 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118ff776a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x0000000118ff8150 base::internal::WorkerThread::RunWorker() + 1024 6 QtWebEngineCore 0x0000000118ff7d34 base::internal::WorkerThread::RunDedicatedWorker() + 20 7 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 15:: MemoryInfra 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118f771db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 16:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118f771db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000118fe262b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000118fa67cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000119001a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 11 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 17: 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 com.apple.GeForceMTLDriver 0x00007fff402cf04e 0x7fff4016b000 + 1458254 3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 18:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff443171ee __CFRunLoopServiceMachPort + 328 3 com.apple.CoreFoundation 0x00007fff4431675c __CFRunLoopRun + 1612 4 com.apple.CoreFoundation 0x00007fff44315ebe CFRunLoopRunSpecific + 455 5 com.apple.AppKit 0x00007fff419154c2 _NSEventThread + 175 6 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 8 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 19:: ThreadPoolSingleThreadSharedBackgroundBlocking1 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011904f2cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000118ff776a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x0000000118ff7e3d base::internal::WorkerThread::RunWorker() + 237 6 QtWebEngineCore 0x0000000118ff7c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20 7 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 10 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 20: 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 libopenblas.0.dylib 0x00000001ba5782eb blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 21: 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 libopenblas.0.dylib 0x00000001ba5782eb blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 22: 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 libopenblas.0.dylib 0x00000001ba5782eb blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 5 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 23:: QFileInfoGatherer 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 QtCore 0x00000001086f975b QWaitConditionPrivate::wait(QDeadlineTimer) + 59 3 QtCore 0x00000001086f969d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93 4 QtWidgets 0x0000000115960c68 QFileInfoGatherer::run() + 136 5 QtCore 0x00000001086f1619 QThreadPrivate::start(void*) + 329 6 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 8 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 24:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff703a022a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff703a076c mach_msg + 60 2 QtWebEngineCore 0x000000011904f492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x0000000118ff7778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x0000000118ff8150 base::internal::WorkerThread::RunWorker() + 1024 5 QtWebEngineCore 0x0000000118ff7cd4 base::internal::WorkerThread::RunPooledWorker() + 20 6 QtWebEngineCore 0x000000011904ae07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 8 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 9 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 25:: QFileInfoGatherer 0 libsystem_kernel.dylib 0x00007fff703a386a __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff7046256e _pthread_cond_wait + 722 2 QtCore 0x00000001086f975b QWaitConditionPrivate::wait(QDeadlineTimer) + 59 3 QtCore 0x00000001086f969d QWaitCondition::wait(QMutex*, QDeadlineTimer) + 93 4 QtWidgets 0x0000000115960c68 QFileInfoGatherer::run() + 136 5 QtCore 0x00000001086f1619 QThreadPrivate::start(void*) + 329 6 libsystem_pthread.dylib 0x00007fff7045f2eb _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff70462249 _pthread_start + 66 8 libsystem_pthread.dylib 0x00007fff7045e40d thread_start + 13 Thread 26: 0 libsystem_pthread.dylib 0x00007fff7045e3f0 start_wqthread + 0 Thread 27: 0 libsystem_pthread.dylib 0x00007fff7045e3f0 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00000001094245c0 rcx: 0x0000000106378a48 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x0000000106378a80 rsp: 0x0000000106378a48 r8: 0x0000000106378f48 r9: 0x2353aad0de64acee r10: 0x000000010942466c r11: 0x0000000000000206 r12: 0x0000000000000307 r13: 0x000000012adb5000 r14: 0x0000000000000006 r15: 0x000000000000002d rip: 0x00007fff703a62c6 rfl: 0x0000000000000206 cr2: 0x000000011f4ea000 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x105e91000 - 0x105e91ff3 +edu.ucsf.cgl.ChimeraX (1.2.3 - 1.2.3.0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/MacOS/ChimeraX 0x105e99000 - 0x1060cfff7 +org.python.python (3.8.8, [c] 2001-2019 Python Software Foundation. - 3.8.8) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/Python 0x1064fe000 - 0x106500ff7 +_heapq.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_heapq.cpython-38-darwin.so 0x106608000 - 0x10660dff7 +zlib.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/zlib.cpython-38-darwin.so 0x106617000 - 0x106619ff7 +_bz2.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_bz2.cpython-38-darwin.so 0x106622000 - 0x106653fff +_lzma.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_lzma.cpython-38-darwin.so 0x106662000 - 0x106663ff7 +grp.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/grp.cpython-38-darwin.so 0x1066ab000 - 0x1066b3fff +math.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/math.cpython-38-darwin.so 0x1066bf000 - 0x1066c0ff7 +_bisect.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_bisect.cpython-38-darwin.so 0x1066c8000 - 0x1066ccff7 +_sha512.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_sha512.cpython-38-darwin.so 0x1066d5000 - 0x1066d6ff7 +_random.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_random.cpython-38-darwin.so 0x1067f9000 - 0x1067fefff +_json.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_json.cpython-38-darwin.so 0x106848000 - 0x10685cff7 +_ssl.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_ssl.cpython-38-darwin.so 0x106875000 - 0x1068cdfff +libssl.1.1.dylib (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/libssl.1.1.dylib 0x1068fc000 - 0x106b12da7 +libcrypto.1.1.dylib (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/libcrypto.1.1.dylib 0x106bb0000 - 0x106bbdfff +_socket.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_socket.cpython-38-darwin.so 0x106c4a000 - 0x106c4dff7 +select.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/select.cpython-38-darwin.so 0x106c57000 - 0x106c5cfff +_struct.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_struct.cpython-38-darwin.so 0x106c69000 - 0x106c6dfff +binascii.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/binascii.cpython-38-darwin.so 0x106cb6000 - 0x106cb9ff7 +_hashlib.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_hashlib.cpython-38-darwin.so 0x106cc3000 - 0x106cc9fff +_blake2.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_blake2.cpython-38-darwin.so 0x106cd3000 - 0x106ce3fff +_sha3.cpython-38-darwin.so (0) /Users/USER/Desktop/ChimeraX-1.2.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_sha3.cpython-38-darwin.so 0x106d6d000 - 0x106d7cfff +_datetime.cpython-38-darwin.so (0) 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com.apple.MediaServices (1.0 - 1) /System/Library/PrivateFrameworks/MediaServices.framework/Versions/A/MediaServices 0x7fff62b58000 - 0x7fff62b80ff7 com.apple.spotlight.metadata.utilities (1.0 - 1191.57) /System/Library/PrivateFrameworks/MetadataUtilities.framework/Versions/A/MetadataUtilities 0x7fff62b81000 - 0x7fff62c0eff7 com.apple.gpusw.MetalTools (1.0 - 1) /System/Library/PrivateFrameworks/MetalTools.framework/Versions/A/MetalTools 0x7fff62c25000 - 0x7fff62c3effb com.apple.MobileAssets (1.0 - 437.250.3) /System/Library/PrivateFrameworks/MobileAsset.framework/Versions/A/MobileAsset 0x7fff62db9000 - 0x7fff62dd4ffb com.apple.MobileKeyBag (2.0 - 1.0) /System/Library/PrivateFrameworks/MobileKeyBag.framework/Versions/A/MobileKeyBag 0x7fff62de7000 - 0x7fff62e5cfff com.apple.Montreal (1.0 - 42.15.9) /System/Library/PrivateFrameworks/Montreal.framework/Versions/A/Montreal 0x7fff62e5d000 - 0x7fff62e87ffb com.apple.MultitouchSupport.framework (2450.1 - 2450.1) /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport 0x7fff630c3000 - 0x7fff630cdfff com.apple.NetAuth (6.2 - 6.2) /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth 0x7fff631a3000 - 0x7fff631bdff7 com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics 0x7fff6392e000 - 0x7fff6397fff3 com.apple.OTSVG (1.0 - ???) /System/Library/PrivateFrameworks/OTSVG.framework/Versions/A/OTSVG 0x7fff64a23000 - 0x7fff64b16fff com.apple.PencilKit (1.0 - 1) /System/Library/PrivateFrameworks/PencilKit.framework/Versions/A/PencilKit 0x7fff64b17000 - 0x7fff64b26ff7 com.apple.PerformanceAnalysis (1.218.2 - 218.2) /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis 0x7fff64b27000 - 0x7fff64b50ff3 com.apple.persistentconnection (1.0 - 1.0) /System/Library/PrivateFrameworks/PersistentConnection.framework/Versions/A/PersistentConnection 0x7fff66557000 - 0x7fff66568ffb com.apple.PowerLog (1.0 - 1) /System/Library/PrivateFrameworks/PowerLog.framework/Versions/A/PowerLog 0x7fff66963000 - 0x7fff669b7ffb com.apple.ProtectedCloudStorage (1.0 - 1) /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage 0x7fff669b8000 - 0x7fff669d6ff7 com.apple.ProtocolBuffer (1 - 263.2) /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer 0x7fff66b54000 - 0x7fff66b57ff3 com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem 0x7fff66b58000 - 0x7fff66b6dff3 com.apple.QuickLookThumbnailing (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookThumbnailing.framework/Versions/A/QuickLookThumbnailing 0x7fff66b6e000 - 0x7fff66bbefff com.apple.ROCKit (27.6 - 27.6) /System/Library/PrivateFrameworks/ROCKit.framework/Versions/A/ROCKit 0x7fff66cfa000 - 0x7fff66d05fff com.apple.xpc.RemoteServiceDiscovery (1.0 - 1336.261.2) /System/Library/PrivateFrameworks/RemoteServiceDiscovery.framework/Versions/A/RemoteServiceDiscovery 0x7fff66d18000 - 0x7fff66d3afff com.apple.RemoteViewServices (2.0 - 128) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices 0x7fff66d3b000 - 0x7fff66d4eff3 com.apple.xpc.RemoteXPC (1.0 - 1336.261.2) /System/Library/PrivateFrameworks/RemoteXPC.framework/Versions/A/RemoteXPC 0x7fff68544000 - 0x7fff68662fff com.apple.Sharing (1288.62 - 1288.62) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing 0x7fff68663000 - 0x7fff68682ffb com.apple.shortcut (2.16 - 101) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut 0x7fff69476000 - 0x7fff69725fff com.apple.SkyLight (1.600.0 - 340.54) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight 0x7fff69ec8000 - 0x7fff69ed4fff com.apple.SpeechRecognitionCore (5.0.21 - 5.0.21) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore 0x7fff6a573000 - 0x7fff6a5afff3 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip 0x7fff6a625000 - 0x7fff6a6b0fc7 com.apple.Symbolication (10.2 - 64490.38.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication 0x7fff6ab87000 - 0x7fff6ab93fff com.apple.private.SystemPolicy (1.0 - 1) /System/Library/PrivateFrameworks/SystemPolicy.framework/Versions/A/SystemPolicy 0x7fff6ab98000 - 0x7fff6aba4ffb com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC 0x7fff6ae0a000 - 0x7fff6aed2ff3 com.apple.TextureIO (3.8.4 - 3.8.1) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO 0x7fff6af88000 - 0x7fff6af89fff com.apple.TrustEvaluationAgent (2.0 - 31.200.1) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent 0x7fff6af8f000 - 0x7fff6b146ffb com.apple.UIFoundation (1.0 - 551.2) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation 0x7fff6bdc2000 - 0x7fff6be9bfff com.apple.ViewBridge (401.1 - 401.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge 0x7fff6c673000 - 0x7fff6c676fff com.apple.dt.XCTTargetBootstrap (1.0 - 14490.66) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap 0x7fff6ca77000 - 0x7fff6ca79ffb com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport 0x7fff6ca7a000 - 0x7fff6ca8ffff com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login 0x7fff6cd43000 - 0x7fff6cd77fff libCRFSuite.dylib (41.15.4) /usr/lib/libCRFSuite.dylib 0x7fff6cd7a000 - 0x7fff6cd84ff7 libChineseTokenizer.dylib (28.15.3) /usr/lib/libChineseTokenizer.dylib 0x7fff6cd85000 - 0x7fff6ce0efff libCoreStorage.dylib (546.50.1) /usr/lib/libCoreStorage.dylib 0x7fff6ce12000 - 0x7fff6ce13ffb libDiagnosticMessagesClient.dylib (107) /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff6ce4a000 - 0x7fff6d0a1ff3 libFosl_dynamic.dylib (18.3.4) /usr/lib/libFosl_dynamic.dylib 0x7fff6d0c1000 - 0x7fff6d0c8fff libMatch.1.dylib (31.200.1) /usr/lib/libMatch.1.dylib 0x7fff6d0f2000 - 0x7fff6d111fff libMobileGestalt.dylib (645.270.1) /usr/lib/libMobileGestalt.dylib 0x7fff6d112000 - 0x7fff6d112fff libOpenScriptingUtil.dylib (179.1) /usr/lib/libOpenScriptingUtil.dylib 0x7fff6d252000 - 0x7fff6d253ffb libSystem.B.dylib (1252.250.1) /usr/lib/libSystem.B.dylib 0x7fff6d2cf000 - 0x7fff6d2d0fff libThaiTokenizer.dylib (2.15.1) /usr/lib/libThaiTokenizer.dylib 0x7fff6d2e2000 - 0x7fff6d2f8ffb libapple_nghttp2.dylib (1.24.1) /usr/lib/libapple_nghttp2.dylib 0x7fff6d2f9000 - 0x7fff6d322ffb libarchive.2.dylib (54.250.1) /usr/lib/libarchive.2.dylib 0x7fff6d323000 - 0x7fff6d3a2fff libate.dylib (1.13.8) /usr/lib/libate.dylib 0x7fff6d3a6000 - 0x7fff6d3a6ff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff6d476000 - 0x7fff6d486ffb libbsm.0.dylib (39.200.18) /usr/lib/libbsm.0.dylib 0x7fff6d487000 - 0x7fff6d494fff libbz2.1.0.dylib (38.200.3) /usr/lib/libbz2.1.0.dylib 0x7fff6d495000 - 0x7fff6d4e8ff7 libc++.1.dylib (400.9.4) /usr/lib/libc++.1.dylib 0x7fff6d4e9000 - 0x7fff6d4feff7 libc++abi.dylib (400.17) /usr/lib/libc++abi.dylib 0x7fff6d4ff000 - 0x7fff6d4ffff3 libcharset.1.dylib (51.200.6) /usr/lib/libcharset.1.dylib 0x7fff6d500000 - 0x7fff6d510ffb libcmph.dylib (6.15.1) /usr/lib/libcmph.dylib 0x7fff6d511000 - 0x7fff6d529ffb libcompression.dylib (52.250.2) /usr/lib/libcompression.dylib 0x7fff6d79e000 - 0x7fff6d7b4fff libcoretls.dylib (155.220.1) /usr/lib/libcoretls.dylib 0x7fff6d7b5000 - 0x7fff6d7b6ff3 libcoretls_cfhelpers.dylib (155.220.1) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff6d954000 - 0x7fff6da4cff7 libcrypto.35.dylib (22.260.1) /usr/lib/libcrypto.35.dylib 0x7fff6dc4f000 - 0x7fff6dc5aff7 libcsfde.dylib (546.50.1) /usr/lib/libcsfde.dylib 0x7fff6dc62000 - 0x7fff6dcb8ff3 libcups.2.dylib (462.12) /usr/lib/libcups.2.dylib 0x7fff6ddec000 - 0x7fff6ddecfff libenergytrace.dylib (17.200.1) /usr/lib/libenergytrace.dylib 0x7fff6dded000 - 0x7fff6de06ffb libexpat.1.dylib (16.1.1) /usr/lib/libexpat.1.dylib 0x7fff6de07000 - 0x7fff6de13fff libexslt.0.dylib (16.5) /usr/lib/libexslt.0.dylib 0x7fff6de1e000 - 0x7fff6de23ff7 libgermantok.dylib (17.15.2) /usr/lib/libgermantok.dylib 0x7fff6de24000 - 0x7fff6de29ff7 libheimdal-asn1.dylib (520.270.1) /usr/lib/libheimdal-asn1.dylib 0x7fff6de54000 - 0x7fff6df44fff libiconv.2.dylib (51.200.6) /usr/lib/libiconv.2.dylib 0x7fff6df45000 - 0x7fff6e1a6ffb libicucore.A.dylib (62141.0.1) /usr/lib/libicucore.A.dylib 0x7fff6e1f3000 - 0x7fff6e1f4fff liblangid.dylib (128.15.1) /usr/lib/liblangid.dylib 0x7fff6e1f5000 - 0x7fff6e20dff3 liblzma.5.dylib (10.200.3) /usr/lib/liblzma.5.dylib 0x7fff6e225000 - 0x7fff6e2c9ff7 libmecab.1.0.0.dylib (779.24.1) /usr/lib/libmecab.1.0.0.dylib 0x7fff6e2ca000 - 0x7fff6e4cefff libmecabra.dylib (779.24.1) /usr/lib/libmecabra.dylib 0x7fff6e6a6000 - 0x7fff6e9f7ff7 libnetwork.dylib (1229.250.15) /usr/lib/libnetwork.dylib 0x7fff6ea89000 - 0x7fff6f20efdf libobjc.A.dylib (756.2) /usr/lib/libobjc.A.dylib 0x7fff6f220000 - 0x7fff6f224ffb libpam.2.dylib (22.200.1) /usr/lib/libpam.2.dylib 0x7fff6f227000 - 0x7fff6f25cfff libpcap.A.dylib (79.250.1) /usr/lib/libpcap.A.dylib 0x7fff6f2b2000 - 0x7fff6f2b5fff libpmenergy.dylib (194.267.1) /usr/lib/libpmenergy.dylib 0x7fff6f2b6000 - 0x7fff6f2b8fff libpmsample.dylib (194.267.1) /usr/lib/libpmsample.dylib 0x7fff6f375000 - 0x7fff6f38dffb libresolv.9.dylib (65.200.2) /usr/lib/libresolv.9.dylib 0x7fff6f38f000 - 0x7fff6f3caff3 libsandbox.1.dylib (851.270.1) /usr/lib/libsandbox.1.dylib 0x7fff6f3de000 - 0x7fff6f3dfff7 libspindump.dylib (267.3) /usr/lib/libspindump.dylib 0x7fff6f3e0000 - 0x7fff6f5bdfff libsqlite3.dylib (274.26) /usr/lib/libsqlite3.dylib 0x7fff6f7d6000 - 0x7fff6f7d9ff7 libutil.dylib (51.200.4) /usr/lib/libutil.dylib 0x7fff6f7da000 - 0x7fff6f7e7fff libxar.1.dylib (417.1) /usr/lib/libxar.1.dylib 0x7fff6f7ec000 - 0x7fff6f8ceff3 libxml2.2.dylib (32.10) /usr/lib/libxml2.2.dylib 0x7fff6f8cf000 - 0x7fff6f8f7ff3 libxslt.1.dylib (16.5) /usr/lib/libxslt.1.dylib 0x7fff6f8f8000 - 0x7fff6f90aff7 libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib 0x7fff700ee000 - 0x7fff700f2ff3 libcache.dylib (81) /usr/lib/system/libcache.dylib 0x7fff700f3000 - 0x7fff700fdff3 libcommonCrypto.dylib (60118.250.2) /usr/lib/system/libcommonCrypto.dylib 0x7fff700fe000 - 0x7fff70105ff7 libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib 0x7fff70106000 - 0x7fff7010fff7 libcopyfile.dylib (146.250.1) /usr/lib/system/libcopyfile.dylib 0x7fff70110000 - 0x7fff70194fc3 libcorecrypto.dylib (602.260.2) /usr/lib/system/libcorecrypto.dylib 0x7fff7021b000 - 0x7fff70254ff7 libdispatch.dylib (1008.270.1) /usr/lib/system/libdispatch.dylib 0x7fff70255000 - 0x7fff70281ff7 libdyld.dylib (655.1.1) /usr/lib/system/libdyld.dylib 0x7fff70282000 - 0x7fff70282ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff70283000 - 0x7fff7028fff3 libkxld.dylib (4903.270.47) /usr/lib/system/libkxld.dylib 0x7fff70290000 - 0x7fff70290ff7 liblaunch.dylib (1336.261.2) /usr/lib/system/liblaunch.dylib 0x7fff70291000 - 0x7fff70296fff libmacho.dylib (927.0.3) /usr/lib/system/libmacho.dylib 0x7fff70297000 - 0x7fff70299ffb libquarantine.dylib (86.220.1) /usr/lib/system/libquarantine.dylib 0x7fff7029a000 - 0x7fff7029bff7 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib 0x7fff7029c000 - 0x7fff702b3ff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib 0x7fff702b4000 - 0x7fff702b4ff7 libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib 0x7fff702b5000 - 0x7fff7033cfff libsystem_c.dylib (1272.250.1) /usr/lib/system/libsystem_c.dylib 0x7fff7033d000 - 0x7fff70340ffb libsystem_configuration.dylib (963.270.3) /usr/lib/system/libsystem_configuration.dylib 0x7fff70341000 - 0x7fff70344ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib 0x7fff70345000 - 0x7fff7034bfff libsystem_darwin.dylib (1272.250.1) /usr/lib/system/libsystem_darwin.dylib 0x7fff7034c000 - 0x7fff70352ff7 libsystem_dnssd.dylib (878.270.2) /usr/lib/system/libsystem_dnssd.dylib 0x7fff70353000 - 0x7fff7039effb libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib 0x7fff7039f000 - 0x7fff703c7ff7 libsystem_kernel.dylib (4903.270.47) /usr/lib/system/libsystem_kernel.dylib 0x7fff703c8000 - 0x7fff70413ff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib 0x7fff70414000 - 0x7fff7043efff libsystem_malloc.dylib (166.270.1) /usr/lib/system/libsystem_malloc.dylib 0x7fff7043f000 - 0x7fff70449ff7 libsystem_networkextension.dylib (767.250.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff7044a000 - 0x7fff70451fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib 0x7fff70452000 - 0x7fff7045bfef libsystem_platform.dylib (177.270.1) /usr/lib/system/libsystem_platform.dylib 0x7fff7045c000 - 0x7fff70466ff7 libsystem_pthread.dylib (330.250.2) /usr/lib/system/libsystem_pthread.dylib 0x7fff70467000 - 0x7fff7046aff7 libsystem_sandbox.dylib (851.270.1) /usr/lib/system/libsystem_sandbox.dylib 0x7fff7046b000 - 0x7fff7046dff3 libsystem_secinit.dylib (30.260.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff7046e000 - 0x7fff70475ff3 libsystem_symptoms.dylib (820.267.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff70476000 - 0x7fff7048bfff libsystem_trace.dylib (906.260.1) /usr/lib/system/libsystem_trace.dylib 0x7fff7048d000 - 0x7fff70492ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff70493000 - 0x7fff704c2fff libxpc.dylib (1336.261.2) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 40 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: 2920713 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=935.6M resident=0K(0%) swapped_out_or_unallocated=935.6M(100%) Writable regions: Total=4.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.7G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 512K 4 Activity Tracing 256K 1 CG backing stores 672K 4 CG image 116K 20 CoreAnimation 84K 14 CoreGraphics 8K 1 CoreImage 20K 4 CoreUI image data 956K 20 CoreUI image file 316K 4 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 4.0G 878 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 2048K 12 reserved VM address space (unallocated) MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated) Mach message 24K 5 Memory Tag 242 12K 1 OpenGL GLSL 384K 5 STACK GUARD 108K 27 Stack 134.2M 28 Stack Guard 56.0M 1 VM_ALLOCATE 290.9M 124 VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated) __DATA 58.2M 582 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 331.3M 214 __TEXT 604.2M 535 __UNICODE 564K 1 mapped file 80.0M 144 shared memory 2868K 24 =========== ======= ======= TOTAL 5.8G 2668 TOTAL, minus reserved VM space 5.5G 2668 Log: UCSF ChimeraX version: 1.2.3 (2021-05-13) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/apadavan/Desktop/Review > Article/Review_Figures/G_loops/7NZ1_S1_Gloop.cxs"" Log from Tue Aug 31 17:25:24 2021UCSF ChimeraX version: 1.2.3 (2021-05-13) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6ZKC 6zkc title: Complex I during turnover, closed [more info...] Chain information for 6zkc #1 --- Chain | Description 1 | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial 2 | Mitochondrial complex I, 24 kDa subunit 3 | NADH:ubiquinone oxidoreductase core subunit S1 4 | Mitochondrial complex I, 49 kDa subunit 5 | NADH:ubiquinone oxidoreductase core subunit S3 6 | Mitochondrial complex I, PSST subunit 9 | Mitochondrial complex I, TYKY subunit A | NADH-ubiquinone oxidoreductase chain 3 H | NADH-ubiquinone oxidoreductase chain 1 J | NADH-ubiquinone oxidoreductase chain 6 K | NADH-ubiquinone oxidoreductase chain 4L L | NADH-ubiquinone oxidoreductase chain 5 M | NADH-ubiquinone oxidoreductase chain 4 N | NADH-ubiquinone oxidoreductase chain 2 V | Mitochondrial complex I, B14.7 subunit W | NADH:ubiquinone oxidoreductase subunit B5 X j | Acyl carrier protein Y | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8 Z | Mitochondrial complex I, PDSW subunit a | Mitochondrial complex I, 10 kDa subunit b | Mitochondrial complex I, 13 kDa subunit c | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial d | NADH:ubiquinone oxidoreductase subunit A9 e | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 f | Mitochondrial complex I, B13 subunit g | NADH:ubiquinone oxidoreductase subunit A6 h | Mitochondrial complex I, B14.5a subunit i | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 k | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial l | NADH:ubiquinone oxidoreductase subunit S5 m | NADH:ubiquinone oxidoreductase subunit A3 n | NADH:ubiquinone oxidoreductase subunit B3 o | NADH dehydrogenase [ubiquinone] 1 subunit C2 p | NADH:ubiquinone oxidoreductase subunit B4 q | Mitochondrial complex I, B16.6 subunit r | Mitochondrial complex I, B17 subunit s | NADH:ubiquinone oxidoreductase subunit B7 t | NADH:ubiquinone oxidoreductase subunit B9 u | NADH:ubiquinone oxidoreductase subunit B2 v | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial w | Mitochondrial complex I, ESSS subunit x | Mitochondrial complex I, KFYI subunit y | Mitochondrial complex I, MNLL subunit z | Mitochondrial complex I, MWFE subunit Non-standard residues in 6zkc #1 --- 3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn- phosphatidylethanolamine) AMP — adenosine monophosphate CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn- glycero-3-phospho)-1',3'-Sn-glycerol) DCQ — 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione (decylubiquinone) FES — FE2/S2 (inorganic) cluster FMN — flavin mononucleotide (riboflavin monophosphate) K — potassium ion MYR — myristic acid NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine) SF4 — iron/sulfur cluster ZMP — S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta- alanyl}amino)ethyl] tetradecanethioate ZN — zinc ion > hide atoms > show cartoons > set bgColor white > name core #1/1 /2 /3 /4 /5 /6 /9 /A /H /J /K /N /M /L > show core surfaces > rainbow core chains palette > ""#DC050C:#E8601C:#F1932D:#F6C141:#F7F056:#CAE0AB:#90C987:#4EB265:#7BAFDE:#5289C7:#1965B0:#882E72:#AE76A3:#D1BBD7"" > transparency core 325 > name accessory #1/a /b /c /d /e /f /g /h /i /j /k /l /m /n /o /p /q /r /s /t > /u /v /w /x /y /z /V /W /X /Y /Z > show accessory surfaces > rainbow accessory chains palette > ""#FEDA8B:#4A7BB7:#D1C1E1:#C3A8D1:#B58FC2:#A778B4:#9B62A7:#8C4E99:#6F4C9B:#6059A9:#5568B8:#4E79C5:#4D8AC6:#4E96BC:#549EB3:#59A5A9:#60AB9E:#69B190:#77B77D:#8CBC68:#A6BE54:#BEBC48:#D1B541:#DDAA3C:#E49C39:#E78C35:#E67932:#E4632D:#DF4828:#DA2222:#B8221E:#95211B:#721E17:#521A13"" > hide suface Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide surfaces > open 7nz1 7nz1 title: Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm [more info...] Chain information for 7nz1 #2 --- Chain | Description B | NADH-quinone oxidoreductase subunit B D | NADH-quinone oxidoreductase subunit C/D E | NADH-quinone oxidoreductase subunit E F | NADH-quinone oxidoreductase subunit F G | NADH-quinone oxidoreductase subunit G I | NADH-quinone oxidoreductase subunit I Non-standard residues in 7nz1 #2 --- CA — calcium ion FES — FE2/S2 (inorganic) cluster FMN — flavin mononucleotide (riboflavin monophosphate) SF4 — iron/sulfur cluster > hide cartoons > show cartoons > hide atoms > show cartoons > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zkc, chain 1 (#1) with 7nz1, chain F (#2), sequence alignment score = 1147.3 RMSD between 348 pruned atom pairs is 1.011 angstroms; (across all 418 pairs: 2.987) > hide #!1 models > hide #!2 models > open /Users/apadavan/Downloads/4hea.pdb Summary of feedback from opening /Users/apadavan/Downloads/4hea.pdb --- warnings | Start residue of secondary structure not found: HELIX 205 205 LEU B 17 VAL B 21 5 5 Start residue of secondary structure not found: HELIX 206 206 THR B 28 HIS B 35 1 8 Start residue of secondary structure not found: HELIX 207 207 TYR B 38 GLU B 47 1 10 Start residue of secondary structure not found: HELIX 208 208 THR B 49 GLY B 61 1 13 Start residue of secondary structure not found: HELIX 209 209 PRO B 71 SER B 77 1 7 291 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (144 ) Cannot find LINK/SSBOND residue HIS (115 ) Cannot find LINK/SSBOND residue SF4 (801 ) Cannot find LINK/SSBOND residue CYS (359 ) Cannot find LINK/SSBOND residue CYS (45 ) 68 messages similar to the above omitted 4hea.pdb title: Crystal structure of the entire respiratory complex I from thermus thermophilus [more info...] Chain information for 4hea.pdb #3 --- Chain | Description 1 | nadh-quinone oxidoreductase subunit 1 2 | nadh-quinone oxidoreductase subunit 2 3 | nadh-quinone oxidoreductase subunit 3 4 | nadh-quinone oxidoreductase subunit 4 5 | nadh-quinone oxidoreductase subunit 5 6 | nadh-quinone oxidoreductase subunit 6 7 | nadh-quinone oxidoreductase subunit 15 9 | nadh-quinone oxidoreductase subunit 9 A | nadh-quinone oxidoreductase subunit 7 H | nadh-quinone oxidoreductase subunit 8 J | nadh-quinone oxidoreductase subunit 10 K | nadh-quinone oxidoreductase subunit 11 L | nadh-quinone oxidoreductase subunit 12 M | nadh-quinone oxidoreductase subunit 13 N | nadh-quinone oxidoreductase subunit 14 W | putative uncharacterized protein TTHA1528 > hide #!3 atoms > show #!3 cartoons > view > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zkc, chain L (#1) with 4hea.pdb, chain L (#3), sequence alignment score = 1220.7 RMSD between 349 pruned atom pairs is 1.057 angstroms; (across all 577 pairs: 3.612) > view > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > hide accessory > hide accessory cartoons > show core surfaces > name core #1/1 /2 /3 /4 /5 /6 /9 /A /H /J /K /N /M /L > show core surfaces > hide #!1 models > show #!1 models > transparency 0 > show #1/c cartoons > show #1/c surfaces > transparency #1/c 50 > hide core cartoons > transparency core 80 > graphics silhouettes true > lighting full > lighting shadows false > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > select #1/3 :388-409 :627-639 282 atoms, 287 bonds, 35 residues, 1 model selected > show sel cartoons > select clear > transparency core 70 > view matrix camera position: 0.79891,0.0089074,0.60139,270.66,0.41675,-0.72915,-0.54283,-80.57,0.43367,0.6843,-0.58624,48.606 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1.35,1,0,0,0,0,1,0,0,0,0,1,0,#1.36,1,0,0,0,0,1,0,0,0,0,1,0,#1.37,1,0,0,0,0,1,0,0,0,0,1,0,#1.38,1,0,0,0,0,1,0,0,0,0,1,0,#1.39,1,0,0,0,0,1,0,0,0,0,1,0,#1.40,1,0,0,0,0,1,0,0,0,0,1,0,#1.41,1,0,0,0,0,1,0,0,0,0,1,0,#1.42,1,0,0,0,0,1,0,0,0,0,1,0,#1.43,1,0,0,0,0,1,0,0,0,0,1,0,#1.44,1,0,0,0,0,1,0,0,0,0,1,0,#1.45,1,0,0,0,0,1,0,0,0,0,1,0,#1.46,1,0,0,0,0,1,0,0,0,0,1,0,#1.47,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.28041,0.52274,0.80506,31.677,-0.11634,-0.85103,0.51206,115.93,0.9528,0.049925,0.29945,139.96,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.41848,-0.89425,0.1587,55.056,0.6826,-0.42495,-0.59453,118.26,0.5991,-0.14047,0.78825,152.2,#3.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > 0.79891,0.0089074,0.60139,270.66,0.41675,-0.72915,-0.54283,-80.57,0.43367,0.6843,-0.58624,48.606 > view matrix camera position: 0.79891,0.0089074,0.60139,300.76,0.41675,-0.72915,-0.54283,-102.02,0.43367,0.6843,-0.58624,19.481 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1.35,1,0,0,0,0,1,0,0,0,0,1,0,#1.36,1,0,0,0,0,1,0,0,0,0,1,0,#1.37,1,0,0,0,0,1,0,0,0,0,1,0,#1.38,1,0,0,0,0,1,0,0,0,0,1,0,#1.39,1,0,0,0,0,1,0,0,0,0,1,0,#1.40,1,0,0,0,0,1,0,0,0,0,1,0,#1.41,1,0,0,0,0,1,0,0,0,0,1,0,#1.42,1,0,0,0,0,1,0,0,0,0,1,0,#1.43,1,0,0,0,0,1,0,0,0,0,1,0,#1.44,1,0,0,0,0,1,0,0,0,0,1,0,#1.45,1,0,0,0,0,1,0,0,0,0,1,0,#1.46,1,0,0,0,0,1,0,0,0,0,1,0,#1.47,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.28041,0.52274,0.80506,31.677,-0.11634,-0.85103,0.51206,115.93,0.9528,0.049925,0.29945,139.96,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,-0.41848,-0.89425,0.1587,55.056,0.6826,-0.42495,-0.59453,118.26,0.5991,-0.14047,0.78825,152.2,#3.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera > 0.79891,0.0089074,0.60139,300.76,0.41675,-0.72915,-0.54283,-102.02,0.43367,0.6843,-0.58624,19.481 > save ""/Users/apadavan/Desktop/Review > Article/Review_Figures/G_loops/6ZKC_S1_Gloop.cxs"" > save ""/Users/apadavan/Desktop/Review > Article/Review_Figures/G_loops/6ZKC_S1_Gloop.png"" width 1594 height 858 > supersample 3 > hide #!1 models > show #!2 models > color #2/G #F1932D > color #2/D #F6C141 > color #2/B #CAE0AB > color #2/I #90C987 > color #2/F #DC050C > color #2/E #E8601C > hide #2 cartoons > show #2 surfaces > color #2/G #F1932D > color #2/D #F6C141 > color #2/B #CAE0AB > color #2/I #90C987 > color #2/F #DC050C > color #2/E #E8601C > transparency 70 > show #2/G cartoons > hide surfaces > show #2 surfaces > hide #2 cartoons > select #2/G :386-433 :681-784 1187 atoms, 1216 bonds, 152 residues, 1 model selected > show sel cartoons > view matrix camera > 0.79891,0.0089074,0.60139,300.76,0.41675,-0.72915,-0.54283,-102.02,0.43367,0.6843,-0.58624,19.481 > select clear > save ""/Users/apadavan/Desktop/Review > Article/Review_Figures/G_loops/7NZ1_S1_Gloop.cxs"" ——— End of log from Tue Aug 31 17:25:24 2021 ——— opened ChimeraX session OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA CorporationHardware: Hardware Overview: Model Name: iMac Model Identifier: iMac14,3 Processor Name: Intel Core i7 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: IM143.0118.B12 SMC Version (system): 2.17f7 Software: System Software Overview: System Version: macOS 10.14.6 (18G87) Kernel Version: Darwin 18.7.0 Time since boot: 15 days 22:42 Graphics/Displays: NVIDIA GeForce GT 750M: Chipset Model: NVIDIA GeForce GT 750M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 1 GB Vendor: NVIDIA (0x10de) Device ID: 0x0fe9 Revision ID: 0x00a2 ROM Revision: 3762 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort HP VH240a: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60 Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: 6CM1160B4N Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No 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: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.3 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.3 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.2 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.4 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.7 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.0 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX