id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3907 Crash in graphics driver Eric Pettersen Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.dev202010262104 (2020-10-26 21:04:12 UTC) Description Last time you used ChimeraX it crashed. Running the NIH3D script on a large structure (5y6p) Process: ChimeraX [8276] Path: /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.2.0 (1.2.0.0) Code Type: X86-64 (Native) Parent Process: tcsh [642] Responsible: Terminal [514] User ID: 501 Date/Time: 2020-11-03 13:54:23.802 -0800 OS Version: Mac OS X 10.15.7 (19H2) Report Version: 12 Anonymous UUID: 1001EC17-01AB-23EF-FBAF-2E1668FB0851 Time Awake Since Boot: 190000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_INSTRUCTION (SIGILL) Exception Codes: 0x0000000000000001, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Application Specific Information: *** CFRetain() called with NULL *** Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff699c433a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff69a80e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff698db93e raise + 26 3 libsystem_platform.dylib 0x00007fff69a755fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff24a71eae IntelVertexArray::extractBuffers(GLDVertexArrayRec*, unsigned long long, unsigned long long) + 118 6 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff24a71e29 glrUpdateVertexArrayBuffers + 13 7 libGPUSupportMercury.dylib 0x00007fff50c4c9e0 gpusLoadCurrentVertexArray + 687 8 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff24a6483e updateDispatch + 1225 9 GLEngine 0x00007fff3a3d8506 gleDoSelectiveDispatchNoErrorCoreGL3 + 544 10 GLEngine 0x00007fff3a36b61f glValidateProgramARB_Exec + 350 11 _ctypes.cpython-38-darwin.so 0x0000000106611caf ffi_call_unix64 + 79 12 _ctypes.cpython-38-darwin.so 0x00000001066124fd ffi_call + 877 13 _ctypes.cpython-38-darwin.so 0x000000010660cdfc _ctypes_callproc + 844 14 _ctypes.cpython-38-darwin.so 0x0000000106606582 PyCFuncPtr_call + 1298 15 org.python.python 0x0000000100f4537b PyObject_Call + 171 16 org.python.python 0x0000000100f9d20e slot_tp_call + 222 17 org.python.python 0x0000000100f44ef6 _PyObject_MakeTpCall + 374 18 org.python.python 0x00000001010238c4 call_function + 660 19 org.python.python 0x0000000101020557 _PyEval_EvalFrameDefault + 26791 20 org.python.python 0x0000000100f45861 function_code_fastcall + 177 21 org.python.python 0x0000000101023792 call_function + 354 22 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 23 org.python.python 0x0000000100f45861 function_code_fastcall + 177 24 org.python.python 0x0000000101023792 call_function + 354 25 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 26 org.python.python 0x0000000100f45861 function_code_fastcall + 177 27 org.python.python 0x0000000101023792 call_function + 354 28 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 29 org.python.python 0x0000000100f45861 function_code_fastcall + 177 30 org.python.python 0x0000000101023792 call_function + 354 31 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 32 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 33 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 34 org.python.python 0x0000000100f4823b method_vectorcall + 171 35 org.python.python 0x0000000101023792 call_function + 354 36 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102 37 org.python.python 0x0000000100f45861 function_code_fastcall + 177 38 org.python.python 0x0000000101023792 call_function + 354 39 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 40 org.python.python 0x0000000100f45861 function_code_fastcall + 177 41 org.python.python 0x0000000101023792 call_function + 354 42 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 43 org.python.python 0x0000000100f45861 function_code_fastcall + 177 44 org.python.python 0x0000000101023792 call_function + 354 45 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 46 org.python.python 0x0000000100f45861 function_code_fastcall + 177 47 org.python.python 0x0000000101023792 call_function + 354 48 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 49 org.python.python 0x0000000100f45861 function_code_fastcall + 177 50 org.python.python 0x0000000101023792 call_function + 354 51 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 52 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 53 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 54 org.python.python 0x0000000100f4823b method_vectorcall + 171 55 org.python.python 0x0000000101023792 call_function + 354 56 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102 57 org.python.python 0x0000000100f45861 function_code_fastcall + 177 58 org.python.python 0x0000000101023792 call_function + 354 59 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 60 org.python.python 0x0000000100f45861 function_code_fastcall + 177 61 org.python.python 0x0000000101023792 call_function + 354 62 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 63 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 64 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 65 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100 66 org.python.python 0x000000010102082f _PyEval_EvalFrameDefault + 27519 67 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 68 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 69 org.python.python 0x0000000100f4823b method_vectorcall + 171 70 org.python.python 0x0000000101023792 call_function + 354 71 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102 72 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 73 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 74 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100 75 org.python.python 0x000000010102082f _PyEval_EvalFrameDefault + 27519 76 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 77 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 78 org.python.python 0x0000000100f4823b method_vectorcall + 171 79 org.python.python 0x0000000101023792 call_function + 354 80 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102 81 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 82 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 83 org.python.python 0x0000000101023792 call_function + 354 84 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 85 org.python.python 0x0000000100f45861 function_code_fastcall + 177 86 org.python.python 0x0000000101023792 call_function + 354 87 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 88 org.python.python 0x0000000100f45861 function_code_fastcall + 177 89 org.python.python 0x0000000101023792 call_function + 354 90 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 91 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 92 org.python.python 0x0000000101019c10 PyEval_EvalCode + 48 93 org.python.python 0x0000000101017040 builtin_exec + 592 94 org.python.python 0x0000000100f835a1 cfunction_vectorcall_FASTCALL + 177 95 org.python.python 0x0000000101023792 call_function + 354 96 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 97 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 98 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 99 org.python.python 0x0000000101023792 call_function + 354 100 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 101 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 102 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 103 org.python.python 0x0000000101023792 call_function + 354 104 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102 105 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 106 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 107 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100 108 org.python.python 0x000000010102082f _PyEval_EvalFrameDefault + 27519 109 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 110 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 111 org.python.python 0x0000000100f4823b method_vectorcall + 171 112 org.python.python 0x0000000101023792 call_function + 354 113 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102 114 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 115 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 116 org.python.python 0x0000000101023792 call_function + 354 117 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 118 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 119 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 120 org.python.python 0x0000000101023792 call_function + 354 121 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 122 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 123 org.python.python 0x0000000101019c10 PyEval_EvalCode + 48 124 org.python.python 0x0000000101017040 builtin_exec + 592 125 org.python.python 0x0000000100f835a1 cfunction_vectorcall_FASTCALL + 177 126 org.python.python 0x0000000101023792 call_function + 354 127 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 128 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 129 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 130 org.python.python 0x0000000101023792 call_function + 354 131 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944 132 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 133 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 134 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100 135 org.python.python 0x0000000101089563 pymain_run_module + 179 136 org.python.python 0x0000000101088c58 Py_RunMain + 1416 137 org.python.python 0x0000000101089443 pymain_main + 403 138 org.python.python 0x000000010108929b Py_Main + 43 139 edu.ucsf.cgl.ChimeraX 0x0000000100f10d79 main + 121 140 libdyld.dylib 0x00007fff6987ccc9 start + 1 Thread 1: 0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010293a27b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 2: 0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010293a27b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 3: 0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010293a27b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 4:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff2f7e2ef5 __CFRunLoopServiceMachPort + 247 3 com.apple.CoreFoundation 0x00007fff2f7e19c2 __CFRunLoopRun + 1319 4 com.apple.CoreFoundation 0x00007fff2f7e0e3e CFRunLoopRunSpecific + 462 5 com.apple.AppKit 0x00007fff2cbf4954 _NSEventThread + 132 6 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 5:: ThreadPoolServiceThread 0 libsystem_kernel.dylib 0x00007fff699c6b96 kevent64 + 10 1 QtWebEngineCore 0x000000011645c73a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x000000011645c597 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 4 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 5 QtWebEngineCore 0x00000001163ef224 base::internal::ServiceThread::Run(base::RunLoop*) + 20 6 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 6:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x00000001163fabe8 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x00000001163fb444 base::internal::WorkerThread::RunWorker() + 644 5 QtWebEngineCore 0x00000001163fb0b4 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20 6 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 7:: Chrome_IOThread 0 libsystem_kernel.dylib 0x00007fff699c6b96 kevent64 + 10 1 QtWebEngineCore 0x000000011645c73a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x000000011645c597 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 4 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 5 QtWebEngineCore 0x000000011a3573c4 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 20 6 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 8:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 9:: CompositorTileWorker1 0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698 2 QtWebEngineCore 0x0000000116449555 base::ConditionVariable::Wait() + 53 3 QtWebEngineCore 0x000000011777ef38 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56 4 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 5 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 6 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 10:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 11:: Chrome_ChildIOThread 0 libsystem_kernel.dylib 0x00007fff699c6b96 kevent64 + 10 1 QtWebEngineCore 0x000000011645c73a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x000000011645c597 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 4 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 5 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 6 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 12:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 13:: VizCompositorThread 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 14:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 15:: ThreadPoolSingleThreadForegroundBlocking0 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x00000001163fabda base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x00000001163fb444 base::internal::WorkerThread::RunWorker() + 644 6 QtWebEngineCore 0x00000001163fb1a4 base::internal::WorkerThread::RunDedicatedWorker() + 20 7 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 16:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143 6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399 7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 17:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60 2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405 3 QtWebEngineCore 0x00000001163fabe8 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x00000001163fb444 base::internal::WorkerThread::RunWorker() + 644 5 QtWebEngineCore 0x00000001163fb144 base::internal::WorkerThread::RunPooledWorker() + 20 6 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 18: 0 libsystem_pthread.dylib 0x00007fff69a7cb68 start_wqthread + 0 Thread 19: 0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698 2 org.python.python 0x0000000101077a01 PyThread_acquire_lock_timed + 337 3 org.python.python 0x00000001010c46df acquire_timed + 111 4 org.python.python 0x00000001010c447c lock_PyThread_acquire_lock + 44 5 org.python.python 0x0000000100f4e6d4 method_vectorcall_VARARGS_KEYWORDS + 324 6 org.python.python 0x0000000101023792 call_function + 354 7 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 8 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 9 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 10 org.python.python 0x0000000101023792 call_function + 354 11 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 12 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534 13 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253 14 org.python.python 0x0000000101023792 call_function + 354 15 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 16 org.python.python 0x0000000100f45861 function_code_fastcall + 177 17 org.python.python 0x0000000101023792 call_function + 354 18 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 19 org.python.python 0x0000000100f45861 function_code_fastcall + 177 20 org.python.python 0x0000000101023792 call_function + 354 21 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755 22 org.python.python 0x0000000100f45861 function_code_fastcall + 177 23 org.python.python 0x0000000100f482d2 method_vectorcall + 322 24 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100 25 org.python.python 0x00000001010c507a t_bootstrap + 74 26 org.python.python 0x0000000101077649 pythread_wrapper + 25 27 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148 28 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00000001080f7dc0 rcx: 0x00007fbb41f8da58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x0000000000000004 rbp: 0x00007fbb41f8da80 rsp: 0x00007fbb41f8da58 r8: 0x00007fbb41f8df48 r9: 0x5932d5e0006cac9f r10: 0x00000001080f7dc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0xffffffffffffffff r14: 0x0000000000000004 r15: 0x0000000000000016 rip: 0x00007fff699c433a rfl: 0x0000000000000246 cr2: 0x000000010150db78 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x100f0d000 - 0x100f10ff3 +edu.ucsf.cgl.ChimeraX (1.2.0 - 1.2.0.0) /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX 0x100f22000 - 0x10116dfff +org.python.python (3.8.5, [c] 2001-2019 Python Software Foundation. - 3.8.5) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/Python 0x1012ae000 - 0x1012b7fff +libintl.8.dylib (0) /usr/local/opt/gettext/lib/libintl.8.dylib 0x1014ca000 - 0x1014cdffb +_heapq.cpython-38-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_heapq.cpython-38-darwin.so 0x1015da000 - 0x1015e1ff3 +zlib.cpython-38-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/zlib.cpython-38-darwin.so 0x1015ee000 - 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libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib 0x7fff66863000 - 0x7fff668eeff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib 0x7fff668ef000 - 0x7fff668f0fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib 0x7fff66908000 - 0x7fff6691efff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib 0x7fff66953000 - 0x7fff669c5ff7 libarchive.2.dylib (72.140.1) /usr/lib/libarchive.2.dylib 0x7fff669c6000 - 0x7fff66a5ffe5 libate.dylib (3.0.1) /usr/lib/libate.dylib 0x7fff66a63000 - 0x7fff66a63ff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff66a64000 - 0x7fff66b28ffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib 0x7fff66b29000 - 0x7fff66b39ffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib 0x7fff66b3a000 - 0x7fff66b46fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib 0x7fff66b47000 - 0x7fff66b99fff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib 0x7fff66b9a000 - 0x7fff66bafffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib 0x7fff66bb0000 - 0x7fff66bb0fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib 0x7fff66bb1000 - 0x7fff66bc2fff libcmph.dylib (8) /usr/lib/libcmph.dylib 0x7fff66bc3000 - 0x7fff66bdafd7 libcompression.dylib (87) /usr/lib/libcompression.dylib 0x7fff66eb4000 - 0x7fff66ecaff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib 0x7fff66ecb000 - 0x7fff66eccfff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff67476000 - 0x7fff67481fff libcsfde.dylib (551) /usr/lib/libcsfde.dylib 0x7fff67489000 - 0x7fff674e8ff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib 0x7fff675f2000 - 0x7fff675f2fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib 0x7fff675f3000 - 0x7fff6760bfff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib 0x7fff67619000 - 0x7fff6761bfff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib 0x7fff6762a000 - 0x7fff6762ffff libgermantok.dylib (24) /usr/lib/libgermantok.dylib 0x7fff67630000 - 0x7fff67639ff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib 0x7fff6763a000 - 0x7fff6772afff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib 0x7fff6772b000 - 0x7fff67982fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib 0x7fff6799c000 - 0x7fff6799dfff liblangid.dylib (133) /usr/lib/liblangid.dylib 0x7fff6799e000 - 0x7fff679b6ff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib 0x7fff679ce000 - 0x7fff67a75ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib 0x7fff67a76000 - 0x7fff67cd8ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib 0x7fff68045000 - 0x7fff68074fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib 0x7fff681a4000 - 0x7fff68620ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib 0x7fff68621000 - 0x7fff68638fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib 0x7fff686c1000 - 0x7fff686f4fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib 0x7fff68707000 - 0x7fff6870bfff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib 0x7fff6870e000 - 0x7fff68744ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib 0x7fff68784000 - 0x7fff68792ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib 0x7fff68793000 - 0x7fff68796ff3 libpmenergy.dylib (214.120.1) /usr/lib/libpmenergy.dylib 0x7fff68797000 - 0x7fff68799fff libpmsample.dylib (214.120.1) /usr/lib/libpmsample.dylib 0x7fff687c8000 - 0x7fff687e0fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff687e2000 - 0x7fff68826ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib 0x7fff6883a000 - 0x7fff6883bff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib 0x7fff6883c000 - 0x7fff68a26ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib 0x7fff68c1c000 - 0x7fff68c76ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib 0x7fff68c77000 - 0x7fff68c7affb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff68c7b000 - 0x7fff68c88ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib 0x7fff68c8e000 - 0x7fff68d70fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib 0x7fff68d74000 - 0x7fff68d9cfff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib 0x7fff68d9d000 - 0x7fff68dafff3 libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff6965e000 - 0x7fff69663ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff69664000 - 0x7fff6966ffff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff69670000 - 0x7fff69677fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff69678000 - 0x7fff69681ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff69682000 - 0x7fff69714fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib 0x7fff69821000 - 0x7fff69861ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff69862000 - 0x7fff69898fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib 0x7fff69899000 - 0x7fff69899ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff6989a000 - 0x7fff698a6ff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib 0x7fff698a7000 - 0x7fff698a7ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib 0x7fff698a8000 - 0x7fff698adff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff698ae000 - 0x7fff698b0ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff698b1000 - 0x7fff698b2ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff698b3000 - 0x7fff698caff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff698cb000 - 0x7fff698cbff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff698cc000 - 0x7fff69953fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff69954000 - 0x7fff69957ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib 0x7fff69958000 - 0x7fff6995bfff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff6995c000 - 0x7fff69964fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff69965000 - 0x7fff6996cfff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff6996d000 - 0x7fff6996effb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff6996f000 - 0x7fff699bcff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff699bd000 - 0x7fff699e9ff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff699ea000 - 0x7fff69a31fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff69a32000 - 0x7fff69a59fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff69a5a000 - 0x7fff69a67ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff69a68000 - 0x7fff69a71ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff69a72000 - 0x7fff69a7afef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff69a7b000 - 0x7fff69a85fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff69a86000 - 0x7fff69a8aff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib 0x7fff69a8b000 - 0x7fff69a8dfff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff69a8e000 - 0x7fff69a95ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff69a96000 - 0x7fff69aacff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff69aae000 - 0x7fff69ab3ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff69ab4000 - 0x7fff69ae9ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 80 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: 766415 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=989.5M resident=0K(0%) swapped_out_or_unallocated=989.5M(100%) Writable regions: Total=12.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=12.7G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 336K 2 CG image 44K 6 CoreAnimation 80K 16 CoreGraphics 8K 1 CoreImage 8K 2 CoreUI image data 936K 14 Dispatch continuations 8192K 1 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 8.2G 1674 MALLOC guard page 32K 7 MALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated) Mach message 24K 3 OpenGL GLSL 256K 3 STACK GUARD 76K 19 Stack 130.6M 20 Stack Guard 56.0M 1 VM_ALLOCATE 4.4G 527 VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated) __DATA 51.8M 540 __DATA_CONST 1260K 67 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 474.3M 196 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 515.6M 508 __UNICODE 564K 1 mapped file 396.9M 49 shared memory 656K 20 =========== ======= ======= TOTAL 14.2G 3690 TOTAL, minus reserved VM space 14.2G 3690 Log: > runscript cx_unified.py --pdb 6e9d > open pdbe_bio:6E9D autoStyle false Summary of feedback from opening 6E9D fetched from pdbe_bio --- warnings | Atom H is not in the residue template for GLY /A:226 Atom H is not in the residue template for GLY /AA:226 Atom H is not in the residue template for GLY /AB:226 Atom H is not in the residue template for GLY /B:226 Atom H is not in the residue template for GLY /BA:226 55 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. note | Fetching compressed 6E9D bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/6e9d-assembly-1.cif.gz 6E9D bioassembly 1 title: Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM Reconstruction of AAV-2 L336C [more info...] Chain information for 6E9D bioassembly 1 #1 --- Chain | Description A AA AB B BA BB C CA CB D DA DB E EA EB F FA FB G GA GB H HA HB I IA J JA K KA L LA M MA N NA O OA P PA Q QA R RA S SA T TA U UA V VA W WA X XA Y YA Z ZA | Capsid protein VP1 Opened 1 biological assemblies for 6E9D > windowsize 512 512 > graphics bgColor white > color name marine 0,50,100 Color 'marine' is opaque, 0% red, 50% green, and 100% blue > color name forest 13.3,54.5,13.3 Color 'forest' is opaque, 13.3% red, 54.5% green, and 13.3% blue > color name tangerine 95.3,51.8,0 Color 'tangerine' is opaque, 95.3% red, 51.8% green, and 0% blue > color name grape 64.3,0,86.7 Color 'grape' is opaque, 64.3% red, 0% green, and 86.7% blue > color name nih_blue 12.5,33.3,54.1 Color 'nih_blue' is opaque, 12.5% red, 33.3% green, and 54.1% blue > color name jmol_carbon 56.5,56.5,56.5 Color 'jmol_carbon' is opaque, 56.5% red, 56.5% green, and 56.5% blue > color name bond_purple 57.6,43.9,85.9 Color 'bond_purple' is opaque, 57.6% red, 43.9% green, and 85.9% blue > color name struts_grey 48,48,48 Color 'struts_grey' is opaque, 48% red, 48% green, and 48% blue > color name carbon_grey 22.2,22.2,22.2 Color 'carbon_grey' is opaque, 22.2% red, 22.2% green, and 22.2% blue > delete solvent > delete H > delete ligand|ions > select protein|nucleic-acid 245880 atoms, 253260 bonds, 30600 residues, 1 model selected > select ~sel Nothing selected > delete sel > ~select Nothing selected > ~nucleotides > ~ribbon > ~display > surface #1 enclose #1 gridSpacing 2.5 > color nih_blue > save 6E9D-surf.png width 512 height 512 supersample 3 > save 6E9D-surf.glb > save 6E9D-surf.x3d > color white > color magenta > color byattribute kd_hydrophobicity protein target rs palette > 16,67,87:white:100,45,0 noValueColor magenta 30600 residues, 1 surfaces, atom kd_hydrophobicity range -4.5 to 4.5 > save 6E9D-surf-hydropathy.png width 512 height 512 supersample 3 > save 6E9D-surf-hydropathy.glb > save 6E9D-surf-hydropathy.x3d > rainbow chains @CA Expected a keyword UCSF ChimeraX version: 1.2.dev202010262104 (2020-10-26) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-14.7.8 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB Boot ROM Version: 236.0.0.0.0 SMC Version (system): 2.32f21 Software: System Software Overview: System Version: macOS 10.15.7 (19H2) Kernel Version: Darwin 19.6.0 Time since boot: 2 days 6:20 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a 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 Automatically Adjust Brightness: No Connection Type: Internal Locale: ('en_US', 'UTF-8') PyQt version: 5.15.1 Compiled Qt version: 5.15.1 Runtime Qt version: 5.15.1 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 cftime: 1.2.1 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.9.3 ChimeraX-AtomicLibrary: 1.1 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: 2.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 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: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202010262104 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 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: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.0.2 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8 ChimeraX-Map: 1.0.1 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: 1.1 ChimeraX-MDcrds: 2.1 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.3.1 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-Read-Pbonds: 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: 1.2.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2.1 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: 1.2.2 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.3.1 ChimeraX-uniprot: 2.0 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: 4.4.2 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 imagecodecs-lite: 2020.1.31 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: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.2 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 netifaces: 0.10.9 networkx: 2.5 numexpr: 2.7.1 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 20.2.3 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.8 psutil: 5.7.2 ptyprocess: 0.6.0 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: 5.15.1 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 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: 6.0.4 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Graphics nonchimerax all ChimeraX