id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4704 Graphics crash, maOS 10.14.1, Intel Iris Plus 655, report 2 kpwulab@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [65073] Path: /Applications/Science/ChimeraX_Daily.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.3.0 (1.3.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [65073] User ID: 501 Date/Time: 2021-05-31 03:34:05.881 +0800 OS Version: Mac OS X 10.14.1 (18B75) Report Version: 12 Bridge OS Version: 5.2 (18P4347) Anonymous UUID: 46243032-1D8F-9011-9F9C-AF784B976DB6 Sleep/Wake UUID: 8FADCFF4-0B9A-490D-964B-1FBE14AE8334 Time Awake Since Boot: 910000 seconds Time Since Wake: 3700 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: 0x00000813 Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff5ded2b86 __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff5df88c50 pthread_kill + 285 2 libsystem_c.dylib 0x00007fff5ddef096 raise + 26 3 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0x000000010a73bbdf pymain_main + 223 141 org.python.python 0x000000010a73baeb Py_Main + 43 142 edu.ucsf.cgl.ChimeraX 0x000000010a5dddc8 main + 120 143 libdyld.dylib 0x00007fff5dd9408d start + 1 Thread 1: 0 libsystem_kernel.dylib 0x00007fff5ded01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5df895cb _pthread_cond_wait + 724 2 libopenblas.0.dylib 0x000000010c0f221f blas_thread_server + 207 3 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 2: 0 libsystem_kernel.dylib 0x00007fff5ded01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5df895cb _pthread_cond_wait + 724 2 libopenblas.0.dylib 0x000000010c0f221f blas_thread_server + 207 3 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 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base::internal::ServiceThread::Run(base::RunLoop*) + 20 6 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 10 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 5:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d828778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x000000011d829150 base::internal::WorkerThread::RunWorker() + 1024 5 QtWebEngineCore 0x000000011d828c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20 6 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 8 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 9 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 6:: Chrome_IOThread 0 libsystem_kernel.dylib 0x00007fff5ded48d6 kevent64 + 10 1 QtWebEngineCore 0x000000011d88ae6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x000000011d88acc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x0000000121757f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102 6 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 10 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 7:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d7a81db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011d87be07 base::(anonymous 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QtWebEngineCore 0x000000011d88acc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 6 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 8 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 9 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 11:: VizCompositorThread 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d7a81db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 12:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d7a81db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 13:: ThreadPoolSingleThreadForegroundBlocking0 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d82876a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x000000011d829150 base::internal::WorkerThread::RunWorker() + 1024 6 QtWebEngineCore 0x000000011d828d34 base::internal::WorkerThread::RunDedicatedWorker() + 20 7 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 10 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 14:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d7a81db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 15:: MemoryInfra 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d7a81db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 16:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d7a81db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x000000011d81362b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x000000011d7d77cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x000000011d832a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d8802cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x000000011d82876a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x000000011d828e3d base::internal::WorkerThread::RunWorker() + 237 6 QtWebEngineCore 0x000000011d828c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20 7 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 10 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 18:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff30ba0da2 __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff30ba02f1 __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff30b9fa28 CFRunLoopRunSpecific + 463 5 com.apple.AppKit 0x00007fff2e0fdadd _NSEventThread + 160 6 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 8 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 19:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff5deccc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5decd174 mach_msg + 60 2 QtWebEngineCore 0x000000011d880492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x000000011d828778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x000000011d829150 base::internal::WorkerThread::RunWorker() + 1024 5 QtWebEngineCore 0x000000011d828cd4 base::internal::WorkerThread::RunPooledWorker() + 20 6 QtWebEngineCore 0x000000011d87be07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff5df86339 _pthread_body + 126 8 libsystem_pthread.dylib 0x00007fff5df892a7 _pthread_start + 70 9 libsystem_pthread.dylib 0x00007fff5df85445 thread_start + 13 Thread 20: 0 libsystem_pthread.dylib 0x00007fff5df85428 start_wqthread + 0 1 ??? 0x0000600036f4b518 0 + 105554038273304 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000116bd95c0 rcx: 0x000000010aa74a48 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x000000010aa74a80 rsp: 0x000000010aa74a48 r8: 0x000000010aa74f48 r9: 0x4ce0679452c8de00 r10: 0x0000000116bd966c r11: 0x0000000000000206 r12: 0x0000000000000307 r13: 0x00007fcc0b9cd818 r14: 0x0000000000000006 r15: 0x000000000000002d rip: 0x00007fff5ded2b86 rfl: 0x0000000000000206 cr2: 0x0000000116bac070 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10a5dd000 - 0x10a5ddff3 +edu.ucsf.cgl.ChimeraX (1.3.0 - 1.3.0.0) /Applications/Science/ChimeraX_Daily.app/Contents/MacOS/ChimeraX 0x10a5e9000 - 0x10a81fff7 +org.python.python (3.8.8, [c] 2001-2019 Python Software Foundation. - 3.8.8) /Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/Python 0x10abfa000 - 0x10abfcff7 +_heapq.cpython-38-darwin.so (0) /Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_heapq.cpython-38-darwin.so 0x10ad04000 - 0x10ad09ff7 +zlib.cpython-38-darwin.so (0) /Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/zlib.cpython-38-darwin.so 0x10ad13000 - 0x10ad15ff7 +_bz2.cpython-38-darwin.so (0) /Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_bz2.cpython-38-darwin.so 0x10ad1e000 - 0x10ad4ffff +_lzma.cpython-38-darwin.so (0) /Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_lzma.cpython-38-darwin.so 0x10ad5e000 - 0x10ad5fff7 +grp.cpython-38-darwin.so (0) 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libcoretls_cfhelpers.dylib (155.220.1) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff5b95d000 - 0x7fff5baedff3 libcrypto.35.dylib (22.200.4) /usr/lib/libcrypto.35.dylib 0x7fff5be21000 - 0x7fff5be2cff7 libcsfde.dylib (546.50.1) /usr/lib/libcsfde.dylib 0x7fff5be35000 - 0x7fff5be8bffb libcups.2.dylib (462.9) /usr/lib/libcups.2.dylib 0x7fff5bfc3000 - 0x7fff5bfc3fff libenergytrace.dylib (17.200.1) /usr/lib/libenergytrace.dylib 0x7fff5bfc4000 - 0x7fff5bfddffb libexpat.1.dylib (16.1.1) /usr/lib/libexpat.1.dylib 0x7fff5bff5000 - 0x7fff5bffaff7 libgermantok.dylib (17.15.2) /usr/lib/libgermantok.dylib 0x7fff5bffb000 - 0x7fff5c000ff7 libheimdal-asn1.dylib (520.220.2) /usr/lib/libheimdal-asn1.dylib 0x7fff5c02c000 - 0x7fff5c11dff7 libiconv.2.dylib (51.200.6) /usr/lib/libiconv.2.dylib 0x7fff5c11e000 - 0x7fff5c381ffb libicucore.A.dylib (62108.0.1) /usr/lib/libicucore.A.dylib 0x7fff5c3ce000 - 0x7fff5c3cffff liblangid.dylib (128.15.1) /usr/lib/liblangid.dylib 0x7fff5c3d0000 - 0x7fff5c3e8fff liblzma.5.dylib (10.200.3) /usr/lib/liblzma.5.dylib 0x7fff5c400000 - 0x7fff5c4b0fff libmecab.1.0.0.dylib (779.19.2) /usr/lib/libmecab.1.0.0.dylib 0x7fff5c4b1000 - 0x7fff5c6eefff libmecabra.dylib (779.19.2) /usr/lib/libmecabra.dylib 0x7fff5c8c6000 - 0x7fff5cc1efff libnetwork.dylib (1229.221.1) /usr/lib/libnetwork.dylib 0x7fff5ccaf000 - 0x7fff5d435fe7 libobjc.A.dylib (750.1) /usr/lib/libobjc.A.dylib 0x7fff5d448000 - 0x7fff5d44cffb libpam.2.dylib (22.200.1) /usr/lib/libpam.2.dylib 0x7fff5d44f000 - 0x7fff5d485ff7 libpcap.A.dylib (79.200.4) /usr/lib/libpcap.A.dylib 0x7fff5d4da000 - 0x7fff5d4ddff7 libpmenergy.dylib (194.220.1) /usr/lib/libpmenergy.dylib 0x7fff5d4de000 - 0x7fff5d4e0fff libpmsample.dylib (194.220.1) /usr/lib/libpmsample.dylib 0x7fff5d59f000 - 0x7fff5d5b7ffb libresolv.9.dylib (65.200.2) /usr/lib/libresolv.9.dylib 0x7fff5d5b9000 - 0x7fff5d5f5ff7 libsandbox.1.dylib (851.220.9) /usr/lib/libsandbox.1.dylib 0x7fff5d609000 - 0x7fff5d60aff7 libspindump.dylib (267.1) /usr/lib/libspindump.dylib 0x7fff5d60b000 - 0x7fff5d7e2fe7 libsqlite3.dylib (274.20) /usr/lib/libsqlite3.dylib 0x7fff5da6f000 - 0x7fff5da72ffb libutil.dylib (51.200.4) /usr/lib/libutil.dylib 0x7fff5da73000 - 0x7fff5da80fff libxar.1.dylib (404) /usr/lib/libxar.1.dylib 0x7fff5da85000 - 0x7fff5db68fff libxml2.2.dylib (32.8) /usr/lib/libxml2.2.dylib 0x7fff5db69000 - 0x7fff5db91ff3 libxslt.1.dylib (16.1) /usr/lib/libxslt.1.dylib 0x7fff5db92000 - 0x7fff5dba4ffb libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib 0x7fff5dc15000 - 0x7fff5dc19ff3 libcache.dylib (81) /usr/lib/system/libcache.dylib 0x7fff5dc1a000 - 0x7fff5dc24ff3 libcommonCrypto.dylib (60118.220.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff5dc25000 - 0x7fff5dc2cfff libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib 0x7fff5dc2d000 - 0x7fff5dc36ff3 libcopyfile.dylib (146.200.3) /usr/lib/system/libcopyfile.dylib 0x7fff5dc37000 - 0x7fff5dcbbfdf libcorecrypto.dylib (602.220.6) /usr/lib/system/libcorecrypto.dylib 0x7fff5dd42000 - 0x7fff5dd7cff7 libdispatch.dylib (1008.220.2) /usr/lib/system/libdispatch.dylib 0x7fff5dd7d000 - 0x7fff5ddacfff libdyld.dylib (635.2) /usr/lib/system/libdyld.dylib 0x7fff5ddad000 - 0x7fff5ddadffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff5ddae000 - 0x7fff5ddbaff7 libkxld.dylib (4903.221.2) /usr/lib/system/libkxld.dylib 0x7fff5ddbb000 - 0x7fff5ddbbff7 liblaunch.dylib (1336.220.5) /usr/lib/system/liblaunch.dylib 0x7fff5ddbc000 - 0x7fff5ddc1fff libmacho.dylib (921) /usr/lib/system/libmacho.dylib 0x7fff5ddc2000 - 0x7fff5ddc4ffb libquarantine.dylib (86.220.1) /usr/lib/system/libquarantine.dylib 0x7fff5ddc5000 - 0x7fff5ddc6ff3 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib 0x7fff5ddc7000 - 0x7fff5dddeff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib 0x7fff5dddf000 - 0x7fff5dddffff libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib 0x7fff5dde0000 - 0x7fff5de68fff libsystem_c.dylib (1272.200.26) /usr/lib/system/libsystem_c.dylib 0x7fff5de69000 - 0x7fff5de6cff7 libsystem_configuration.dylib (963.200.27) /usr/lib/system/libsystem_configuration.dylib 0x7fff5de6d000 - 0x7fff5de70ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib 0x7fff5de71000 - 0x7fff5de77ffb libsystem_darwin.dylib (1272.200.26) /usr/lib/system/libsystem_darwin.dylib 0x7fff5de78000 - 0x7fff5de7eff7 libsystem_dnssd.dylib (878.200.35) /usr/lib/system/libsystem_dnssd.dylib 0x7fff5de7f000 - 0x7fff5decbff3 libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib 0x7fff5decc000 - 0x7fff5def3ff7 libsystem_kernel.dylib (4903.221.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff5def4000 - 0x7fff5df3fff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib 0x7fff5df40000 - 0x7fff5df64ff7 libsystem_malloc.dylib (166.220.1) /usr/lib/system/libsystem_malloc.dylib 0x7fff5df65000 - 0x7fff5df70ff3 libsystem_networkextension.dylib (767.220.1) /usr/lib/system/libsystem_networkextension.dylib 0x7fff5df71000 - 0x7fff5df78fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib 0x7fff5df79000 - 0x7fff5df82fef libsystem_platform.dylib (177.200.16) /usr/lib/system/libsystem_platform.dylib 0x7fff5df83000 - 0x7fff5df8dfff libsystem_pthread.dylib (330.220.2) /usr/lib/system/libsystem_pthread.dylib 0x7fff5df8e000 - 0x7fff5df91ff7 libsystem_sandbox.dylib (851.220.9) /usr/lib/system/libsystem_sandbox.dylib 0x7fff5df92000 - 0x7fff5df94ff3 libsystem_secinit.dylib (30.220.1) /usr/lib/system/libsystem_secinit.dylib 0x7fff5df95000 - 0x7fff5df9cff7 libsystem_symptoms.dylib (820.227.2) /usr/lib/system/libsystem_symptoms.dylib 0x7fff5df9d000 - 0x7fff5dfb2ff7 libsystem_trace.dylib (906.220.1) /usr/lib/system/libsystem_trace.dylib 0x7fff5dfb4000 - 0x7fff5dfb9ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff5dfba000 - 0x7fff5dfeafff libxpc.dylib (1336.220.5) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 5 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: 786125 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=810.5M resident=0K(0%) swapped_out_or_unallocated=810.5M(100%) Writable regions: Total=147.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=147.1G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 2 CG backing stores 1160K 3 CG image 144K 17 CoreAnimation 108K 8 CoreGraphics 8K 2 CoreImage 24K 3 CoreUI image data 2524K 23 CoreUI image file 416K 7 Foundation 28K 3 Kernel Alloc Once 8K 2 MALLOC 146.3G 279 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 128.4M 3 reserved VM address space (unallocated) MALLOC_NANO (reserved) 128.0M 2 reserved VM address space (unallocated) Mach message 24K 3 Memory Tag 242 12K 2 OpenGL GLSL 384K 6 STACK GUARD 80K 21 Stack 130.7M 22 Stack Guard 56.0M 2 VM_ALLOCATE 376.6M 72 VM_ALLOCATE (reserved) 32.0M 2 reserved VM address space (unallocated) __DATA 47.3M 476 __FONT_DATA 4K 2 __GLSLBUILTINS 5176K 2 __LINKEDIT 307.4M 140 __TEXT 503.1M 454 __UNICODE 564K 2 mapped file 84.8M 104 shared memory 5212K 23 =========== ======= ======= TOTAL 148.1G 1666 TOTAL, minus reserved VM space 147.8G 1666 Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kpwu/Documents/Research-IBC-AS/project-synuclein in > calcium/maps/aSyn-Ca-model-0525-fiber-700.pdb"" Summary of feedback from opening /Users/kpwu/Documents/Research-IBC- AS/project-synuclein in calcium/maps/aSyn-Ca-model-0525-fiber-700.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Created by DsigNA Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 9654495 messages similar to the above omitted Chain information for aSyn-Ca-model-0525-fiber-700.pdb #1 --- Chain | Description A B C D E F G M O P Q R S T U | No description available OpenGL version: 4.1 INTEL-12.2.17 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 16 GB Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0) Software: System Software Overview: System Version: macOS 10.14.1 (18B75) Kernel Version: Darwin 18.2.0 Time since boot: 18 days 4:27 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 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 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: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 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: 2.0 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: 1.1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 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: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 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: 2.0 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: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 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 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 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: 1.2.3 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: 0.29.20 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: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 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: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Graphics nonchimerax all ChimeraX