id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5328 Crash in AtomSearchTree implementation chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.3.dev202109251824 (2021-09-25 18:24:47 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [18326] Path: /Volumes/VOLUME/*/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX Identifier: ChimeraX Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [18326] User ID: 501 Date/Time: 2021-09-28 23:16:46.953 -0400 OS Version: Mac OS X 10.15.7 (19H2) Report Version: 12 Bridge OS Version: 4.6 (17P6610) Anonymous UUID: 14DA238E-DDD2-6AA3-AC40-9404AFB54528 Sleep/Wake UUID: 7644EDEB-4300-49AD-861E-16B4FFA3EC3C Time Awake Since Boot: 66000 seconds Time Since Wake: 6300 seconds System Integrity Protection: enabled Notes: Translocated Process Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0: --> __TEXT 000000010d69c000-000000010d69d000 [ 4K] r-x/r-x SM=COW /var/folders/*/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff70ea233a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff70f5ee60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff70db993e raise + 26 3 libsystem_platform.dylib 0x00007fff70f535fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 libatomsearch.dylib 0x000000014b4f8c74 _Node::_Node(std::__1::vector > const&, bool, double) + 116 6 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 7 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 8 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 9 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 10 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 11 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 12 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 13 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 14 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 15 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 16 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 17 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 18 libatomsearch.dylib 0x000000014b4f97c7 _Node::_Node(std::__1::vector > const&, bool, double) + 3015 19 libatomsearch.dylib 0x000000014b4f972f _Node::_Node(std::__1::vector > const&, bool, double) + 2863 20 libatomsearch.dylib 0x000000014b4f7f67 AtomSearchTree::AtomSearchTree(std::__1::vector > const&, bool, double) + 455 21 ast.cpython-38-darwin.so 0x000000014b839f0a __pyx_tp_new_8chimerax_11atom_search_3ast_CyAtomSearchTree(_typeobject*, _object*, _object*) + 2826 22 org.python.python 0x000000010d71a702 type_call + 50 23 org.python.python 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144 org.python.python 0x000000010d7f9aeb Py_Main + 43 145 edu.ucsf.cgl.ChimeraX 0x000000010d69cdc8 main + 120 146 libdyld.dylib 0x00007fff70d5acc9 start + 1 Thread 1:: ThreadPoolServiceThread 0 libsystem_kernel.dylib 0x00007fff70ea4b96 kevent64 + 10 1 QtWebEngineCore 0x000000012505be6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330 2 QtWebEngineCore 0x000000012505bcc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167 3 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 4 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 5 QtWebEngineCore 0x0000000124fefa94 base::internal::ServiceThread::Run(base::RunLoop*) + 20 6 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 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base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124f791db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 5:: CompositorTileWorker1 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 QtWebEngineCore 0x0000000125048e18 base::ConditionVariable::Wait() + 104 3 QtWebEngineCore 0x00000001263005f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56 4 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 5 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 6 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 6:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x0000000124f7920f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223 4 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 5 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 6 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 7 QtWebEngineCore 0x000000012504ce07 base::(anonymous 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1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124f791db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 10:: ThreadPoolSingleThreadForegroundBlocking0 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124ff976a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x0000000124ffa150 base::internal::WorkerThread::RunWorker() + 1024 6 QtWebEngineCore 0x0000000124ff9d34 base::internal::WorkerThread::RunDedicatedWorker() + 20 7 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 11:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124f791db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 12:: MemoryInfra 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124f791db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 13:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124f791db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 14:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff36e85ef5 __CFRunLoopServiceMachPort + 247 3 com.apple.CoreFoundation 0x00007fff36e849c2 __CFRunLoopRun + 1319 4 com.apple.CoreFoundation 0x00007fff36e83e3e CFRunLoopRunSpecific + 462 5 com.apple.AppKit 0x00007fff34297954 _NSEventThread + 132 6 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 15:: ThreadPoolSingleThreadSharedBackgroundBlocking1 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124ff976a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42 5 QtWebEngineCore 0x0000000124ff9e3d base::internal::WorkerThread::RunWorker() + 237 6 QtWebEngineCore 0x0000000124ff9c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20 7 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 8 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 16:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x00000001250512cf base::WaitableEvent::Wait() + 31 4 QtWebEngineCore 0x0000000124f791db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171 5 QtWebEngineCore 0x0000000124fe462b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139 6 QtWebEngineCore 0x0000000124fa87cb base::RunLoop::Run() + 395 7 QtWebEngineCore 0x0000000125003a7d base::Thread::ThreadMain() + 413 8 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 9 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 10 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 17: 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010e7c027b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 18: 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010e7c027b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 19: 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010e7c027b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 20: 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010e7c027b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 21: 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 libopenblas.0.dylib 0x000000010e7c027b blas_thread_server + 507 3 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 22:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff70e9bdfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff70e9c170 mach_msg + 60 2 QtWebEngineCore 0x0000000125051492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x0000000124ff9778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x0000000124ffa150 base::internal::WorkerThread::RunWorker() + 1024 5 QtWebEngineCore 0x0000000124ff9cd4 base::internal::WorkerThread::RunPooledWorker() + 20 6 QtWebEngineCore 0x000000012504ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 23: 0 libsystem_pthread.dylib 0x00007fff70f5ab68 start_wqthread + 0 Thread 24: 0 libsystem_pthread.dylib 0x00007fff70f5ab68 start_wqthread + 0 Thread 25: 0 libsystem_pthread.dylib 0x00007fff70f5ab68 start_wqthread + 0 Thread 26: 0 libsystem_pthread.dylib 0x00007fff70f5ab68 start_wqthread + 0 Thread 27: 0 libsystem_pthread.dylib 0x00007fff70f5ab68 start_wqthread + 0 Thread 28: 0 libsystem_kernel.dylib 0x00007fff70e9e882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff70f5f425 _pthread_cond_wait + 698 2 org.python.python 0x000000010d7e9b2c PyThread_acquire_lock_timed + 700 3 org.python.python 0x000000010d836c4f acquire_timed + 111 4 org.python.python 0x000000010d836d60 lock_PyThread_acquire_lock + 48 5 org.python.python 0x000000010d6d0ef5 method_vectorcall_VARARGS_KEYWORDS + 373 6 org.python.python 0x000000010d79660c call_function + 444 7 org.python.python 0x000000010d79344a _PyEval_EvalFrameDefault + 25642 8 org.python.python 0x000000010d797454 _PyEval_EvalCodeWithName + 2804 9 org.python.python 0x000000010d6c856e _PyFunction_Vectorcall + 270 10 org.python.python 0x000000010d79660c call_function + 444 11 org.python.python 0x000000010d79344a _PyEval_EvalFrameDefault + 25642 12 org.python.python 0x000000010d797454 _PyEval_EvalCodeWithName + 2804 13 org.python.python 0x000000010d6c856e _PyFunction_Vectorcall + 270 14 org.python.python 0x000000010d79660c call_function + 444 15 org.python.python 0x000000010d79344a _PyEval_EvalFrameDefault + 25642 16 org.python.python 0x000000010d6c83d0 function_code_fastcall + 128 17 org.python.python 0x000000010d79660c call_function + 444 18 org.python.python 0x000000010d79344a _PyEval_EvalFrameDefault + 25642 19 org.python.python 0x000000010d6c83d0 function_code_fastcall + 128 20 org.python.python 0x000000010d79660c call_function + 444 21 org.python.python 0x000000010d79344a _PyEval_EvalFrameDefault + 25642 22 org.python.python 0x000000010d6c83d0 function_code_fastcall + 128 23 org.python.python 0x000000010d6caadb method_vectorcall + 235 24 org.python.python 0x000000010d6c7dad PyVectorcall_Call + 109 25 org.python.python 0x000000010d83664a t_bootstrap + 74 26 org.python.python 0x000000010d7e9619 pythread_wrapper + 25 27 libsystem_pthread.dylib 0x00007fff70f5f109 _pthread_start + 148 28 libsystem_pthread.dylib 0x00007fff70f5ab8b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000117ff6dc0 rcx: 0x00007f8087355a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007f8087355a80 rsp: 0x00007f8087355a58 r8: 0x00007f8087355f48 r9: 0x0c50a48981c3af4f r10: 0x0000000117ff6dc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff70ea233a rfl: 0x0000000000000246 cr2: 0x000000014b8b1000 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10d69c000 - 0x10d69cff3 +edu.ucsf.cgl.ChimeraX (1.2.5 - 1.2.5.0) /var/folders/*/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX 0x10d6a7000 - 0x10d8ddff7 +org.python.python (3.8.8, [c] 2001-2019 Python Software Foundation. - 3.8.8) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/Python 0x10da3c000 - 0x10da3eff7 +_heapq.cpython-38-darwin.so (0) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_heapq.cpython-38-darwin.so 0x10da46000 - 0x10da4bff7 +zlib.cpython-38-darwin.so (0) 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0x10db19000 - 0x10db71fff +libssl.1.1.dylib (0) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/libssl.1.1.dylib 0x10dba0000 - 0x10ddb6da7 +libcrypto.1.1.dylib (0) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/libcrypto.1.1.dylib 0x10de54000 - 0x10de61fff +_socket.cpython-38-darwin.so (0) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_socket.cpython-38-darwin.so 0x10de6e000 - 0x10de71ff7 +select.cpython-38-darwin.so (0) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/select.cpython-38-darwin.so 0x10de7b000 - 0x10de80fff +_struct.cpython-38-darwin.so (0) /var/folders/*/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_struct.cpython-38-darwin.so 0x10de8d000 - 0x10de91fff 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0x7fff6fbd4ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib 0x7fff6fbe5000 - 0x7fff6fbe9fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib 0x7fff6fbec000 - 0x7fff6fc22ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib 0x7fff6fc62000 - 0x7fff6fc70ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib 0x7fff6fc71000 - 0x7fff6fc74ff3 libpmenergy.dylib (214.120.1) /usr/lib/libpmenergy.dylib 0x7fff6fc75000 - 0x7fff6fc77fff libpmsample.dylib (214.120.1) /usr/lib/libpmsample.dylib 0x7fff6fca6000 - 0x7fff6fcbefff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff6fcc0000 - 0x7fff6fd04ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib 0x7fff6fd05000 - 0x7fff6fd17ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib 0x7fff6fd18000 - 0x7fff6fd19ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib 0x7fff6fd1a000 - 0x7fff6ff04ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib 0x7fff6fff8000 - 0x7fff70025ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib 0x7fff700fa000 - 0x7fff70154ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib 0x7fff70155000 - 0x7fff70158ffb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff70159000 - 0x7fff70166ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib 0x7fff7016c000 - 0x7fff7024efff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib 0x7fff70252000 - 0x7fff7027afff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib 0x7fff7027b000 - 0x7fff7028dff3 libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff70b3c000 - 0x7fff70b41ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff70b42000 - 0x7fff70b4dfff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff70b4e000 - 0x7fff70b55fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff70b56000 - 0x7fff70b5fff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff70b60000 - 0x7fff70bf2fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib 0x7fff70cff000 - 0x7fff70d3fff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff70d40000 - 0x7fff70d76fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib 0x7fff70d77000 - 0x7fff70d77ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff70d78000 - 0x7fff70d84ff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib 0x7fff70d85000 - 0x7fff70d85ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib 0x7fff70d86000 - 0x7fff70d8bff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff70d8c000 - 0x7fff70d8eff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff70d8f000 - 0x7fff70d90ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff70d91000 - 0x7fff70da8ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff70da9000 - 0x7fff70da9ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff70daa000 - 0x7fff70e31fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff70e32000 - 0x7fff70e35ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib 0x7fff70e36000 - 0x7fff70e39fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff70e3a000 - 0x7fff70e42fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff70e43000 - 0x7fff70e4afff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff70e4b000 - 0x7fff70e4cffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff70e4d000 - 0x7fff70e9aff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff70e9b000 - 0x7fff70ec7ff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff70ec8000 - 0x7fff70f0ffff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff70f10000 - 0x7fff70f37fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff70f38000 - 0x7fff70f45ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff70f46000 - 0x7fff70f4fff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff70f50000 - 0x7fff70f58fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff70f59000 - 0x7fff70f63fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff70f64000 - 0x7fff70f68ff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib 0x7fff70f69000 - 0x7fff70f6bfff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff70f6c000 - 0x7fff70f73ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff70f74000 - 0x7fff70f8aff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff70f8c000 - 0x7fff70f91ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff70f92000 - 0x7fff70fc7ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 11 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: 50115 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%) Writable regions: Total=2.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 640K 5 Activity Tracing 256K 1 CG backing stores 1232K 2 CG image 460K 35 CoreAnimation 788K 25 CoreGraphics 8K 1 CoreImage 32K 4 CoreUI image data 3592K 29 Foundation 24K 2 Kernel Alloc Once 8K 1 MALLOC 1.3G 1483 MALLOC guard page 32K 7 MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) Mach message 40K 7 OpenGL GLSL 384K 5 STACK GUARD 112K 28 Stack 157.7M 29 Stack Guard 56.0M 1 VM_ALLOCATE 226.9M 315 VM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated) __DATA 66.5M 564 __DATA_CONST 132K 6 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 481.4M 148 __OBJC_RO 32.3M 1 __OBJC_RW 1904K 1 __TEXT 574.9M 528 __UNICODE 564K 1 mapped file 428.7M 81 shared memory 2980K 29 =========== ======= ======= TOTAL 3.6G 3344 TOTAL, minus reserved VM space 3.3G 3344 System Profile: Network Service: Wi-Fi, AirPort, en0 bridge_os_version: Bridge OS 4.6 (17P6610) Boot Volume File System Type: apfs bridge_model: iBridge2,14 Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, DDR4, 2667 MHz, Micron, 8ATF1G64HZ-2G6E1 Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, DDR4, 2667 MHz, Micron, 8ATF1G64HZ-2G6E1 USB Device: USB 3.1 Bus USB Device: Apple T2 Bus USB Device: Composite Device USB Device: Touch Bar Backlight USB Device: Touch Bar Display USB Device: Apple Internal Keyboard / Trackpad USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 55.3 Thunderbolt Bus: MacBook Pro, Apple Inc., 55.3 Model: MacBookPro16,1, BootROM 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0), 6 processors, 6-Core Intel Core i7, 2.6 GHz, 16 GB, SMC Graphics: kHW_IntelUHDGraphics630Item, Intel UHD Graphics 630, spdisplays_builtin Graphics: kHW_AMDRadeonPro5300MItem, AMD Radeon Pro 5300M, spdisplays_pcie_device, 4 GB AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Apr 7 2020 13:09:12 version 9.30.357.41.32.5.49 FWID 01-617711e7 Bluetooth: Version 7.0.6f7, 3 services, 27 devices, 1 incoming serial ports Log: UCSF ChimeraX version: 1.3.dev202109251824 (2021-09-25) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/premisatheesan/Downloads/1bf2cb2b7fc127c8 5/c3jclC_.5.pdb"" Chain information for c3jclC_.5.pdb #1 --- Chain | Description ? | No description available OpenGL version: 4.1 ATI-3.10.18 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H2) Kernel Version: Darwin 19.6.0 Time since boot: 4 days 14:38 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.01.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1 charset-normalizer: 2.0.6 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.1 ChimeraX-AtomicLibrary: 4.1.4 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202109251824 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.1 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.1 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2 ChimeraX-ModelPanel: 1.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.3 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 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: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.4 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.10.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.4.0 html2text: 2020.1.16 idna: 3.2 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.8.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.20 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.1 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.0 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Structure Analysis can't reproduce Tom Goddard all ChimeraX