id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1428 ISOLDE: crash in Distance_Restraint_Mgr destructor chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-18.0.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-11-07) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [25503] Path: /Applications/ChimeraX06.app/Contents/MacOS/ChimeraX Identifier: ChimeraX Version: 0.6.0 (0.6.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [25503] User ID: 502 Date/Time: 2018-11-08 08:42:37.293 +0000 OS Version: Mac OS X 10.14 (18A391) Report Version: 12 Anonymous UUID: 93DF4E87-45ED-D785-6E93-DB772A884336 Sleep/Wake UUID: 3FEECE74-C75A-4D92-80A1-D6E4B48B042A Time Awake Since Boot: 140000 seconds Time Since Wake: 12000 seconds System Integrity Protection: disabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff5a4a2b86 __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff5a558c50 pthread_kill + 285 2 libsystem_c.dylib 0x00007fff5a3bf096 raise + 26 3 libsystem_platform.dylib 0x00007fff5a54db3d _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 molc.cpython-36m-darwin.so 0x00000001212aa73f isolde::Distance_Restraint_Mgr::~Distance_Restraint_Mgr() + 303 6 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AudioThread 0 libsystem_kernel.dylib 0x00007fff5a49cc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5a49d174 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff2d2d005e __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff2d2cf5ad __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff2d2cece4 CFRunLoopRunSpecific + 463 5 QtWebEngineCore 0x0000000113b908ef 0x112f71000 + 12712175 6 QtWebEngineCore 0x0000000113b90284 0x112f71000 + 12710532 7 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 8 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 9 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 10 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 11 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 12 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 13 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 14:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x00007fff5a49cc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5a49d174 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff2d2d005e __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff2d2cf5ad __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff2d2cece4 CFRunLoopRunSpecific + 463 5 QtWebEngineCore 0x0000000113b908ef 0x112f71000 + 12712175 6 QtWebEngineCore 0x0000000113b90284 0x112f71000 + 12710532 7 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 8 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 9 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 10 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 11 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 12 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 13 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 15:: Chrome_ChildIOThread 0 libsystem_kernel.dylib 0x00007fff5a4a3052 kevent + 10 1 QtWebEngineCore 0x000000011409e3b9 0x112f71000 + 18011065 2 QtWebEngineCore 0x000000011409b6ad 0x112f71000 + 17999533 3 QtWebEngineCore 0x0000000113b8f97f 0x112f71000 + 12708223 4 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 5 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 6 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 7 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 8 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 9 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 10 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 16:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5a4a4b8e poll + 10 1 QtCore 0x00000001125ef3e0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544 2 QtCore 0x00000001125f0a59 QEventDispatcherUNIX::processEvents(QFlags) + 857 3 QtCore 0x0000000112598082 QEventLoop::exec(QFlags) + 418 4 QtWebEngineCore 0x0000000112f92a0a 0x112f71000 + 137738 5 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 6 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 7 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 8 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 9 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 17:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5a4a4b8e poll + 10 1 QtCore 0x00000001125ef3e0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544 2 QtCore 0x00000001125f0a59 QEventDispatcherUNIX::processEvents(QFlags) + 857 3 QtCore 0x0000000112598082 QEventLoop::exec(QFlags) + 418 4 QtWebEngineCore 0x0000000112f92a0a 0x112f71000 + 137738 5 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 6 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 7 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 8 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 9 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 18:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5a4a4b8e poll + 10 1 QtCore 0x00000001125ef3e0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544 2 QtCore 0x00000001125f0a59 QEventDispatcherUNIX::processEvents(QFlags) + 857 3 QtCore 0x0000000112598082 QEventLoop::exec(QFlags) + 418 4 QtWebEngineCore 0x0000000112f92a0a 0x112f71000 + 137738 5 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 6 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 7 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 8 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 9 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 19:: PowerSaveBlocker 0 libsystem_kernel.dylib 0x00007fff5a49cc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5a49d174 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff2d2d005e __CFRunLoopServiceMachPort + 337 3 com.apple.CoreFoundation 0x00007fff2d2cf5ad __CFRunLoopRun + 1654 4 com.apple.CoreFoundation 0x00007fff2d2cece4 CFRunLoopRunSpecific + 463 5 QtWebEngineCore 0x0000000113b908ef 0x112f71000 + 12712175 6 QtWebEngineCore 0x0000000113b90284 0x112f71000 + 12710532 7 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 8 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 9 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 10 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 11 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 12 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 13 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 20:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff5a4a4b8e poll + 10 1 QtCore 0x00000001125ef3e0 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544 2 QtCore 0x00000001125f0a59 QEventDispatcherUNIX::processEvents(QFlags) + 857 3 QtCore 0x0000000112598082 QEventLoop::exec(QFlags) + 418 4 QtWebEngineCore 0x0000000112f92a0a 0x112f71000 + 137738 5 QtWebEngineCore 0x0000000113b8d0ee 0x112f71000 + 12697838 6 QtWebEngineCore 0x0000000113bb1511 0x112f71000 + 12846353 7 QtWebEngineCore 0x0000000113be534b 0x112f71000 + 13058891 8 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 9 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 10 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 11 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 21:: BrowserBlockingWorker2/288531 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 QtWebEngineCore 0x0000000113bdfbff 0x112f71000 + 13036543 3 QtWebEngineCore 0x0000000113bdf2c6 0x112f71000 + 13034182 4 QtWebEngineCore 0x0000000113be316d 0x112f71000 + 13050221 5 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 6 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 8 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 22:: BrowserBlockingWorker3/267415 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 QtWebEngineCore 0x0000000113bdfbff 0x112f71000 + 13036543 3 QtWebEngineCore 0x0000000113bdf2c6 0x112f71000 + 13034182 4 QtWebEngineCore 0x0000000113be316d 0x112f71000 + 13050221 5 QtWebEngineCore 0x0000000113bde647 0x112f71000 + 13030983 6 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 7 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 8 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 23: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 24: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 25: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 26: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 27: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 28: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 29: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 30: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMM.dylib 0x0000000129e46f91 OpenMM::threadBody(void*) + 145 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 31: 0 libsystem_kernel.dylib 0x00007fff5a4a01b2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff5a5595cb _pthread_cond_wait + 724 2 libOpenMMOpenCL.dylib 0x000000012a0b2ccd threadBody(void*) + 109 3 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 4 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 5 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 32: 0 libsystem_pthread.dylib 0x00007fff5a555408 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 33:: Dispatch queue: opencl_runtime 0 libsystem_kernel.dylib 0x00007fff5a49cc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5a49d174 mach_msg + 60 2 com.apple.framework.IOKit 0x00007fff2fd0dedb io_connect_method + 374 3 com.apple.framework.IOKit 0x00007fff2fd0dd3d IOConnectCallMethod + 244 4 com.apple.framework.IOKit 0x00007fff2fd0e54a IOConnectCallStructMethod + 38 5 com.apple.IOAccelerator 0x00007fff4b0f5c4c IOAccelContextSubmitDataBuffersExt2 + 248 6 com.apple.IOAccelerator 0x00007fff4b0f5b4e IOAccelContextSubmitDataBuffers + 29 7 libGPUSupportMercury.dylib 0x00007fff48d3fb24 gpusQueueSubmitDataBuffers + 117 8 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff2454e68b IntelCLCommandBuffer::getNew(GLDQueueRec*) + 31 9 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff2454e581 intelSubmitCLCommands(GLDQueueRec*, unsigned int) + 69 10 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff2454e4cc CHAL_INTEL::ChalContext::ChalFlush() + 82 11 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff24551311 CHAL_INTEL::ChalContext::ChalExecuteKernel(GLDKernelRec*, unsigned int, unsigned long*, unsigned long*, unsigned long*, unsigned long, void**, unsigned long*, unsigned int*, GLDFenceRec*) + 1257 12 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff24550def gldExecuteKernel + 493 13 com.apple.opencl 0x00007fff35e52d14 0x7fff35e3f000 + 81172 14 com.apple.opencl 0x00007fff35e6ade5 0x7fff35e3f000 + 179685 15 com.apple.opencl 0x00007fff35e6cd66 0x7fff35e3f000 + 187750 16 libdispatch.dylib 0x00007fff5a315dcb _dispatch_client_callout + 8 17 libdispatch.dylib 0x00007fff5a31c120 _dispatch_lane_serial_drain + 618 18 libdispatch.dylib 0x00007fff5a31cbd8 _dispatch_lane_invoke + 388 19 libdispatch.dylib 0x00007fff5a325084 _dispatch_workloop_worker_thread + 603 20 libsystem_pthread.dylib 0x00007fff5a55561c _pthread_wqthread + 409 21 libsystem_pthread.dylib 0x00007fff5a555415 start_wqthread + 13 Thread 34: 0 libsystem_pthread.dylib 0x00007fff5a555408 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 35: 0 libsystem_pthread.dylib 0x00007fff5a555408 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 36: 0 libsystem_pthread.dylib 0x00007fff5a555408 start_wqthread + 0 Thread 37: 0 libsystem_pthread.dylib 0x00007fff5a555408 start_wqthread + 0 1 ??? 0x0000000054485244 0 + 1414025796 Thread 38: 0 libsystem_kernel.dylib 0x00007fff5a49cc2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff5a49d174 mach_msg + 60 2 com.apple.framework.IOKit 0x00007fff2fd0dedb io_connect_method + 374 3 com.apple.framework.IOKit 0x00007fff2fd0e83b IOConnectCallScalarMethod + 76 4 com.apple.IOAccelerator 0x00007fff4b0f62fa IOAccelContextFinishFenceEvent + 41 5 libGPUSupportMercury.dylib 0x00007fff48d4107a gldFinishFenceOnQueue + 127 6 com.apple.opencl 0x00007fff35e52ec4 0x7fff35e3f000 + 81604 7 com.apple.opencl 0x00007fff35e69244 0x7fff35e3f000 + 172612 8 com.apple.opencl 0x00007fff35e690e8 clWaitForEvents + 185 9 libOpenMMOpenCL.dylib 0x000000012a195ee8 OpenMM::OpenCLNonbondedUtilities::computeInteractions(int, bool, bool) + 568 10 libOpenMMOpenCL.dylib 0x000000012a0ea0e8 OpenMM::OpenCLCalcForcesAndEnergyKernel::finishComputation(OpenMM::ContextImpl&, bool, bool, int, bool&) + 88 11 libOpenMM.dylib 0x0000000129de62bb OpenMM::ContextImpl::calcForcesAndEnergy(bool, bool, int) + 267 12 libOpenMM.dylib 0x0000000129e47bee OpenMM::VariableLangevinIntegrator::step(int) + 94 13 openmm.cpython-36m-darwin.so 0x000000012063e2f7 isolde::OpenMM_Thread_Handler::_step_threaded(unsigned long) + 375 14 openmm.cpython-36m-darwin.so 0x00000001206416f2 void* std::__1::__thread_proxy >, void (isolde::OpenMM_Thread_Handler::*)(unsigned long), isolde::OpenMM_Thread_Handler*, unsigned long> >(void*) + 66 15 libsystem_pthread.dylib 0x00007fff5a55633d _pthread_body + 126 16 libsystem_pthread.dylib 0x00007fff5a5592a7 _pthread_start + 70 17 libsystem_pthread.dylib 0x00007fff5a555425 thread_start + 13 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00000001123865c0 rcx: 0x000000010eda2a48 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x000000010eda2a80 rsp: 0x000000010eda2a48 r8: 0x000000010eda2f48 r9: 0x179159fc26372bb3 r10: 0x000000011238666c r11: 0x0000000000000287 r12: 0x0000000000000307 r13: 0x0000600006f88060 r14: 0x000000000000000b r15: 0x000000000000002d rip: 0x00007fff5a4a2b86 rfl: 0x0000000000000286 cr2: 0x000000010ebe5060 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10e997000 - 0x10e997ff3 +edu.ucsf.cgl.ChimeraX (0.6.0 - 0.6.0.0) /Applications/ChimeraX06.app/Contents/MacOS/ChimeraX 0x10e99d000 - 0x10eb61ff7 +org.python.python (3.6.4, [c] 2001-2017 Python Software Foundation. - 3.6.4) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/Python 0x10ef69000 - 0x10ef6aff7 +_heapq.cpython-36m-darwin.so (0) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/_heapq.cpython-36m-darwin.so 0x10f0b7000 - 0x10f0bbff7 +_struct.cpython-36m-darwin.so (0) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/_struct.cpython-36m-darwin.so 0x10f185000 - 0x10f191fff +_ssl.cpython-36m-darwin.so (0) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/_ssl.cpython-36m-darwin.so 0x10f1a1000 - 0x10f1aaffb +_socket.cpython-36m-darwin.so (0) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/_socket.cpython-36m-darwin.so 0x10f1f6000 - 0x10f1fafff +math.cpython-36m-darwin.so (0) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/math.cpython-36m-darwin.so 0x10f201000 - 0x10f203ffb +select.cpython-36m-darwin.so (0) /Applications/ChimeraX06.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/select.cpython-36m-darwin.so 0x10f249000 - 0x10f24cff3 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- 0x7fff58a81fff libmecab.1.0.0.dylib (779.15.23) /usr/lib/libmecab.1.0.0.dylib 0x7fff58a82000 - 0x7fff58cbffff libmecabra.dylib (779.15.23) /usr/lib/libmecabra.dylib 0x7fff58e97000 - 0x7fff591effff libnetwork.dylib (1229.200.109) /usr/lib/libnetwork.dylib 0x7fff59280000 - 0x7fff59a06fe7 libobjc.A.dylib (750) /usr/lib/libobjc.A.dylib 0x7fff59a07000 - 0x7fff59a08fff libodfde.dylib (24.50.1) /usr/lib/libodfde.dylib 0x7fff59a19000 - 0x7fff59a1dffb libpam.2.dylib (22.200.1) /usr/lib/libpam.2.dylib 0x7fff59a20000 - 0x7fff59a56ff7 libpcap.A.dylib (79.200.4) /usr/lib/libpcap.A.dylib 0x7fff59b70000 - 0x7fff59b88ffb libresolv.9.dylib (65.200.2) /usr/lib/libresolv.9.dylib 0x7fff59b8a000 - 0x7fff59bc6ff7 libsandbox.1.dylib (851.201.1) /usr/lib/libsandbox.1.dylib 0x7fff59bc7000 - 0x7fff59bd9ff7 libsasl2.2.dylib (211) /usr/lib/libsasl2.2.dylib 0x7fff59bda000 - 0x7fff59bdbffb libspindump.dylib (266) /usr/lib/libspindump.dylib 0x7fff59bdc000 - 0x7fff59db3fe7 libsqlite3.dylib (274.20) /usr/lib/libsqlite3.dylib 0x7fff59dd6000 - 0x7fff59e0fff7 libssl.0.9.8.dylib (76.200.2) /usr/lib/libssl.0.9.8.dylib 0x7fff59eb6000 - 0x7fff59f03fff libssl.44.dylib (22.200.4) /usr/lib/libssl.44.dylib 0x7fff59f04000 - 0x7fff59f55ff7 libstdc++.6.dylib (104.1) /usr/lib/libstdc++.6.dylib 0x7fff5a040000 - 0x7fff5a043ffb libutil.dylib (51.200.4) /usr/lib/libutil.dylib 0x7fff5a044000 - 0x7fff5a051fff libxar.1.dylib (404) /usr/lib/libxar.1.dylib 0x7fff5a056000 - 0x7fff5a139fff libxml2.2.dylib (32.6) /usr/lib/libxml2.2.dylib 0x7fff5a13a000 - 0x7fff5a162ff3 libxslt.1.dylib (16.1) /usr/lib/libxslt.1.dylib 0x7fff5a163000 - 0x7fff5a175ffb libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib 0x7fff5a1e6000 - 0x7fff5a1eaff3 libcache.dylib (81) /usr/lib/system/libcache.dylib 0x7fff5a1eb000 - 0x7fff5a1f5ff3 libcommonCrypto.dylib (60118.200.6) /usr/lib/system/libcommonCrypto.dylib 0x7fff5a1f6000 - 0x7fff5a1fdfff libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib 0x7fff5a1fe000 - 0x7fff5a207ff3 libcopyfile.dylib (146.200.3) /usr/lib/system/libcopyfile.dylib 0x7fff5a208000 - 0x7fff5a28cfff libcorecrypto.dylib (602.200.50) /usr/lib/system/libcorecrypto.dylib 0x7fff5a312000 - 0x7fff5a34cff7 libdispatch.dylib (1008.200.78) /usr/lib/system/libdispatch.dylib 0x7fff5a34d000 - 0x7fff5a37cfff libdyld.dylib (625.13) /usr/lib/system/libdyld.dylib 0x7fff5a37d000 - 0x7fff5a37dffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff5a37e000 - 0x7fff5a38aff7 libkxld.dylib (4903.201.2) /usr/lib/system/libkxld.dylib 0x7fff5a38b000 - 0x7fff5a38bff7 liblaunch.dylib (1336.201.2) /usr/lib/system/liblaunch.dylib 0x7fff5a38c000 - 0x7fff5a391fff libmacho.dylib (917) /usr/lib/system/libmacho.dylib 0x7fff5a392000 - 0x7fff5a394ff3 libquarantine.dylib (86.200.11) /usr/lib/system/libquarantine.dylib 0x7fff5a395000 - 0x7fff5a396ff3 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib 0x7fff5a397000 - 0x7fff5a3aeff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib 0x7fff5a3af000 - 0x7fff5a3affff libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib 0x7fff5a3b0000 - 0x7fff5a438fff libsystem_c.dylib (1272.200.26) /usr/lib/system/libsystem_c.dylib 0x7fff5a439000 - 0x7fff5a43cff7 libsystem_configuration.dylib (963.200.27) /usr/lib/system/libsystem_configuration.dylib 0x7fff5a43d000 - 0x7fff5a440ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib 0x7fff5a441000 - 0x7fff5a447ffb libsystem_darwin.dylib (1272.200.26) /usr/lib/system/libsystem_darwin.dylib 0x7fff5a448000 - 0x7fff5a44eff7 libsystem_dnssd.dylib (878.200.35) /usr/lib/system/libsystem_dnssd.dylib 0x7fff5a44f000 - 0x7fff5a49bff3 libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib 0x7fff5a49c000 - 0x7fff5a4c3ff7 libsystem_kernel.dylib (4903.201.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff5a4c4000 - 0x7fff5a50fff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib 0x7fff5a510000 - 0x7fff5a534ff7 libsystem_malloc.dylib (166.200.60) /usr/lib/system/libsystem_malloc.dylib 0x7fff5a535000 - 0x7fff5a540ffb libsystem_networkextension.dylib (767.200.40) /usr/lib/system/libsystem_networkextension.dylib 0x7fff5a541000 - 0x7fff5a548fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib 0x7fff5a549000 - 0x7fff5a552fef libsystem_platform.dylib (177.200.16) /usr/lib/system/libsystem_platform.dylib 0x7fff5a553000 - 0x7fff5a55dfff libsystem_pthread.dylib (330.201.1) /usr/lib/system/libsystem_pthread.dylib 0x7fff5a55e000 - 0x7fff5a561ff7 libsystem_sandbox.dylib (851.201.1) /usr/lib/system/libsystem_sandbox.dylib 0x7fff5a562000 - 0x7fff5a564ff7 libsystem_secinit.dylib (30.200.13) /usr/lib/system/libsystem_secinit.dylib 0x7fff5a565000 - 0x7fff5a56cff7 libsystem_symptoms.dylib (820.207.88) /usr/lib/system/libsystem_symptoms.dylib 0x7fff5a56d000 - 0x7fff5a582ff7 libsystem_trace.dylib (906.200.86) /usr/lib/system/libsystem_trace.dylib 0x7fff5a584000 - 0x7fff5a589ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff5a58a000 - 0x7fff5a5bafff libxpc.dylib (1336.201.2) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 444 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: 13901623 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=738.4M resident=0K(0%) swapped_out_or_unallocated=738.4M(100%) Writable regions: Total=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 4 Activity Tracing 256K 2 CG backing stores 51.5M 20 CG image 272K 35 CoreAnimation 484K 72 CoreGraphics 8K 2 CoreImage 208K 25 CoreUI image data 4552K 52 CoreUI image file 360K 7 Foundation 28K 4 Kernel Alloc Once 8K 2 MALLOC 763.5M 536 MALLOC guard page 32K 9 MALLOC_LARGE (reserved) 1024K 6 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 2 reserved VM address space (unallocated) Memory Tag 242 12K 2 Memory Tag 251 32K 2 OpenCL 10.7M 28 OpenCL (reserved) 32K 2 reserved VM address space (unallocated) OpenGL GLSL 512K 7 STACK GUARD 152K 39 Stack 184.8M 40 Stack Guard 56.0M 2 VM_ALLOCATE 111.4M 391 __DATA 63.3M 650 __FONT_DATA 4K 2 __GLSLBUILTINS 5176K 2 __LINKEDIT 248.7M 252 __TEXT 489.6M 607 __UNICODE 560K 2 mapped file 82.4M 97 shared memory 10.5M 23 =========== ======= ======= TOTAL 2.4G 2894 TOTAL, minus reserved VM space 2.0G 2894 Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.8 (2018-11-07) How to cite UCSF ChimeraX > open /Users/jozef/Downloads/hPCP17_xC15-cluster1_1.pdb Summary of feedback from opening /Users/jozef/Downloads/hPCP17_xC15-cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME=""complex_26w.pdb0"" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_26.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for hPCP17_xC15-cluster1_1.pdb #1 --- Chain | Description A | No description available B | No description available > set bgColor white OpenGL version: 4.1 NVIDIA-12.0.19 355.11.10.50.10.103 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party fixed all ChimeraX