id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5413 Dual display crash hrishikesh.das@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-20.6.0-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 [3053] Path: /private/var/folders/*/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.1.1 (1.1.1.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [3053] User ID: 501 Date/Time: 2021-10-14 19:51:40.150 +0200 OS Version: macOS 11.6 (20G165) Report Version: 12 Bridge OS Version: 5.5 (18P4759a) Anonymous UUID: 250318AF-B0C7-4CAC-6AA5-6AB535BC3FE0 Sleep/Wake UUID: 9BB514DF-39FC-4CA0-926C-F0561964D0D7 Time Awake Since Boot: 15000 seconds Time Since Wake: 31 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: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff2042292e __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff204515bd pthread_kill + 263 2 libsystem_c.dylib 0x00007fff20335bd5 raise + 26 3 libsystem_platform.dylib 0x00007fff20496d7d _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 libqcocoa.dylib 0x00000001234647a1 0x123445000 + 128929 6 libqcocoa.dylib 0x000000012345e3c2 0x123445000 + 103362 7 libqcocoa.dylib 0x000000012345de4b 0x123445000 + 101963 8 QtGui 0x0000000118d3170c QWindowPrivate::create(bool, unsigned long long) + 140 9 QtGui 0x0000000118d30978 QWindowPrivate::setTopLevelScreen(QScreen*, bool) + 744 10 QtGui 0x0000000118d5771c QScreen::~QScreen() + 444 11 QtGui 0x0000000118d5778e QScreen::~QScreen() + 14 12 QtGui 0x0000000118d0a6aa QWindowSystemInterface::handleScreenRemoved(QPlatformScreen*) + 58 13 libqcocoa.dylib 0x000000012344efed 0x123445000 + 40941 14 com.apple.Foundation 0x00007fff212ae01a -[__NSObserver _doit:] + 287 15 com.apple.CoreFoundation 0x00007fff2053ea53 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12 16 com.apple.CoreFoundation 0x00007fff205da4d9 ___CFXRegistrationPost_block_invoke + 49 17 com.apple.CoreFoundation 0x00007fff205da454 _CFXRegistrationPost + 496 18 com.apple.CoreFoundation 0x00007fff2050fcce _CFXNotificationPost + 736 19 com.apple.Foundation 0x00007fff21281bb8 -[NSNotificationCenter postNotificationName:object:userInfo:] + 59 20 com.apple.AppKit 0x00007fff23880daa ___NSApplicationReactToScreenInvalidation_block_invoke + 1015 21 com.apple.AppKit 0x00007fff23880712 _NSApplicationReactToScreenInvalidation + 129 22 com.apple.AppKit 0x00007fff22ede806 -[NSApplication(ScreenHandling) _reactToDockChanged] + 146 23 com.apple.AppKit 0x00007fff22ede05b _NSCGSDockMessageReceive + 268 24 com.apple.HIToolbox 0x00007fff287b6326 DockCallback(unsigned int, unsigned int, void*, void*) + 1987 25 com.apple.HIServices 0x00007fff257de1ee dockClientNotificationProc + 217 26 com.apple.SkyLight 0x00007fff24cf8f35 (anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*) + 1071 27 com.apple.SkyLight 0x00007fff24f9ade8 CGSDatagramReadStream::dispatchMainQueueDatagrams() + 202 28 com.apple.SkyLight 0x00007fff24f9ad0f invocation function for block in CGSDatagramReadStream::mainQueueWakeup() + 18 29 libdispatch.dylib 0x00007fff202a6623 _dispatch_call_block_and_release + 12 30 libdispatch.dylib 0x00007fff202a7806 _dispatch_client_callout + 8 31 libdispatch.dylib 0x00007fff202b3b4f _dispatch_main_queue_callback_4CF + 940 32 com.apple.CoreFoundation 0x00007fff20585f18 __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9 33 com.apple.CoreFoundation 0x00007fff20548112 __CFRunLoopRun + 2755 34 com.apple.CoreFoundation 0x00007fff20546f8c CFRunLoopRunSpecific + 563 35 com.apple.HIToolbox 0x00007fff2878f1f3 RunCurrentEventLoopInMode + 292 36 com.apple.HIToolbox 0x00007fff2878ef55 ReceiveNextEventCommon + 587 37 com.apple.HIToolbox 0x00007fff2878ecf3 _BlockUntilNextEventMatchingListInModeWithFilter + 70 38 com.apple.AppKit 0x00007fff22d50172 _DPSNextEvent + 864 39 com.apple.AppKit 0x00007fff22d4e945 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364 40 com.apple.AppKit 0x00007fff22d40c69 -[NSApplication run] + 586 41 libqcocoa.dylib 0x000000012347ade3 0x123445000 + 220643 42 QtCore 0x000000011943793f QEventLoop::exec(QFlags) + 431 43 QtCore 0x000000011943c932 QCoreApplication::exec() + 130 44 QtWidgets.so 0x00000001141a27d2 meth_QApplication_exec_(_object*, _object*) + 82 45 org.python.python 0x000000010756e382 _PyMethodDef_RawFastCallKeywords + 226 46 org.python.python 0x000000010756d8b9 _PyCFunction_FastCallKeywords + 41 47 org.python.python 0x0000000107642b60 call_function + 656 48 org.python.python 0x000000010763f817 _PyEval_EvalFrameDefault + 26567 49 org.python.python 0x000000010756dd61 function_code_fastcall + 177 50 org.python.python 0x0000000107642bd4 call_function + 772 51 org.python.python 0x000000010763f817 _PyEval_EvalFrameDefault + 26567 52 org.python.python 0x0000000107643a2c _PyEval_EvalCodeWithName + 3276 53 org.python.python 0x000000010756d879 _PyFunction_FastCallKeywords + 217 54 org.python.python 0x0000000107642bd4 call_function + 772 55 org.python.python 0x000000010763f8ae _PyEval_EvalFrameDefault + 26718 56 org.python.python 0x0000000107643a2c _PyEval_EvalCodeWithName + 3276 57 org.python.python 0x0000000107638fb0 PyEval_EvalCode + 48 58 org.python.python 0x0000000107636547 builtin_exec + 583 59 org.python.python 0x000000010756e52d _PyMethodDef_RawFastCallKeywords + 653 60 org.python.python 0x000000010756d8b9 _PyCFunction_FastCallKeywords + 41 61 org.python.python 0x0000000107642b60 call_function + 656 62 org.python.python 0x000000010763f8ae _PyEval_EvalFrameDefault + 26718 63 org.python.python 0x0000000107643a2c _PyEval_EvalCodeWithName + 3276 64 org.python.python 0x000000010756d879 _PyFunction_FastCallKeywords + 217 65 org.python.python 0x0000000107642bd4 call_function + 772 66 org.python.python 0x000000010763f8ae _PyEval_EvalFrameDefault + 26718 67 org.python.python 0x0000000107643a2c _PyEval_EvalCodeWithName + 3276 68 org.python.python 0x000000010756d377 _PyFunction_FastCallDict + 455 69 org.python.python 0x000000010769daf3 pymain_run_module + 147 70 org.python.python 0x000000010769cbdc pymain_main + 5900 71 org.python.python 0x000000010769b4c3 Py_Main + 51 72 edu.ucsf.cgl.ChimeraX 0x0000000107541dc8 main + 120 73 libdyld.dylib 0x00007fff2046cf3d start + 1 Thread 1: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x0000000108eafc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 2: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x0000000108eafc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 3: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x0000000108eafc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 4: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x0000000108eafc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 5: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x0000000108eafc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 6:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff2054949f __CFRunLoopServiceMachPort + 316 3 com.apple.CoreFoundation 0x00007fff20547b7f __CFRunLoopRun + 1328 4 com.apple.CoreFoundation 0x00007fff20546f8c CFRunLoopRunSpecific + 563 5 com.apple.AppKit 0x00007fff22ed623a _NSEventThread + 124 6 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 7: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x000000012a1c6c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 8: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x000000012a1c6c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 9: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x000000012a1c6c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 10: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x000000012a1c6c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 11: 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 libopenblasp-r0.3.7.dylib 0x000000012a1c6c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 12:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe22f 0x11be5c000 + 35267119 4 QtWebEngineCore 0x000000011dfb205d 0x11be5c000 + 34955357 5 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 6 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 13:: DnsConfigService 0 libsystem_kernel.dylib 0x00007fff20420c4a kevent + 10 1 QtWebEngineCore 0x000000011e2bf9a9 0x11be5c000 + 38156713 2 QtWebEngineCore 0x000000011e2bccbd 0x11be5c000 + 38145213 3 QtWebEngineCore 0x000000011e073cdc 0x11be5c000 + 35749084 4 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 5 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 6 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 7 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 14:: TaskSchedulerServiceThread 0 libsystem_kernel.dylib 0x00007fff20420c4a kevent + 10 1 QtWebEngineCore 0x000000011e2bf9a9 0x11be5c000 + 38156713 2 QtWebEngineCore 0x000000011e2bccbd 0x11be5c000 + 38145213 3 QtWebEngineCore 0x000000011e073cc4 0x11be5c000 + 35749060 4 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 5 QtWebEngineCore 0x000000011e01ca74 0x11be5c000 + 35392116 6 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 15:: TaskSchedulerForegroundWorker 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe421 0x11be5c000 + 35267617 4 QtWebEngineCore 0x000000011e015d28 0x11be5c000 + 35364136 5 QtWebEngineCore 0x000000011e01665b 0x11be5c000 + 35366491 6 QtWebEngineCore 0x000000011e0162c4 0x11be5c000 + 35365572 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 16:: TaskSchedulerForegroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe421 0x11be5c000 + 35267617 4 QtWebEngineCore 0x000000011e015d28 0x11be5c000 + 35364136 5 QtWebEngineCore 0x000000011e01665b 0x11be5c000 + 35366491 6 QtWebEngineCore 0x000000011e0162c4 0x11be5c000 + 35365572 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 17:: TaskSchedulerBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe421 0x11be5c000 + 35267617 4 QtWebEngineCore 0x000000011e015d28 0x11be5c000 + 35364136 5 QtWebEngineCore 0x000000011e01665b 0x11be5c000 + 35366491 6 QtWebEngineCore 0x000000011e016234 0x11be5c000 + 35365428 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc 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35749060 4 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 5 QtWebEngineCore 0x000000011d949fe4 0x11be5c000 + 28237796 6 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 20:: TaskSchedulerSingleThreadSharedBackgroundBlocking0 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe22f 0x11be5c000 + 35267119 4 QtWebEngineCore 0x000000011e015d1a 0x11be5c000 + 35364122 5 QtWebEngineCore 0x000000011e0163bf 0x11be5c000 + 35365823 6 QtWebEngineCore 0x000000011e016264 0x11be5c000 + 35365476 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 21:: CompositorTileWorker1/71939 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 QtWebEngineCore 0x000000011e06bfa8 0x11be5c000 + 35717032 3 QtWebEngineCore 0x000000011eff24c8 0x11be5c000 + 51995848 4 QtWebEngineCore 0x000000011e02c694 0x11be5c000 + 35456660 5 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 6 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 22:: AudioThread 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe22f 0x11be5c000 + 35267119 4 QtWebEngineCore 0x000000011dfb205d 0x11be5c000 + 34955357 5 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 6 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 23:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dfb2052 0x11be5c000 + 34955346 4 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 5 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 6 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 7 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 24:: Chrome_ChildIOThread 0 libsystem_kernel.dylib 0x00007fff20420c4a kevent + 10 1 QtWebEngineCore 0x000000011e2bf9a9 0x11be5c000 + 38156713 2 QtWebEngineCore 0x000000011e2bccbd 0x11be5c000 + 38145213 3 QtWebEngineCore 0x000000011e073cdc 0x11be5c000 + 35749084 4 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 5 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 6 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 7 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 25:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe22f 0x11be5c000 + 35267119 4 QtWebEngineCore 0x000000011dfb205d 0x11be5c000 + 34955357 5 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 6 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 26:: TaskSchedulerSingleThreadForegroundBlocking1 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe22f 0x11be5c000 + 35267119 4 QtWebEngineCore 0x000000011e015d1a 0x11be5c000 + 35364122 5 QtWebEngineCore 0x000000011e01665b 0x11be5c000 + 35366491 6 QtWebEngineCore 0x000000011e016324 0x11be5c000 + 35365668 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 27:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe22f 0x11be5c000 + 35267119 4 QtWebEngineCore 0x000000011dfb205d 0x11be5c000 + 34955357 5 QtWebEngineCore 0x000000011dfdb085 0x11be5c000 + 35123333 6 QtWebEngineCore 0x000000011e02d9bc 0x11be5c000 + 35461564 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 28:: QFileInfoGatherer 0 libsystem_kernel.dylib 0x00007fff2041ecde __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff20451e49 _pthread_cond_wait + 1298 2 QtCore 0x000000011927c8ab 0x119252000 + 174251 3 QtCore 0x000000011927c80c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 4 QtWidgets 0x000000011897b762 0x118740000 + 2340706 5 QtCore 0x00000001192740b3 0x119252000 + 139443 6 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 29:: TaskSchedulerForegroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff2041c2ba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2041c62c mach_msg + 60 2 QtWebEngineCore 0x000000011dffe32d 0x11be5c000 + 35267373 3 QtWebEngineCore 0x000000011dffe421 0x11be5c000 + 35267617 4 QtWebEngineCore 0x000000011e015d28 0x11be5c000 + 35364136 5 QtWebEngineCore 0x000000011e01665b 0x11be5c000 + 35366491 6 QtWebEngineCore 0x000000011e0162c4 0x11be5c000 + 35365572 7 QtWebEngineCore 0x000000011e06d717 0x11be5c000 + 35723031 8 libsystem_pthread.dylib 0x00007fff204518fc _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2044d443 thread_start + 15 Thread 30: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 31: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 32: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 33: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 34: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 35: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 36: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 37: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 38: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 39: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 40: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 41: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 42: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 43: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 44: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 45: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 46: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 47: 0 libsystem_pthread.dylib 0x00007fff2044d420 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00000001146ffe00 rcx: 0x00007fb93b577a58 rdx: 0x0000000000000000 rdi: 0x0000000000000103 rsi: 0x000000000000000b rbp: 0x00007fb93b577a80 rsp: 0x00007fb93b577a58 r8: 0x00007fb93b577f48 r9: 0x49d917a004aef2a5 r10: 0x00000001146ffe00 r11: 0x0000000000000246 r12: 0x0000000000000103 r13: 0x0000600002224dc0 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff2042292e rfl: 0x0000000000000246 cr2: 0x00000001077a8fa4 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Thread 0 instruction stream: c0 74 06 f0 41 ff 0f 75-08 4c 89 ff e8 6b 90 3d .t..A..u.L...k.= 00 48 8b 03 48 63 48 08-48 8d 04 c8 48 63 4d d4 .H..HcH.H...HcM. 4c 89 74 c8 10 eb 0b 48-89 df e8 2f 90 3d 00 4c L.t....H.../.=.L 89 30 48 89 d8 48 83 c4-08 5b 41 5c 41 5d 41 5e .0H..H...[A\A]A^ 41 5f 5d c3 66 66 66 2e-0f 1f 84 00 00 00 00 00 A_].fff......... 55 48 89 e5 48 8b 47 08-48 8b 08 48 85 c9 74 0d UH..H.G.H..H..t. 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0x7fff3dafdfff com.apple.sidecar-ui (1.0 - 231) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI 0x7fff3e120000 - 0x7fff3e182fff com.apple.ImageCaptureCore (1711.5.2 - 1711.5.2) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore 0x7fff3e183000 - 0x7fff3e1a8fff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters 0x7fff3e864000 - 0x7fff3e990fff com.apple.AnnotationKit (1.0 - 383.6) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit 0x7fff3e991000 - 0x7fff3ee31fff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer 0x7fff3ee32000 - 0x7fff3ef1afff com.apple.PDFKit (1.0 - 950.40.3) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit 0x7fff3fc61000 - 0x7fff3fcdefff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput 0x7fff40e15000 - 0x7fff40e1efff com.apple.IOAccelMemoryInfo (1.0 - 1) /System/Library/PrivateFrameworks/IOAccelMemoryInfo.framework/Versions/A/IOAccelMemoryInfo 0x7fff40e79000 - 0x7fff40e7cfff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz 0x7fff412a1000 - 0x7fff412bffff libCGInterfaces.dylib (544.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff4384e000 - 0x7fff43ac1fff com.apple.RawCamera.bundle (9.10.0 - 1450.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff46394000 - 0x7fff4639ffff libGPUSupportMercury.dylib (18.5.9) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib 0x7fff479ca000 - 0x7fff47a0afff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics 0x7fff51640000 - 0x7fff5166dfff com.apple.HelpData (2.3 - 201) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData 0x7fff5166e000 - 0x7fff51688fff com.apple.shortcut (2.16 - 118) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut 0x7fff51689000 - 0x7fff51728fff com.apple.Symbolication (12.5 - 64544.70.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication 0x7fff53fb0000 - 0x7fff53fe6fff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit 0x7fff555dd000 - 0x7fff555e0fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback 0x7fff5dd18000 - 0x7fff5e1a7fff com.apple.driver.AppleIntelKBLGraphicsMTLDriver (16.5.2 - 16.0.5) /System/Library/Extensions/AppleIntelKBLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsMTLDriver 0x7fff5e1a8000 - 0x7fff5ec0bfff libSC.dylib (4.6.20) /System/Library/Extensions/AMDShared.bundle/Contents/PlugIns/libSC.dylib 0x7fff5ef40000 - 0x7fff5ff27fff com.apple.driver.AppleIntelKBLGraphicsGLDriver (16.5.2 - 16.0.5) /System/Library/Extensions/AppleIntelKBLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelKBLGraphicsGLDriver 0x7fff696d9000 - 0x7fff696ddfff libmetal_timestamp.dylib (31001.192.1) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib 0x7fff6bb24000 - 0x7fff6bb2afff libCoreFSCache.dylib (200.11) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib 0x7fff6bb2b000 - 0x7fff6bb2ffff libCoreVMClient.dylib (200.11) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x7fff6bb30000 - 0x7fff6bb3ffff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff6bb40000 - 0x7fff6bb42fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib 0x7fff6bb43000 - 0x7fff6bb4bfff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff6bb4c000 - 0x7fff6bb7ffff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6bb80000 - 0x7fff6bbbcfff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6bbbd000 - 0x7fff6bd50fff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x7fff6bd51000 - 0x7fff6bd5bfff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6bd5c000 - 0x7fff6bed9fff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine 0x7fff6beda000 - 0x7fff6bf02fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x7fff6d19b000 - 0x7fff6d1f3fff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6e13d000 - 0x7fff6e18cfff ATIRadeonX6000SCLib.dylib (4.6.20) /System/Library/Extensions/AMDRadeonX6000GLDriver.bundle/Contents/MacOS/ATIRadeonX6000SCLib.dylib 0x7fff6e29d000 - 0x7fff6e2a4fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff6e2a5000 - 0x7fff6e38cfff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio 0x7fff6f90e000 - 0x7fff6f920fff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging 0x7fff73c1e000 - 0x7fff73c29fff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics 0x7fff73e3f000 - 0x7fff73e57fff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed 0x7fff779cf000 - 0x7fff779d6fff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 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: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%) Writable regions: Total=1.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.6G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 1152K 9 Activity Tracing 256K 1 CG backing stores 22.6M 13 CG image 328K 45 CoreAnimation 192K 26 CoreGraphics 24K 5 CoreServices 624K 2 CoreUI image data 5312K 54 Foundation 32K 2 Kernel Alloc Once 8K 1 MALLOC 514.2M 389 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 188K 47 Stack 159.4M 48 Stack Guard 56.0M 1 VM_ALLOCATE 250.3M 546 VM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated) __DATA 44.4M 699 __DATA_CONST 23.4M 267 __DATA_DIRTY 1213K 170 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 553.9M 227 __OBJC_RO 70.3M 1 __OBJC_RW 2496K 2 __TEXT 685.2M 648 __UNICODE 588K 1 mapped file 262.6M 50 shared memory 792K 22 =========== ======= ======= TOTAL 3.2G 3298 TOTAL, minus reserved VM space 2.6G 3298 Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/final_figures_images/interfac2.cxs Log from Thu Oct 14 19:05:50 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfac2.cxs > format session Window position QRect(1738,1679 551x162) outside any known screen, using primary screen Log from Thu Oct 14 18:19:53 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interface1.cxs > format session Log from Thu Oct 14 17:28:27 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs Log from Thu Oct 14 16:42:53 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs Log from Thu Oct 14 15:32:31 2021UCSF 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/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/dimer_pol_to_submit/complex_model- > coot-4.pdb Chain information for complex_model-coot-4.pdb #1 --- Chain | Description A B | No description available > set bgColor white > lighting soft > graphics silhouettes true > dssp > set silhouetteWidth 1 > select #1:219-355 1994 atoms, 2022 bonds, 274 residues, 1 model selected > color sel #176e6dff > select #1:356-604 4000 atoms, 4088 bonds, 498 residues, 1 model selected > color sel #878787ff > select #1:605-623 322 atoms, 330 bonds, 38 residues, 1 model selected > color sel #af2e79ff > select #1:624-1230 9262 atoms, 9510 bonds, 4 pseudobonds, 1168 residues, 2 models selected > color (#!1 & sel) #44a14fff > select #1:711-790 1236 atoms, 1264 bonds, 160 residues, 1 model selected > color sel #f9a036ff > select #1:1085-1109 34 atoms, 30 bonds, 4 pseudobonds, 4 residues, 2 models selected > color (#!1 & sel) #a264ffff > select clear > select #1.1 4 pseudobonds, 1 model selected > select clear > color sel #176e6dff > select clear > view > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs > view > select /A:1085 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select clear > select /A:1085 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select clear > select clear > select /A:1085 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > select clear > hide cartoons > show atoms > select /A:1085@C 1 atom, 1 residue, 1 model selected > select /A:1109@N 1 atom, 1 residue, 1 model selected > select clear > hide atoms > show cartoons > show sel atoms > hide sel cartoons > select clear > show cartoons > hide cartoons > show cartoons > chain_trace_atmos Unknown command: chain_trace_atmos > chain_trace_atoms Unknown command: chain_trace_atoms > select clear > select clear > chain_trace_atoms Unknown command: chain_trace_atoms > hide sel atoms > show sel atoms > hide sel cartoons > select clear > polymers(missing_structure_treatment=0, consider_chains_ids=True) Unknown command: polymers(missing_structure_treatment=0, consider_chains_ids=True) > polymers (missing_structure_treatment=0, consider_chains_ids=True) Unknown command: polymers (missing_structure_treatment=0, consider_chains_ids=True) > select clear > hide #1.1 models > hide atoms > show cartoons > select clear > view > dssp > view > connect_structure Unknown command: connect_structure > connect_structure (#1/a:1085-1109) Unknown command: connect_structure (#1/a:1085-1109) > connect_structure (#1:1085-1109) Unknown command: connect_structure (#1:1085-1109) > view > preset cartoons/nucleotides cylinders/stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs opened ChimeraX session > view > hide cartoons > select #1:711-790 1236 atoms, 1264 bonds, 160 residues, 1 model selected > show sel cartoons > select #1:605-623 322 atoms, 330 bonds, 38 residues, 1 model selected > show sel cartoons > select clear > view > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/dimer_thumb_hairpin.png > width 1775 height 1780 supersample 3 > select clear > show cartoons > view > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > color (#!1 & sel) light gray > surface (#!1 & sel) > color (#!1 & sel) light gray > select clear > color #1.2#!1 gray > undo > select /B 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > transparency (#!1 & sel) 50 > select clear > transparency #1.2#!1 0 > color #1.2#!1 white > undo > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > color (#!1 & sel) dim gray > select clear > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > color (#!1 & sel) light gray > select clear > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > color (#!1 & sel) white > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfaces.png > width 1775 height 1780 supersample 3 > select #1/B:605-623 161 atoms, 165 bonds, 19 residues, 1 model selected > select #1/A:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > select #1/B:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > color sel dim gray > select clear > surface hidePatches #1.2#!1 > select #1/A:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > color (#!1 & sel) gray > select #1/B:605-623 161 atoms, 165 bonds, 19 residues, 1 model selected > color sel #af2e79ff > select #1/B:623-1230 4638 atoms, 4763 bonds, 2 pseudobonds, 585 residues, 2 models selected > select #1/A:623-1230 4638 atoms, 4763 bonds, 2 pseudobonds, 585 residues, 2 models selected > color (#!1 & sel) #44a14fff > select #1/A:605-623 161 atoms, 165 bonds, 19 residues, 1 model selected > color (#!1 & sel) #af2e79ff > select #1:1085-1109 34 atoms, 30 bonds, 4 pseudobonds, 4 residues, 2 models selected > color (#!1 & sel) #a264ffff > select #1:219-355 1994 atoms, 2022 bonds, 274 residues, 1 model selected > color (#!1 & sel) #176e6dff > select clear > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > select clear > select #1:218-355 2012 atoms, 2040 bonds, 276 residues, 1 model selected > color (#!1 & sel) #176e6dff > color (#!1 & sel) #176e6dff > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/dimer_colored_domain.png > width 1775 height 1780 supersample 3 > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs > select #1:711-790 1236 atoms, 1264 bonds, 160 residues, 1 model selected > color (#!1 & sel) #f9b928ff > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs opened ChimeraX session Drag select of 14 residues > show sel atoms > color sel byhetero > view sel > select clear > view > select /B:754@CB 1 atom, 1 residue, 1 model selected Drag select of 62 atoms, 18 residues, 59 bonds > hide sel cartoons > select clear Drag select of 33 atoms, 38 bonds Drag select of 21 atoms, 3 residues, 21 bonds > select clear > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > color (#!1 & sel) light gray > color sel byhetero > select clear Drag select of 143 atoms, 16 residues, 147 bonds Drag select of 32 atoms, 1 residues, 36 bonds > hide sel atoms > show sel cartoons > show sel cartoons > select clear > hide atoms > hide atoms > show cartoons > show cartoons > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > color sel skyblue > surface (#!1 & sel) > color sel skyblue > select clear > dssp > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfaces.png > width 1752 height 1924 supersample 4 > select #1/B:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > color sel light gray > color sel gray > select clear > select #1/B:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > color sel light gray > select clear > hide surfaces > select #1/B:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > select #1/356-605 Nothing selected > select #1:356-605 4014 atoms, 4102 bonds, 500 residues, 1 model selected > color (#!1 & sel) light gray > select #1:711-790 1236 atoms, 1264 bonds, 160 residues, 1 model selected > color (#!1 & sel) #f9a036ff > select clear > select #1/B:356-605 2007 atoms, 2051 bonds, 250 residues, 1 model selected > select #1:711-790 1236 atoms, 1264 bonds, 160 residues, 1 model selected > select #1:218-355 2012 atoms, 2040 bonds, 276 residues, 1 model selected > color (#!1 & sel) #176e6dff > select clear > select #1:623-1230 9276 atoms, 9526 bonds, 4 pseudobonds, 1170 residues, 2 models selected > color (#!1 & sel) #44a14fff > select #1:711-790 1236 atoms, 1264 bonds, 160 residues, 1 model selected > color (#!1 & sel) #f9a036ff > select clear > select #1:1085-1109 34 atoms, 30 bonds, 4 pseudobonds, 4 residues, 2 models selected > color (#!1 & sel) #a264ffff > select #1:605-623 322 atoms, 330 bonds, 38 residues, 1 model selected > color (#!1 & sel) #af2e79ff > select clear > view > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/for_figure_final.cxs > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/dimer_colored_domain.png > width 1752 height 1924 supersample 4 > select /B 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > select /A 7798 atoms, 7987 bonds, 2 pseudobonds, 990 residues, 2 models selected > surface (#!1 & sel) > color sel skyblue > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfaces.png > width 1752 height 1924 supersample 4 > hide surfaces Drag select of 9 residues > show sel atoms > hide sel cartoons > color sel byhetero > select clear Drag select of 4 atoms, 11 residues, 2 bonds > hide sel atoms > select clear Drag select of 7 residues Drag select of 6 residues > show sel atoms > view sel > view > show sel atoms > show sel atoms > color sel byhetero > color sel byhetero > hide sel cartoons Drag select of 16 atoms, 1 residues, 18 bonds Drag select of 13 atoms, 15 bonds Drag select of 6 atoms, 1 residues, 8 bonds > view sel > show sel atoms > hide sel cartoons > view sel > show sel atoms > hide sel cartoons > color sel byhetero > show sel atoms > hide sel cartoons > hide sel cartoons > color sel byhetero > view sel > view sel > show sel atoms > hide sel cartoons > color sel byhetero > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interface1.cxs opened ChimeraX session > hide atoms > show cartoons > view > show sel atoms > hide sel atoms > select /B:603 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:603 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:602 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > color sel byhetero > color sel byhetero > show sel atoms > color sel byhetero > show sel atoms > color sel byhetero > show sel atoms > color sel byhetero > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfac2.cxs opened ChimeraX session > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hide atoms > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfac2.cxs > select #1/B:604,602,601 #1/A:610,608,497,615 66 atoms, 64 bonds, 7 residues, 1 model selected > show sel atoms > color sel byhetero > view sel > color sel byhetero > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interface2_atomic.png > width 1725 height 1773 supersample 3 > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interface2_atomic.png > width 1725 height 1773 supersample 4 > view > select #1/B:604,602,601 #1/A:610,608,497,615 66 atoms, 64 bonds, 7 residues, 1 model selected > view sel > color sel byhetero > color sel byhetero > select clear > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interface2_atomic.png > width 1725 height 1773 supersample 4 > save > /Users/hrishikeshdas/Documents/Projects/mtRNApol/mtPol_7SRNA/interfac2.cxs opened ChimeraX session OpenGL version: 4.1 ATI-4.6.20 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 System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0) Software: System Software Overview: System Version: macOS 11.6 (20G165) Kernel Version: Darwin 20.6.0 Time since boot: 6:14 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 Family: Supported, Metal GPUFamily macOS 2 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.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 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: Yes Connection Type: Internal 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-Phenix: 0.3 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 MolecularDynamicsViewer: 1.1 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 Send2Trash: 1.7.1 SEQCROW: 0.25.2 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 Window Toolkit nonchimerax all ChimeraX