id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4142 Crash in QtWebEngineCore in updateDirtyNodes() rsarsam@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-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 [62027] Path: /Applications/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 [62027] User ID: 501 Date/Time: 2021-01-17 20:54:32.439 -0800 OS Version: Mac OS X 10.15.7 (19H114) Report Version: 12 Bridge OS Version: 5.1 (18P3030) Anonymous UUID: 8A9DFDBC-D330-0813-0D35-02485F687BD2 Sleep/Wake UUID: 183A6E6B-7B81-464E-A971-882F4E081CA6 Time Awake Since Boot: 1300000 seconds Time Since Wake: 12000 seconds System Integrity Protection: enabled 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 000000010a0d8000-000000010a0d9000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff68aa133a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff68b5de60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff689b893e raise + 26 3 libsystem_platform.dylib 0x00007fff68b525fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 QtWebEngineCore 0x00000001226c7726 0x12269a000 + 186150 6 QtWebEngineCore 0x00000001226c6969 0x12269a000 + 182633 7 QtWebEngineCore 0x00000001226b6a65 0x12269a000 + 117349 8 QtQuick 0x00000001290f8a5c QQuickWindowPrivate::updateDirtyNode(QQuickItem*) + 2908 9 QtQuick 0x00000001290e7d39 QQuickWindowPrivate::updateDirtyNodes() + 1017 10 QtQuick 0x00000001290e772f QQuickWindowPrivate::syncSceneGraph() + 271 11 QtQuick 0x00000001291bcfbc QQuickRenderControl::sync() + 28 12 QtQuickWidgets 0x0000000129a3c46a 0x129a37000 + 21610 13 QtQuickWidgets 0x0000000129a3c598 0x129a37000 + 21912 14 QtCore 0x000000011ff50ab6 QObject::event(QEvent*) + 102 15 QtWidgets 0x000000011f2784da QWidget::event(QEvent*) + 4826 16 QtQuickWidgets 0x0000000129a402ce QQuickWidget::event(QEvent*) + 782 17 QtWebEngineWidgets 0x000000012266d0e7 0x122652000 + 110823 18 QtWidgets 0x000000011f23b67d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 19 QtWidgets 0x000000011f23ca82 QApplication::notify(QObject*, QEvent*) + 594 20 QtWidgets.so 0x000000011edfb3ca sipQApplication::notify(QObject*, QEvent*) + 234 21 QtCore 0x000000011ff27324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 22 QtCore 0x000000011ff8093f QTimerInfoList::activateTimers() + 991 23 libqcocoa.dylib 0x0000000129c5a032 0x129c25000 + 217138 24 com.apple.CoreFoundation 0x00007fff2e8c2d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 25 com.apple.CoreFoundation 0x00007fff2e8c2cf1 __CFRunLoopDoSource0 + 103 26 com.apple.CoreFoundation 0x00007fff2e8c2b0b __CFRunLoopDoSources0 + 209 27 com.apple.CoreFoundation 0x00007fff2e8c183a __CFRunLoopRun + 927 28 com.apple.CoreFoundation 0x00007fff2e8c0e3e CFRunLoopRunSpecific + 462 29 com.apple.HIToolbox 0x00007fff2d4edabd RunCurrentEventLoopInMode + 292 30 com.apple.HIToolbox 0x00007fff2d4ed7d5 ReceiveNextEventCommon + 584 31 com.apple.HIToolbox 0x00007fff2d4ed579 _BlockUntilNextEventMatchingListInModeWithFilter + 64 32 com.apple.AppKit 0x00007fff2bb33039 _DPSNextEvent + 883 33 com.apple.AppKit 0x00007fff2bb31880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352 34 com.apple.AppKit 0x00007fff2bb2358e -[NSApplication run] + 658 35 libqcocoa.dylib 0x0000000129c5ade3 0x129c25000 + 220643 36 QtCore 0x000000011ff2293f QEventLoop::exec(QFlags) + 431 37 QtCore 0x000000011ff27932 QCoreApplication::exec() + 130 38 QtWidgets.so 0x000000011eeea7d2 meth_QApplication_exec_(_object*, _object*) + 82 39 org.python.python 0x000000010a107382 _PyMethodDef_RawFastCallKeywords + 226 40 org.python.python 0x000000010a1068b9 _PyCFunction_FastCallKeywords + 41 41 org.python.python 0x000000010a1dbb60 call_function + 656 42 org.python.python 0x000000010a1d8817 _PyEval_EvalFrameDefault + 26567 43 org.python.python 0x000000010a106d61 function_code_fastcall + 177 44 org.python.python 0x000000010a1dbbd4 call_function + 772 45 org.python.python 0x000000010a1d8817 _PyEval_EvalFrameDefault + 26567 46 org.python.python 0x000000010a1dca2c _PyEval_EvalCodeWithName + 3276 47 org.python.python 0x000000010a106879 _PyFunction_FastCallKeywords + 217 48 org.python.python 0x000000010a1dbbd4 call_function + 772 49 org.python.python 0x000000010a1d88ae _PyEval_EvalFrameDefault + 26718 50 org.python.python 0x000000010a1dca2c _PyEval_EvalCodeWithName + 3276 51 org.python.python 0x000000010a1d1fb0 PyEval_EvalCode + 48 52 org.python.python 0x000000010a1cf547 builtin_exec + 583 53 org.python.python 0x000000010a10752d _PyMethodDef_RawFastCallKeywords + 653 54 org.python.python 0x000000010a1068b9 _PyCFunction_FastCallKeywords + 41 55 org.python.python 0x000000010a1dbb60 call_function + 656 56 org.python.python 0x000000010a1d88ae _PyEval_EvalFrameDefault + 26718 57 org.python.python 0x000000010a1dca2c _PyEval_EvalCodeWithName + 3276 58 org.python.python 0x000000010a106879 _PyFunction_FastCallKeywords + 217 59 org.python.python 0x000000010a1dbbd4 call_function + 772 60 org.python.python 0x000000010a1d88ae _PyEval_EvalFrameDefault + 26718 61 org.python.python 0x000000010a1dca2c _PyEval_EvalCodeWithName + 3276 62 org.python.python 0x000000010a106377 _PyFunction_FastCallDict + 455 63 org.python.python 0x000000010a236af3 pymain_run_module + 147 64 org.python.python 0x000000010a235bdc pymain_main + 5900 65 org.python.python 0x000000010a2344c3 Py_Main + 51 66 edu.ucsf.cgl.ChimeraX 0x000000010a0d8dc8 main + 120 67 libdyld.dylib 0x00007fff68959cc9 start + 1 Thread 1: 0 libsystem_kernel.dylib 0x00007fff68a9d882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff68b5e425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x000000010ba10c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 2: 0 libsystem_kernel.dylib 0x00007fff68a9d882 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0x00007fff68b59b8b thread_start + 15 Thread 8:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 com.apple.CoreFoundation 0x00007fff2e8c2ef5 __CFRunLoopServiceMachPort + 247 3 com.apple.CoreFoundation 0x00007fff2e8c19c2 __CFRunLoopRun + 1319 4 com.apple.CoreFoundation 0x00007fff2e8c0e3e CFRunLoopRunSpecific + 462 5 com.apple.AppKit 0x00007fff2bcd4954 _NSEventThread + 132 6 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 9:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c22f 0x12269a000 + 35267119 4 QtWebEngineCore 0x00000001247f005d 0x12269a000 + 34955357 5 QtWebEngineCore 0x0000000124819085 0x12269a000 + 35123333 6 QtWebEngineCore 0x000000012486b9bc 0x12269a000 + 35461564 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 10:: DnsConfigService 0 libsystem_kernel.dylib 0x00007fff68a9f766 kevent + 10 1 QtWebEngineCore 0x0000000124afd9a9 0x12269a000 + 38156713 2 QtWebEngineCore 0x0000000124afacbd 0x12269a000 + 38145213 3 QtWebEngineCore 0x00000001248b1cdc 0x12269a000 + 35749084 4 QtWebEngineCore 0x0000000124819085 0x12269a000 + 35123333 5 QtWebEngineCore 0x000000012486b9bc 0x12269a000 + 35461564 6 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 7 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 11:: TaskSchedulerServiceThread 0 libsystem_kernel.dylib 0x00007fff68a9f766 kevent + 10 1 QtWebEngineCore 0x0000000124afd9a9 0x12269a000 + 38156713 2 QtWebEngineCore 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libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 13:: TaskSchedulerForegroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c421 0x12269a000 + 35267617 4 QtWebEngineCore 0x0000000124853d28 0x12269a000 + 35364136 5 QtWebEngineCore 0x000000012485465b 0x12269a000 + 35366491 6 QtWebEngineCore 0x00000001248542c4 0x12269a000 + 35365572 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 14:: TaskSchedulerBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c421 0x12269a000 + 35267617 4 QtWebEngineCore 0x0000000124853d28 0x12269a000 + 35364136 5 QtWebEngineCore 0x000000012485465b 0x12269a000 + 35366491 6 QtWebEngineCore 0x0000000124854234 0x12269a000 + 35365428 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 15:: TaskSchedulerBackgroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c421 0x12269a000 + 35267617 4 QtWebEngineCore 0x0000000124853d28 0x12269a000 + 35364136 5 QtWebEngineCore 0x000000012485465b 0x12269a000 + 35366491 6 QtWebEngineCore 0x0000000124854234 0x12269a000 + 35365428 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 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0x000000012483c22f 0x12269a000 + 35267119 4 QtWebEngineCore 0x0000000124853d1a 0x12269a000 + 35364122 5 QtWebEngineCore 0x00000001248543bf 0x12269a000 + 35365823 6 QtWebEngineCore 0x0000000124854264 0x12269a000 + 35365476 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 18:: CompositorTileWorker1/69635 0 libsystem_kernel.dylib 0x00007fff68a9d882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff68b5e425 _pthread_cond_wait + 698 2 QtWebEngineCore 0x00000001248a9fa8 0x12269a000 + 35717032 3 QtWebEngineCore 0x00000001258304c8 0x12269a000 + 51995848 4 QtWebEngineCore 0x000000012486a694 0x12269a000 + 35456660 5 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 6 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 19:: AudioThread 0 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QtWebEngineCore 0x0000000124afacbd 0x12269a000 + 38145213 3 QtWebEngineCore 0x00000001248b1cdc 0x12269a000 + 35749084 4 QtWebEngineCore 0x0000000124819085 0x12269a000 + 35123333 5 QtWebEngineCore 0x000000012486b9bc 0x12269a000 + 35461564 6 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 7 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 23:: TaskSchedulerSingleThreadForegroundBlocking1 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c22f 0x12269a000 + 35267119 4 QtWebEngineCore 0x0000000124853d1a 0x12269a000 + 35364122 5 QtWebEngineCore 0x000000012485465b 0x12269a000 + 35366491 6 QtWebEngineCore 0x0000000124854324 0x12269a000 + 35365668 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 24:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c22f 0x12269a000 + 35267119 4 QtWebEngineCore 0x00000001247f005d 0x12269a000 + 34955357 5 QtWebEngineCore 0x0000000124819085 0x12269a000 + 35123333 6 QtWebEngineCore 0x000000012486b9bc 0x12269a000 + 35461564 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 25:: QFileInfoGatherer 0 libsystem_kernel.dylib 0x00007fff68a9d882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff68b5e425 _pthread_cond_wait + 698 2 QtCore 0x000000011fd678ab 0x11fd3d000 + 174251 3 QtCore 0x000000011fd6780c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 4 QtWidgets 0x000000011f466762 0x11f22b000 + 2340706 5 QtCore 0x000000011fd5f0b3 0x11fd3d000 + 139443 6 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 26:: TaskSchedulerForegroundWorker 0 libsystem_kernel.dylib 0x00007fff68a9adfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68a9b170 mach_msg + 60 2 QtWebEngineCore 0x000000012483c32d 0x12269a000 + 35267373 3 QtWebEngineCore 0x000000012483c421 0x12269a000 + 35267617 4 QtWebEngineCore 0x0000000124853d28 0x12269a000 + 35364136 5 QtWebEngineCore 0x000000012485465b 0x12269a000 + 35366491 6 QtWebEngineCore 0x00000001248542c4 0x12269a000 + 35365572 7 QtWebEngineCore 0x00000001248ab717 0x12269a000 + 35723031 8 libsystem_pthread.dylib 0x00007fff68b5e109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff68b59b8b thread_start + 15 Thread 27: 0 libsystem_pthread.dylib 0x00007fff68b59b68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000116c7ddc0 rcx: 0x00007f808008fa58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007f808008fa80 rsp: 0x00007f808008fa58 r8: 0x00007f808008ff48 r9: 0x99bc798147de9ccb r10: 0x0000000116c7ddc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff68aa133a rfl: 0x0000000000000246 cr2: 0x000000010a341fa4 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10a0d8000 - 0x10a0d8ff3 +edu.ucsf.cgl.ChimeraX (1.1.1 - 1.1.1.0) /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX 0x10a0e3000 - 0x10a2defff +org.python.python (3.7.8, [c] 2001-2019 Python Software Foundation. - 3.7.8) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/Python 0x10a66d000 - 0x10a66eff7 +_heapq.cpython-37m-darwin.so (0) 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0x7fff62893ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login 0x7fff628c5000 - 0x7fff628d1ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata 0x7fff65356000 - 0x7fff65362ff9 libAudioStatistics.dylib (1104.95) /usr/lib/libAudioStatistics.dylib 0x7fff65363000 - 0x7fff65396ffa libAudioToolboxUtility.dylib (1104.95) /usr/lib/libAudioToolboxUtility.dylib 0x7fff6539d000 - 0x7fff653d1fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib 0x7fff653d4000 - 0x7fff653defff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib 0x7fff653df000 - 0x7fff65467fff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib 0x7fff6546a000 - 0x7fff6546cff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff654b2000 - 0x7fff65669ffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib 0x7fff65690000 - 0x7fff65696ff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib 0x7fff65778000 - 0x7fff6577ffff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib 0x7fff657ae000 - 0x7fff657ceff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib 0x7fff6584e000 - 0x7fff6592bff7 libSMC.dylib (20) /usr/lib/libSMC.dylib 0x7fff65940000 - 0x7fff65941fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib 0x7fff65942000 - 0x7fff659cdff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib 0x7fff659ce000 - 0x7fff659cffff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib 0x7fff659e7000 - 0x7fff659fdfff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib 0x7fff65a32000 - 0x7fff65aa4ff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib 0x7fff65aa5000 - 0x7fff65b3efe5 libate.dylib (3.0.1) /usr/lib/libate.dylib 0x7fff65b42000 - 0x7fff65b42ff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff65b43000 - 0x7fff65c07ffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib 0x7fff65c08000 - 0x7fff65c18ffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib 0x7fff65c19000 - 0x7fff65c25fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib 0x7fff65c26000 - 0x7fff65c78fff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib 0x7fff65c79000 - 0x7fff65c8effb libc++abi.dylib (902) /usr/lib/libc++abi.dylib 0x7fff65c8f000 - 0x7fff65c8ffff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib 0x7fff65c90000 - 0x7fff65ca1fff libcmph.dylib (8) /usr/lib/libcmph.dylib 0x7fff65ca2000 - 0x7fff65cb9fd7 libcompression.dylib (87) /usr/lib/libcompression.dylib 0x7fff65f93000 - 0x7fff65fa9ff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib 0x7fff65faa000 - 0x7fff65fabfff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff6644e000 - 0x7fff66552fef libcrypto.44.dylib (47.140.1) /usr/lib/libcrypto.44.dylib 0x7fff66555000 - 0x7fff66560fff libcsfde.dylib (551) /usr/lib/libcsfde.dylib 0x7fff66568000 - 0x7fff665c7ff7 libcups.2.dylib (483.7) /usr/lib/libcups.2.dylib 0x7fff665c9000 - 0x7fff6662eff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib 0x7fff666d1000 - 0x7fff666d1fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib 0x7fff666d2000 - 0x7fff666eafff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib 0x7fff666f8000 - 0x7fff666fafff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib 0x7fff66709000 - 0x7fff6670efff libgermantok.dylib (24) /usr/lib/libgermantok.dylib 0x7fff6670f000 - 0x7fff66718ff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib 0x7fff66719000 - 0x7fff66809fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib 0x7fff6680a000 - 0x7fff66a61fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib 0x7fff66a79000 - 0x7fff66a7afff liblangid.dylib (133) /usr/lib/liblangid.dylib 0x7fff66a7b000 - 0x7fff66a93ff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib 0x7fff66aab000 - 0x7fff66b52ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib 0x7fff66b53000 - 0x7fff66db5ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib 0x7fff67122000 - 0x7fff67151fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib 0x7fff67281000 - 0x7fff676fdff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib 0x7fff676fe000 - 0x7fff67715fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib 0x7fff6779e000 - 0x7fff677d1fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib 0x7fff677d2000 - 0x7fff677d3ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib 0x7fff677e4000 - 0x7fff677e8fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib 0x7fff677eb000 - 0x7fff67821ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib 0x7fff67861000 - 0x7fff6786fff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib 0x7fff678a5000 - 0x7fff678bdfff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff678bf000 - 0x7fff67903ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib 0x7fff67904000 - 0x7fff67916ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib 0x7fff67917000 - 0x7fff67918ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib 0x7fff67919000 - 0x7fff67b03ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib 0x7fff67bf7000 - 0x7fff67c24ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib 0x7fff67cf9000 - 0x7fff67d53ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib 0x7fff67d54000 - 0x7fff67d57ffb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff67d58000 - 0x7fff67d65ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib 0x7fff67d6b000 - 0x7fff67e4dfff libxml2.2.dylib (33.7) /usr/lib/libxml2.2.dylib 0x7fff67e51000 - 0x7fff67e79fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib 0x7fff67e7a000 - 0x7fff67e8cff3 libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff6873b000 - 0x7fff68740ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff68741000 - 0x7fff6874cfff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff6874d000 - 0x7fff68754fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff68755000 - 0x7fff6875eff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff6875f000 - 0x7fff687f1fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib 0x7fff688fe000 - 0x7fff6893eff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff6893f000 - 0x7fff68975fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib 0x7fff68976000 - 0x7fff68976ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff68977000 - 0x7fff68983ff3 libkxld.dylib (6153.141.10) /usr/lib/system/libkxld.dylib 0x7fff68984000 - 0x7fff68984ff7 liblaunch.dylib (1738.140.2) /usr/lib/system/liblaunch.dylib 0x7fff68985000 - 0x7fff6898aff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff6898b000 - 0x7fff6898dff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff6898e000 - 0x7fff6898fff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff68990000 - 0x7fff689a7ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff689a8000 - 0x7fff689a8ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff689a9000 - 0x7fff68a30fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff68a31000 - 0x7fff68a34ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib 0x7fff68a35000 - 0x7fff68a38fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff68a39000 - 0x7fff68a41fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff68a42000 - 0x7fff68a49fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff68a4a000 - 0x7fff68a4bffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff68a4c000 - 0x7fff68a99ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff68a9a000 - 0x7fff68ac6ff7 libsystem_kernel.dylib (6153.141.10) /usr/lib/system/libsystem_kernel.dylib 0x7fff68ac7000 - 0x7fff68b0efff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff68b0f000 - 0x7fff68b36fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff68b37000 - 0x7fff68b44ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff68b45000 - 0x7fff68b4eff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff68b4f000 - 0x7fff68b57fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff68b58000 - 0x7fff68b62fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff68b63000 - 0x7fff68b67ff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib 0x7fff68b68000 - 0x7fff68b6afff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff68b6b000 - 0x7fff68b72ffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib 0x7fff68b73000 - 0x7fff68b89ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib 0x7fff68b8b000 - 0x7fff68b90ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff68b91000 - 0x7fff68bc6ffe libxpc.dylib (1738.140.2) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 47 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: 1172508 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=955.3M resident=0K(0%) swapped_out_or_unallocated=955.3M(100%) Writable regions: Total=7.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=7.1G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 1024K 8 Activity Tracing 256K 1 CG backing stores 34.8M 6 CG image 732K 41 CoreAnimation 5620K 111 CoreGraphics 8K 1 CoreImage 28K 3 CoreUI image data 4468K 38 Foundation 20K 2 Kernel Alloc Once 8K 1 MALLOC 4.9G 776 MALLOC guard page 48K 9 MALLOC_MEDIUM (reserved) 1.4G 16 reserved VM address space (unallocated) MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated) OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 108K 27 Stack 149.2M 28 Stack Guard 56.0M 1 VM_ALLOCATE 332.3M 730 VM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated) __DATA 64.4M 561 __DATA_CONST 132K 6 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 414.2M 146 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 541.1M 519 __UNICODE 564K 1 mapped file 361.1M 92 shared memory 672K 22 =========== ======= ======= TOTAL 8.5G 3161 TOTAL, minus reserved VM space 6.8G 3161 Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-3.10.19 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1554.60.15.0.0 (iBridge: 18.16.13030.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H114) Kernel Version: Darwin 19.6.0 Time since boot: 15 days 12:26 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: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 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 LG Ultra HD: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: Thunderbolt/DisplayPort 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-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-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Window Toolkit can't reproduce Eric Pettersen all ChimeraX