id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8579 Crash clearing aniso_u6 chimerax-bug-report@… Tristan Croll "The following bug report has been submitted: Platform: macOS-11.6.8-arm64-arm-64bit ChimeraX Version: 1.6.dev202302242240 (2023-02-24 22:40:11 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000102a7bd40 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py"", line 853 in _set_aniso_u6 File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/sanity_check.py"", line 12 in remove_invalid_anisou File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 670 in _anisou_sanity_check File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 639 in add_model File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 597 in __init__ File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 170 in _get_symmetry_handler File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 159 in get_symmetry_handler File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py"", line 815 in _change_selected_model File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py"", line 771 in change_selected_model File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py"", line 434 in selected_model File ""/Users/gaurideak/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/ui/main_win.py"", line 157 in _set_selected_model File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 284 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main Process: ChimeraX [51041] Path: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.6.0 (1.6.0.0) Code Type: ARM-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [51041] User ID: 505 Date/Time: 2023-02-28 13:52:36.426 +0000 OS Version: macOS 11.6.8 (20G730) Report Version: 12 Anonymous UUID: B16EDD29-2A7F-435D-FF80-7678024D959D Sleep/Wake UUID: C61CF1E4-2A5E-4702-8778-29BFA60C5DEB Time Awake Since Boot: 3100000 seconds Time Since Wake: 8600 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 0x0000000000000008 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0x8: --> __TEXT 1028cc000-1028d0000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x0000000197818e28 __pthread_kill + 8 1 libsystem_pthread.dylib 0x000000019784b43c pthread_kill + 292 2 libsystem_c.dylib 0x000000019772ae10 raise + 32 3 libsystem_platform.dylib 0x0000000197896c44 _sigtramp + 56 4 libmolc.dylib 0x0000000128c62ec4 clear_atom_aniso_u6 + 32 5 libmolc.dylib 0x0000000128c62ec4 clear_atom_aniso_u6 + 32 6 libffi.dylib 0x00000001a4714050 ffi_call_SYSV + 80 7 libffi.dylib 0x00000001a471c9e4 ffi_call_int + 948 8 _ctypes.cpython-39-darwin.so 0x0000000113552944 _ctypes_callproc + 1404 9 _ctypes.cpython-39-darwin.so 0x000000011354bc10 PyCFuncPtr_call + 1168 10 org.python.python 0x0000000102b0c870 _PyObject_MakeTpCall + 360 11 org.python.python 0x0000000102be2bc8 call_function + 512 12 org.python.python 0x0000000102be0284 _PyEval_EvalFrameDefault + 23232 13 org.python.python 0x0000000102b0cffc function_code_fastcall + 112 14 org.python.python 0x0000000102b0df84 object_vacall + 256 15 org.python.python 0x0000000102b0e1ac PyObject_CallFunctionObjArgs + 48 16 org.python.python 0x0000000102b162ec property_descr_set + 80 17 org.python.python 0x0000000102b53fa4 _PyObject_GenericSetAttrWithDict + 184 18 org.python.python 0x0000000102b53384 PyObject_SetAttr + 132 19 org.python.python 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org.python.python 0x0000000102b0cf80 _PyFunction_Vectorcall + 256 65 QtCore.abi3.so 0x00000001164de124 PyQtSlot::call(_object*, _object*) const + 68 66 QtCore.abi3.so 0x00000001164ddfac PyQtSlot::invoke(void**, _object*, void*, bool) const + 292 67 QtCore.abi3.so 0x00000001164defa0 PyQtSlotProxy::unislot(void**) + 92 68 QtCore.abi3.so 0x00000001164def10 PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 68 69 QtCore 0x00000001167c0a50 0x116710000 + 723536 70 QtGui 0x0000000119c4d148 QAction::activate(QAction::ActionEvent) + 368 71 QtWidgets 0x00000001194c0600 0x119320000 + 1705472 72 QtWidgets 0x00000001194be12c 0x119320000 + 1696044 73 QtWidgets 0x00000001194c4e30 QMenu::mouseReleaseEvent(QMouseEvent*) + 484 74 QtWidgets.abi3.so 0x0000000118d9f13c sipQMenu::mouseReleaseEvent(QMouseEvent*) + 148 75 QtWidgets 0x0000000119374f70 QWidget::event(QEvent*) + 132 76 QtWidgets 0x00000001194c54d0 QMenu::event(QEvent*) + 1228 77 QtWidgets.abi3.so 0x0000000118d9e754 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0x000000011994b754 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 1788 90 QtGui 0x00000001199a0580 QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 396 91 libqcocoa.dylib 0x000000011b7062a4 0x11b6f0000 + 90788 92 com.apple.CoreFoundation 0x0000000197949e54 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 28 93 com.apple.CoreFoundation 0x0000000197949da0 __CFRunLoopDoSource0 + 208 94 com.apple.CoreFoundation 0x0000000197949a8c __CFRunLoopDoSources0 + 268 95 com.apple.CoreFoundation 0x0000000197948414 __CFRunLoopRun + 820 96 com.apple.CoreFoundation 0x0000000197947968 CFRunLoopRunSpecific + 600 97 com.apple.HIToolbox 0x000000019f871280 RunCurrentEventLoopInMode + 292 98 com.apple.HIToolbox 0x000000019f870f0c ReceiveNextEventCommon + 320 99 com.apple.HIToolbox 0x000000019f870db4 _BlockUntilNextEventMatchingListInModeWithFilter + 72 100 com.apple.AppKit 0x000000019a13c08c _DPSNextEvent + 836 101 com.apple.AppKit 0x000000019a13aa2c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1292 102 com.apple.AppKit 0x000000019a12c878 -[NSApplication run] + 596 103 libqcocoa.dylib 0x000000011b7050d8 0x11b6f0000 + 86232 104 QtCore 0x0000000116780994 QEventLoop::exec(QFlags) + 532 105 QtWidgets 0x00000001194c3a98 0x119320000 + 1718936 106 QtWidgets 0x00000001194c393c QMenu::exec(QPoint const&, QAction*) + 52 107 QtWidgets 0x00000001194d42ac 0x119320000 + 1786540 108 QtCore 0x00000001167c0ce4 0x116710000 + 724196 109 QtWidgets 0x0000000119428760 0x119320000 + 1083232 110 QtWidgets 0x00000001194292e8 QAbstractButton::mousePressEvent(QMouseEvent*) + 232 111 QtWidgets.abi3.so 0x0000000118e3aed4 sipQPushButton::mousePressEvent(QMouseEvent*) + 148 112 QtWidgets 0x0000000119374f70 QWidget::event(QEvent*) + 132 113 QtWidgets.abi3.so 0x0000000118e3b85c sipQPushButton::event(QEvent*) + 224 114 QtWidgets 0x000000011932b520 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272 115 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168 org.python.python 0x0000000102c3d4e8 Py_RunMain + 764 169 org.python.python 0x0000000102c3dd54 pymain_main + 340 170 org.python.python 0x0000000102c3dbf4 Py_Main + 36 171 edu.ucsf.cgl.ChimeraX 0x00000001028cfd54 main + 128 172 libdyld.dylib 0x0000000197869430 start + 4 Thread 1: 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000103addb60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 4 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 2: 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000103addb60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 4 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 3: 0 libsystem_kernel.dylib 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libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 22:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aee078 0x280000000 + 61792376 5 QtWebEngineCore 0x0000000283aedb8c 0x280000000 + 61791116 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 23:: Chrome_IOThread 0 libsystem_kernel.dylib 0x000000019781bea8 kevent64 + 8 1 QtWebEngineCore 0x0000000283b2eed0 0x280000000 + 62058192 2 QtWebEngineCore 0x0000000283b2ed70 0x280000000 + 62057840 3 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 4 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 5 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 6 QtWebEngineCore 0x00000002817fbc9c 0x280000000 + 25148572 7 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 8 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 9 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 10 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 24:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283b288d8 0x280000000 + 62032088 4 QtWebEngineCore 0x0000000283a694d4 0x280000000 + 61248724 5 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 6 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 7 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 8 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 9 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 10 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 11 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 25:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aee078 0x280000000 + 61792376 5 QtWebEngineCore 0x0000000283aedc10 0x280000000 + 61791248 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 26:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aee078 0x280000000 + 61792376 5 QtWebEngineCore 0x0000000283aedc10 0x280000000 + 61791248 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 27:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aedd84 0x280000000 + 61791620 5 QtWebEngineCore 0x0000000283aedc10 0x280000000 + 61791248 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 28:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283a69470 0x280000000 + 61248624 4 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 5 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 6 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 7 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 8 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 9 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 10 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 29:: Chrome_ChildIOThread 0 libsystem_kernel.dylib 0x000000019781bea8 kevent64 + 8 1 QtWebEngineCore 0x0000000283b2eed0 0x280000000 + 62058192 2 QtWebEngineCore 0x0000000283b2ed70 0x280000000 + 62057840 3 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 4 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 5 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 6 QtWebEngineCore 0x000000028613ab8c 0x280000000 + 101952396 7 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 8 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 9 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 10 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 30:: CompositorTileWorker1 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 QtWebEngineCore 0x0000000283b215c4 0x280000000 + 62002628 3 QtWebEngineCore 0x000000028585b024 0x280000000 + 92647460 4 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 5 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 6 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 31:: ThreadPoolSingleThreadSharedForeground0 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aee078 0x280000000 + 61792376 5 QtWebEngineCore 0x0000000283aedc3c 0x280000000 + 61791292 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 32:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283b288d8 0x280000000 + 62032088 4 QtWebEngineCore 0x0000000283a694d4 0x280000000 + 61248724 5 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 6 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 7 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 8 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 9 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 10 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 11 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 33:: VizCompositorThread 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283b288d8 0x280000000 + 62032088 4 QtWebEngineCore 0x0000000283a694d4 0x280000000 + 61248724 5 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 6 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 7 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 8 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 9 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 10 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 11 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 34:: NetworkService 0 libsystem_kernel.dylib 0x000000019781bea8 kevent64 + 8 1 QtWebEngineCore 0x0000000283b2eed0 0x280000000 + 62058192 2 QtWebEngineCore 0x0000000283b2ed70 0x280000000 + 62057840 3 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 4 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 5 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 6 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 7 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 8 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 9 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 35:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283b288d8 0x280000000 + 62032088 4 QtWebEngineCore 0x0000000283a694d4 0x280000000 + 61248724 5 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 6 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 7 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 8 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 9 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 10 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 11 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 36:: ThreadPoolSingleThreadForegroundBlocking1 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aee078 0x280000000 + 61792376 5 QtWebEngineCore 0x0000000283aedc68 0x280000000 + 61791336 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 37:: Thread (pooled) 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 QtCore 0x00000001168e82f4 0x116710000 + 1934068 3 QtCore 0x00000001168e7fac 0x116710000 + 1933228 4 QtCore 0x00000001168e7ed8 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x00000001168e2630 0x116710000 + 1910320 6 QtCore 0x00000001168de374 0x116710000 + 1893236 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 38:: Thread (pooled) 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 QtCore 0x00000001168e82f4 0x116710000 + 1934068 3 QtCore 0x00000001168e7fac 0x116710000 + 1933228 4 QtCore 0x00000001168e7ed8 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x00000001168e2630 0x116710000 + 1910320 6 QtCore 0x00000001168de374 0x116710000 + 1893236 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 39:: Thread (pooled) 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 QtCore 0x00000001168e82f4 0x116710000 + 1934068 3 QtCore 0x00000001168e7fac 0x116710000 + 1933228 4 QtCore 0x00000001168e7ed8 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x00000001168e2630 0x116710000 + 1910320 6 QtCore 0x00000001168de374 0x116710000 + 1893236 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 40:: Thread (pooled) 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 QtCore 0x00000001168e82f4 0x116710000 + 1934068 3 QtCore 0x00000001168e7fac 0x116710000 + 1933228 4 QtCore 0x00000001168e7ed8 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x00000001168e2630 0x116710000 + 1910320 6 QtCore 0x00000001168de374 0x116710000 + 1893236 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 41:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283b288d8 0x280000000 + 62032088 4 QtWebEngineCore 0x0000000283a694d4 0x280000000 + 61248724 5 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 6 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 7 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 8 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 9 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 10 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 11 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 42:: Dispatch queue: com.apple.root.user-interactive-qos 0 libsystem_kernel.dylib 0x0000000197810de8 semaphore_timedwait_trap + 8 1 libdispatch.dylib 0x000000019769c4a4 _dispatch_sema4_timedwait + 64 2 libdispatch.dylib 0x000000019769cab4 _dispatch_semaphore_wait_slow + 76 3 com.apple.AppKit 0x000000019aa2e0a4 __22-[NSCGSLocalFence set]_block_invoke_2 + 164 4 com.apple.QuartzCore 0x000000019dbee1ac CA::Transaction::run_commit_handlers(CATransactionPhase) + 120 5 com.apple.QuartzCore 0x000000019dd374a0 CA::Context::commit_transaction(CA::Transaction*, double, double*) + 740 6 com.apple.QuartzCore 0x000000019dbed310 CA::Transaction::commit() + 684 7 com.apple.AppKit 0x000000019a18f718 NSPerformVisuallyAtomicChange + 160 8 com.apple.AppKit 0x000000019a3b4bb4 __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 116 9 libdispatch.dylib 0x000000019769a128 _dispatch_call_block_and_release + 32 10 libdispatch.dylib 0x000000019769bec0 _dispatch_client_callout + 20 11 libdispatch.dylib 0x00000001976ad7b0 _dispatch_root_queue_drain + 688 12 libdispatch.dylib 0x00000001976ade90 _dispatch_worker_thread2 + 112 13 libsystem_pthread.dylib 0x0000000197847860 _pthread_wqthread + 216 14 libsystem_pthread.dylib 0x00000001978465d4 start_wqthread + 8 Thread 43: 0 libsystem_pthread.dylib 0x00000001978465cc start_wqthread + 0 Thread 44: 0 libsystem_pthread.dylib 0x00000001978465cc start_wqthread + 0 Thread 45:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aee078 0x280000000 + 61792376 5 QtWebEngineCore 0x0000000283aedb8c 0x280000000 + 61791116 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 46:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 com.apple.CoreFoundation 0x000000019794a0d0 __CFRunLoopServiceMachPort + 372 3 com.apple.CoreFoundation 0x000000019794859c __CFRunLoopRun + 1212 4 com.apple.CoreFoundation 0x0000000197947968 CFRunLoopRunSpecific + 600 5 com.apple.AppKit 0x000000019a2bad44 _NSEventThread + 196 6 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 7 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 47:: MemoryInfra 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283b288d8 0x280000000 + 62032088 4 QtWebEngineCore 0x0000000283a694d4 0x280000000 + 61248724 5 QtWebEngineCore 0x0000000283ad6c6c 0x280000000 + 61697132 6 QtWebEngineCore 0x0000000283a98510 0x280000000 + 61441296 7 QtWebEngineCore 0x0000000283af9794 0x280000000 + 61839252 8 QtWebEngineCore 0x0000000283af990c 0x280000000 + 61839628 9 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 10 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 11 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 48:: ThreadPoolSingleThreadSharedBackgroundBlocking2 0 libsystem_kernel.dylib 0x0000000197810d94 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x0000000197811144 mach_msg + 76 2 QtWebEngineCore 0x0000000283b28aec 0x280000000 + 62032620 3 QtWebEngineCore 0x0000000283aed56c 0x280000000 + 61789548 4 QtWebEngineCore 0x0000000283aedd84 0x280000000 + 61791620 5 QtWebEngineCore 0x0000000283aedbb8 0x280000000 + 61791160 6 QtWebEngineCore 0x0000000283b22a28 0x280000000 + 62007848 7 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 8 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 49: 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 libopenblasp-r0.3.20.dylib 0x00000002a63f30cc blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 4 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 50: 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 libopenblasp-r0.3.20.dylib 0x00000002a63f30cc blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 4 libsystem_pthread.dylib 0x00000001978465e0 thread_start + 8 Thread 51: 0 libsystem_kernel.dylib 0x0000000197814508 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000019784bdac _pthread_cond_wait + 1248 2 libopenblasp-r0.3.20.dylib 0x00000002a63f30cc blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000019784b878 _pthread_start + 320 4 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Support/ChimeraX/*/_openmm_async.cpython-39-darwin.so 0x2a77a0000 - 0x2a77cbfff +mcsplit.cpython-39-darwin.so (0) /Users/USER/Library/Application Support/ChimeraX/*/mcsplit.cpython-39-darwin.so 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=14.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=14.7G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 512K 4 Activity Tracing 256K 1 CG backing stores 3264K 6 CG image 2640K 22 CG raster data 2208K 3 CoreAnimation 4848K 23 CoreGraphics 32K 2 CoreUI image data 3168K 24 Foundation 16K 1 Kernel Alloc Once 32K 1 MALLOC 12.7G 226 MALLOC guard page 192K 10 MALLOC_MEDIUM (reserved) 912.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) Mach message 96K 4 OpenGL GLSL 384K 4 STACK GUARD 944K 59 Stack 196.5M 60 Stack Guard 56.0M 1 VM_ALLOCATE 272.6M 752 VM_ALLOCATE (reserved) 384.0M 2 reserved VM address space (unallocated) __AUTH 1031K 267 __AUTH_CONST 15.2M 457 __DATA 22.8M 755 __DATA_CONST 28.1M 736 __DATA_DIRTY 1813K 213 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 537.7M 289 __OBJC_CONST 3315K 257 __OBJC_RO 75.1M 1 __OBJC_RW 2576K 1 __TEXT 651.0M 758 __UNICODE 588K 1 mapped file 273.1M 53 shared memory 3280K 22 =========== ======= ======= TOTAL 16.3G 5026 TOTAL, minus reserved VM space 14.8G 5026 ===== Log before crash start ===== UCSF ChimeraX version: 1.6.dev202302242240 (2023-02-24) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open /Users/gaurideak/Desktop/structure_versions/Tb_NCP_v8.7.pdb format pdb Chain information for Tb_NCP_v8.7.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D H | No description available E | No description available F | No description available G | No description available I | No description available J | No description available ui tool show ""Command Line Interface"" isolde start set selectionWidth 4 Populating font family aliases took 189 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 95 residues in model #1 to IUPAC-IUB standards. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.dev202302242240 (2023-02-24) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 71.7.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: en_GB.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 7459.141.1 OS Loader Version: 6723.140.2 Software: System Software Overview: System Version: macOS 11.6.8 (20G730) Kernel Version: Darwin 20.6.0 Time since boot: 110 days 19:19 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Resolution: 2880 x 1800 UI Looks like: 1440 x 900 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.11.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.0.1 ChimeraX-AddCharge: 1.5.8 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.8 ChimeraX-AtomicLibrary: 10.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.20.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202302242240 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.11 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.8 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.6.13 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.27.2 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.0.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.4 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.2.0 jupyterlab-widgets: 3.0.5 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.0.0 prompt-toolkit: 3.0.37 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.0.2 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.5 zipp: 3.15.0" defect closed moderate Structure Editing duplicate Eric Pettersen Tom Goddard Zach Pearson all ChimeraX