id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8457 Crash clearing aniso_u6 chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-11.5.1-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x0000000102627d40 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py"", line 846 in _set_aniso_u6 File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py"", line 12 in remove_invalid_anisou File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 667 in _anisou_sanity_check File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 636 in add_model File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 594 in __init__ File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 170 in _get_symmetry_handler File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 159 in get_symmetry_handler File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 814 in _change_selected_model File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 771 in change_selected_model File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 433 in selected_model File ""/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/ui/main_win.py"", line 157 in _set_selected_model File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 283 in event_loop File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 884 in init File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1035 in File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main Process: ChimeraX [12742] Path: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.5.0 (1.5.0.0) Code Type: ARM-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [12742] User ID: 501 Date/Time: 2023-02-08 16:33:23.933 +0900 OS Version: macOS 11.5.1 (20G80) Report Version: 12 Anonymous UUID: A143588D-7754-31A9-9C73-363555E3C01C Sleep/Wake UUID: 2C05A555-40F5-4714-BF9C-55BC4FBFE11D Time Awake Since Boot: 21000 seconds Time Since Wake: 2200 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 102198000-10219c000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x000000018e814e68 __pthread_kill + 8 1 libsystem_pthread.dylib 0x000000018e84743c pthread_kill + 292 2 libsystem_c.dylib 0x000000018e726e10 raise + 32 3 libsystem_platform.dylib 0x000000018e892c44 _sigtramp + 56 4 libmolc.dylib 0x0000000170de3054 clear_atom_aniso_u6 + 32 5 libmolc.dylib 0x0000000170de3054 clear_atom_aniso_u6 + 32 6 libffi.dylib 0x000000019b70c050 ffi_call_SYSV + 80 7 libffi.dylib 0x000000019b7149e4 ffi_call_int + 948 8 _ctypes.cpython-39-darwin.so 0x000000010fb16944 _ctypes_callproc + 1404 9 _ctypes.cpython-39-darwin.so 0x000000010fb0fc10 PyCFuncPtr_call + 1168 10 org.python.python 0x00000001021f8870 _PyObject_MakeTpCall + 360 11 org.python.python 0x00000001022cebc8 call_function + 512 12 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232 13 org.python.python 0x00000001021f8ffc function_code_fastcall + 112 14 org.python.python 0x00000001021f9f84 object_vacall + 256 15 org.python.python 0x00000001021fa1ac PyObject_CallFunctionObjArgs + 48 16 org.python.python 0x00000001022022ec property_descr_set + 80 17 org.python.python 0x000000010223ffa4 _PyObject_GenericSetAttrWithDict + 184 18 org.python.python 0x000000010223f384 PyObject_SetAttr + 132 19 org.python.python 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168 org.python.python 0x00000001023294e8 Py_RunMain + 764 169 org.python.python 0x0000000102329d54 pymain_main + 340 170 org.python.python 0x0000000102329bf4 Py_Main + 36 171 edu.ucsf.cgl.ChimeraX 0x000000010219bd54 main + 128 172 libdyld.dylib 0x000000018e865430 start + 4 Thread 1: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 2: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 4:: ThreadPoolServiceThread 0 libsystem_kernel.dylib 0x000000018e817ee8 kevent64 + 8 1 QtWebEngineCore 0x00000001636197c8 0x160000000 + 56727496 2 QtWebEngineCore 0x00000001636196f8 0x160000000 + 56727288 3 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 6 QtWebEngineCore 0x00000001635aa1a8 0x160000000 + 56271272 7 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 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thread_start + 8 Thread 11:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548 4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244 5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264 6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 12:: CompositorTileWorker1 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtWebEngineCore 0x00000001635e6048 0x160000000 + 56516680 3 QtWebEngineCore 0x000000016519afe4 0x160000000 + 85569508 4 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 5 libsystem_pthread.dylib 0x000000018e847878 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QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 6 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 7 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 8 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 9 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 15:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224 4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248 5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 16:: VizCompositorThread 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x000000016353753c 0x160000000 + 55801148 4 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 5 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 6 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 7 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 8 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 9 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 10 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 17:: NetworkService 0 libsystem_kernel.dylib 0x000000018e817ee8 kevent64 + 8 1 QtWebEngineCore 0x00000001636197c8 0x160000000 + 56727496 2 QtWebEngineCore 0x00000001636196f8 0x160000000 + 56727288 3 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 6 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 7 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 8 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 9 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 18:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224 4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248 5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 19:: ThreadPoolSingleThreadForegroundBlocking0 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548 4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244 5 QtWebEngineCore 0x00000001635b5d78 0x160000000 + 56319352 6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 20:: Thread (pooled) 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236 3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396 4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940 6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 21:: Thread (pooled) 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236 3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396 4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940 6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 22:: Thread (pooled) 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236 3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396 4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940 6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 23:: Thread (pooled) 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236 3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396 4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940 6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 24:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224 4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248 5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 25: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 26: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 27:: ThreadPoolBackgroundWorker 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548 4 QtWebEngineCore 0x00000001635b5e84 0x160000000 + 56319620 5 QtWebEngineCore 0x00000001635b5c9c 0x160000000 + 56319132 6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 28:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548 4 QtWebEngineCore 0x00000001635b5e84 0x160000000 + 56319620 5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264 6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 29:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 com.apple.CoreFoundation 0x000000018e946d00 __CFRunLoopServiceMachPort + 372 3 com.apple.CoreFoundation 0x000000018e9451cc __CFRunLoopRun + 1212 4 com.apple.CoreFoundation 0x000000018e944598 CFRunLoopRunSpecific + 600 5 com.apple.AppKit 0x00000001912b4738 _NSEventThread + 196 6 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 7 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 30:: MemoryInfra 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224 4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248 5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836 6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340 7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424 8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816 9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 31:: ThreadPoolSingleThreadSharedBackgroundBlocking1 0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8 1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76 2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788 3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548 4 QtWebEngineCore 0x00000001635b5e84 0x160000000 + 56319620 5 QtWebEngineCore 0x00000001635b5cc8 0x160000000 + 56319176 6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 32: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 33: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 34: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 35: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 36: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 37: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 38: 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360 3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 39:: Thread (pooled) 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236 3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396 4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940 6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 40:: Thread (pooled) 0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8 1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248 2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236 3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396 4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940 6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444 7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320 8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8 Thread 41:: Dispatch queue: com.apple.root.user-interactive-qos 0 libsystem_kernel.dylib 0x000000018e80ce28 semaphore_timedwait_trap + 8 1 libdispatch.dylib 0x000000018e6984a4 _dispatch_sema4_timedwait + 64 2 libdispatch.dylib 0x000000018e698ab4 _dispatch_semaphore_wait_slow + 76 3 com.apple.AppKit 0x0000000191a276e0 __22-[NSCGSLocalFence set]_block_invoke_2 + 164 4 com.apple.QuartzCore 0x0000000194be4578 CA::Transaction::run_commit_handlers(CATransactionPhase) + 120 5 com.apple.QuartzCore 0x0000000194d2d86c CA::Context::commit_transaction(CA::Transaction*, double, double*) + 740 6 com.apple.QuartzCore 0x0000000194be36dc CA::Transaction::commit() + 684 7 com.apple.AppKit 0x000000019118910c NSPerformVisuallyAtomicChange + 160 8 com.apple.AppKit 0x00000001913ae5cc __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 116 9 libdispatch.dylib 0x000000018e696128 _dispatch_call_block_and_release + 32 10 libdispatch.dylib 0x000000018e697ec0 _dispatch_client_callout + 20 11 libdispatch.dylib 0x000000018e6a97b0 _dispatch_root_queue_drain + 688 12 libdispatch.dylib 0x000000018e6a9e90 _dispatch_worker_thread2 + 112 13 libsystem_pthread.dylib 0x000000018e843860 _pthread_wqthread + 216 14 libsystem_pthread.dylib 0x000000018e8425d4 start_wqthread + 8 Thread 42: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 43: 0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0 Thread 0 crashed with ARM Thread State (64-bit): x0: 0x0000000000000000 x1: 0x0000000000000000 x2: 0x0000000000000001 x3: 0x000000018e88fead x4: 0x0000000128047c18 x5: 0x68430aff5cbb020d x6: 0x000000016dc5ec10 x7: 0x000000010fe047b0 x8: 0x11e015912671960a x9: 0x11e015902413eb4a x10: 0x0000000000001bba x11: 0x0000000205797b5e x12: 0x0000000205797b5e x13: 0x0000000000000004 x14: 0x0000000000000881 x15: 0x000000008000001f x16: 0x0000000000000148 x17: 0x00000001fd2c6e90 x18: 0x0000000138953940 x19: 0x000000000000000b x20: 0x0000000102627d40 x21: 0x0000000000000103 x22: 0x0000000102627e20 x23: 0x000000016dc5ed50 x24: 0x0000000000000002 x25: 0x0000000000000008 x26: 0x0000000000000008 x27: 0x0000000000000002 x28: 0x000000016dc5ed08 fp: 0x0000000128047b50 lr: 0x000000018e84743c sp: 0x0000000128047b30 pc: 0x000000018e814e68 cpsr: 0x40000000 far: 0x0000000128047bb0 esr: 0x56000080 Binary Images: 0x102198000 - 0x10219bfff +edu.ucsf.cgl.ChimeraX (1.5.0 - 1.5.0.0) /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX 0x1021b4000 - 0x102423fff +org.python.python (3.9.11, [c] 2001-2021 Python Software Foundation. - 3.9.11) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python 0x10256c000 - 0x1025ebfff dyld (852.2) /usr/lib/dyld 0x1028c0000 - 0x1028c3fff +_heapq.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_heapq.cpython-39-darwin.so 0x1028d4000 - 0x1028dbfff +binascii.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/binascii.cpython-39-darwin.so 0x1028ec000 - 0x1028effff +_bz2.cpython-39-darwin.so (0) 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/System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics 0x1da173000 - 0x1da18cfff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed 0x1e1d68000 - 0x1e1d6ffff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib 0x28b624000 - 0x28b627fff +lib_util.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/lib_util.dylib 0x28e6fc000 - 0x28e717fff com.apple.security.csparser (3.0 - 59754.140.13) /System/Library/Frameworks/Security.framework/PlugIns/csparser.bundle/Contents/MacOS/csparser 0x290404000 - 0x290413fff +numpy_formathandler.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL_accelerate/numpy_formathandler.cpython-39-darwin.so 0x2906b8000 - 0x2906bffff +nones_formathandler.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL_accelerate/nones_formathandler.cpython-39-darwin.so 0x29b948000 - 0x29b973fff +libccp4.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libccp4.dylib 0x29cf7c000 - 0x29cfb7fff +libclipper_cx.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libclipper_cx.dylib 0x29d0c4000 - 0x29d0c7fff +_c_internal_utils.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/_c_internal_utils.cpython-39-darwin.so 0x29d734000 - 0x29d7d3fff +libmmdb2.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libmmdb2.dylib 0x29db00000 - 0x29db2bfff +mcsplit.cpython-39-darwin.so (0) /Users/USER/Library/Application Support/ChimeraX/*/mcsplit.cpython-39-darwin.so 0x29dcd8000 - 0x29dce7fff +_ribbons.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/_ribbons.cpython-39-darwin.so 0x29dd28000 - 0x29de7ffff +libclipper.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libclipper.dylib 0x29e0f0000 - 0x29e10bfff +_path.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/_path.cpython-39-darwin.so 0x2a2300000 - 0x2a270ffff +clipper_python.cpython-39-darwin.so (0) /Users/USER/Library/Application Support/ChimeraX/*/clipper_python.cpython-39-darwin.so 0x2a2a00000 - 0x2a2a87fff +ft2font.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/ft2font.cpython-39-darwin.so 0x2a2ac0000 - 0x2a2ad7fff +_cext.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/kiwisolver/_cext.cpython-39-darwin.so 0x2a2f40000 - 0x2a2f5bfff +_image.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/_image.cpython-39-darwin.so 0x2a3130000 - 0x2a3157fff +_backend_agg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/backends/_backend_agg.cpython-39-darwin.so 0x2a3608000 - 0x2a366bfff +mmcif.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/mmcif.cpython-39-darwin.so 0x2a369c000 - 0x2a36bffff +_pdbio.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/pdb/_pdbio.cpython-39-darwin.so 0x2a7dc8000 - 0x2a7e1bfff +_mmcif.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/_mmcif.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=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%) Writable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 1 CG backing stores 3264K 6 CG image 480K 22 CoreAnimation 208K 13 CoreGraphics 32K 2 CoreUI image data 3744K 28 Foundation 16K 1 Kernel Alloc Once 32K 1 MALLOC 620.4M 90 MALLOC guard page 192K 10 MALLOC_MEDIUM (reserved) 872.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) Mach message 64K 4 OpenGL GLSL 384K 4 STACK GUARD 688K 43 Stack 188.0M 44 Stack Guard 56.0M 1 VM_ALLOCATE 279.5M 588 VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated) __AUTH 1031K 266 __AUTH_CONST 15.2M 461 __DATA 19.4M 625 __DATA_CONST 25.7M 623 __DATA_DIRTY 1813K 213 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 525.2M 173 __OBJC_CONST 3311K 257 __OBJC_RO 75.1M 1 __OBJC_RW 2576K 1 __TEXT 581.0M 646 __UNICODE 588K 1 mapped file 1.7G 257 shared memory 3248K 25 =========== ======= ======= TOTAL 5.2G 4422 TOTAL, minus reserved VM space 4.0G 4422 ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ISOLDE > set selectionWidth 4 Populating font family aliases took 604 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > open > /Users/seiyahirai/Desktop/Research/Kimura_T/E97K/modeling/Large/E97K_job112_postprocess_masked.mrc Opened E97K_job112_postprocess_masked.mrc as #1, grid size 256,256,256, pixel 1.06, shown at level 0.00434, step 1, values float32 > open > /Users/seiyahirai/Desktop/Research/Kimura_T/E97K/modeling/Large/E97Km7_ISOLDE_A93-99.pdb Chain information for E97Km7_ISOLDE_A93-99.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 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: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 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: 16 GB System Firmware Version: 6723.140.2 OS Loader Version: 6723.140.2 Software: System Software Overview: System Version: macOS 11.5.1 (20G80) Kernel Version: Darwin 20.6.0 Time since boot: 9 days 22:46 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: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.19.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.5 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Structure Editing fixed Eric Pettersen Tom Goddard Zach Pearson all ChimeraX