id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7374 Crash destroying tool during garbage collection simone.ritchey@… Richard Scheltema "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. I had just used the visualization button to edit the cut-off color and was moving around to model to get a view of it. Fatal Python error: Segmentation fault Thread 0x0000700013dec000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000010e1cbe00 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 157 in asArray File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 2776 in set_matrix File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 767 in set_projection_matrix File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 675 in _use_shader File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 751 in _opengl_shader File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 648 in shader File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 790 in _draw_geometry File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 759 in draw_self File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 752 in draw File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1539 in _draw_multiple File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1526 in draw_opaque File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1550 in draw_depth File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 231 in _draw_scene File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 165 in draw File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1021 in File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main Process: ChimeraX [1716] Path: /Applications/ChimeraX-1.4.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.4.0 (1.4.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [1716] User ID: 501 Date/Time: 2022-08-02 16:08:31.910 -0500 OS Version: macOS 11.1 (20C69) Report Version: 12 Anonymous UUID: C23B016C-A05B-49F4-7A04-7F2E7B85AC6E Sleep/Wake UUID: 9481B9B3-6BDF-4459-B8B3-744CC759C18C Time Awake Since Boot: 10000 seconds Time Since Wake: 1700 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: EXC_I386_GPFLT Exception Note: EXC_CORPSE_NOTIFY Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff2033f462 __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff2036d610 pthread_kill + 263 2 libsystem_c.dylib 0x00007fff2024fba3 raise + 26 3 libsystem_platform.dylib 0x00007fff203b1d7d _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 QtWidgets 0x000000010d4f9dc7 QGridLayout::~QGridLayout() + 39 6 QtWidgets.abi3.so 0x000000010cf6a438 non-virtual thunk to 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61 org.python.python 0x000000010322f2a2 _PyEval_EvalFrameDefault + 25554 62 org.python.python 0x0000000103159d28 function_code_fastcall + 104 63 org.python.python 0x0000000103231e0c call_function + 732 64 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 65 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611 66 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289 67 org.python.python 0x0000000103231e0c call_function + 732 68 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 69 org.python.python 0x0000000103159d28 function_code_fastcall + 104 70 org.python.python 0x0000000103231e0c call_function + 732 71 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 72 org.python.python 0x0000000103159d28 function_code_fastcall + 104 73 org.python.python 0x0000000103231e0c call_function + 732 74 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 75 org.python.python 0x0000000103159d28 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com.apple.CoreFoundation 0x00007fff204636ce CFRunLoopRunSpecific + 563 132 com.apple.HIToolbox 0x00007fff286e86d0 RunCurrentEventLoopInMode + 292 133 com.apple.HIToolbox 0x00007fff286e84cc ReceiveNextEventCommon + 709 134 com.apple.HIToolbox 0x00007fff286e81ef _BlockUntilNextEventMatchingListInModeWithFilter + 64 135 com.apple.AppKit 0x00007fff22c80de9 _DPSNextEvent + 883 136 com.apple.AppKit 0x00007fff22c7f5af -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366 137 com.apple.AppKit 0x00007fff22c71b0a -[NSApplication run] + 586 138 libqcocoa.dylib 0x000000011bf9748c 0x11bf7e000 + 103564 139 QtCore 0x000000010c8f1516 QEventLoop::exec(QFlags) + 486 140 QtCore 0x000000010c8e83e5 QCoreApplication::exec() + 133 141 QtWidgets.abi3.so 0x000000010d0d690a meth_QApplication_exec(_object*, _object*) + 90 142 org.python.python 0x000000010319871d cfunction_call + 125 143 org.python.python 0x00000001031595b7 _PyObject_MakeTpCall + 359 144 org.python.python 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25: 0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0 Thread 26:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff20338e7e mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff203391f0 mach_msg + 60 2 QtWebEngineCore 0x00000001145a89c6 0x110678000 + 66259398 3 QtWebEngineCore 0x000000011456cd5f 0x110678000 + 66014559 4 QtWebEngineCore 0x000000011456d80c 0x110678000 + 66017292 5 QtWebEngineCore 0x000000011456d40d 0x110678000 + 66016269 6 QtWebEngineCore 0x00000001145a14a8 0x110678000 + 66229416 7 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224 8 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15 Thread 27: 0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0 Thread 28: 0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0 Thread 29: 0 libsystem_kernel.dylib 0x00007fff2033b8e2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff2036de6f _pthread_cond_wait + 1254 2 org.python.python 0x000000010328879c PyThread_acquire_lock_timed + 700 3 org.python.python 0x00000001032d769f acquire_timed + 111 4 org.python.python 0x00000001032d77b0 lock_PyThread_acquire_lock + 48 5 org.python.python 0x000000010316214e method_vectorcall_VARARGS_KEYWORDS + 350 6 org.python.python 0x0000000103231e0c call_function + 732 7 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 8 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611 9 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289 10 org.python.python 0x0000000103231e0c call_function + 732 11 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 12 org.python.python 0x0000000103232b03 _PyEval_EvalCode + 2611 13 org.python.python 0x0000000103159cb1 _PyFunction_Vectorcall + 289 14 org.python.python 0x0000000103231e0c call_function + 732 15 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 16 org.python.python 0x0000000103159d28 function_code_fastcall + 104 17 org.python.python 0x0000000103231e0c call_function + 732 18 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 19 org.python.python 0x0000000103159d28 function_code_fastcall + 104 20 org.python.python 0x0000000103231e0c call_function + 732 21 org.python.python 0x000000010322f27e _PyEval_EvalFrameDefault + 25518 22 org.python.python 0x0000000103159d28 function_code_fastcall + 104 23 org.python.python 0x000000010315bdb2 method_vectorcall + 274 24 org.python.python 0x00000001032d7046 t_bootstrap + 70 25 org.python.python 0x00000001032882f9 pythread_wrapper + 25 26 libsystem_pthread.dylib 0x00007fff2036d950 _pthread_start + 224 27 libsystem_pthread.dylib 0x00007fff2036947b thread_start + 15 Thread 30: 0 libsystem_pthread.dylib 0x00007fff20369458 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010e1cbe00 rcx: 0x00007faf44955a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007faf44955a80 rsp: 0x00007faf44955a58 r8: 0x00007faf44955f48 r9: 0x484b8db02a8808c8 r10: 0x000000010e1cbe00 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x00007faf389a3af0 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff2033f462 rfl: 0x0000000000000246 cr2: 0x00007faf44955f48 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Thread 0 instruction stream: 49 8b 87 60 01 00 00 48-85 c0 74 59 49 8b 0e 48 I..`...H..tYI..H 85 c9 74 07 8b 09 83 f9-02 7c 15 4c 89 f7 31 f6 ..t......|.L..1. 31 d2 31 c9 e8 ef 5b 00-00 49 8b 87 60 01 00 00 1.1...[..I..`... 49 8b 8f 58 01 00 00 48-8b 19 48 83 c1 08 49 89 I..X...H..H...I. 8f 58 01 00 00 48 83 c0-ff 49 89 87 60 01 00 00 .X...H...I..`... 48 85 db 74 b2 48 8b 3b-48 85 ff 74 9b 48 8b 07 H..t.H.;H..t.H.. [ff]50 08 eb 93 49 8b 9f-e8 00 00 00 48 85 db 74 .P...I......H..t .H...[A^A_].f. 0f 1f 84 00 00 00 00 00-55 48 89 e5 53 50 48 89 ........UH..SPH. Thread 0 last branch register state not available. 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795) /System/Library/PrivateFrameworks/CalDAV.framework/Versions/A/CalDAV 0x7fff34726000 - 0x7fff347c4fff com.apple.CoreSuggestions (1.0 - 1115.505) /System/Library/PrivateFrameworks/CoreSuggestions.framework/Versions/A/CoreSuggestions 0x7fff347c5000 - 0x7fff3495bfff com.apple.ical.EventKit (3.0 - 1414.3.1) /System/Library/Frameworks/EventKit.framework/Versions/A/EventKit 0x7fff3495c000 - 0x7fff34c32fff com.apple.CalendarPersistence (8.0 - 1071.3.2) /System/Library/PrivateFrameworks/CalendarPersistence.framework/Versions/A/CalendarPersistence 0x7fff34c33000 - 0x7fff34c59fff com.apple.CalendarAgentLink (8.0 - 250) /System/Library/PrivateFrameworks/CalendarAgentLink.framework/Versions/A/CalendarAgentLink 0x7fff34c5a000 - 0x7fff34c64fff com.apple.RTCReporting (11.70.5 - 11.70.5) /System/Library/PrivateFrameworks/RTCReporting.framework/Versions/A/RTCReporting 0x7fff34e49000 - 0x7fff34e4bfff com.apple.ConstantClasses (1.0 - 1) /System/Library/PrivateFrameworks/ConstantClasses.framework/Versions/A/ConstantClasses 0x7fff34e63000 - 0x7fff34e79fff com.apple.CoreML.AppleNeuralEngine (1.0 - 1) /System/Library/PrivateFrameworks/AppleNeuralEngine.framework/Versions/A/AppleNeuralEngine 0x7fff34ecd000 - 0x7fff34f39fff com.apple.audio.midi.CoreMIDI (2.0 - 88) /System/Library/Frameworks/CoreMIDI.framework/Versions/A/CoreMIDI 0x7fff34fdf000 - 0x7fff34fe2fff com.apple.Cocoa (6.11 - 23) /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa 0x7fff3502d000 - 0x7fff3540afff com.apple.AppleMediaServices (1.0 - 1) /System/Library/PrivateFrameworks/AppleMediaServices.framework/Versions/A/AppleMediaServices 0x7fff35442000 - 0x7fff35882fff com.apple.MediaRemote (1.0 - 1) /System/Library/PrivateFrameworks/MediaRemote.framework/Versions/A/MediaRemote 0x7fff35b54000 - 0x7fff35b5bfff com.apple.DisplayServicesFW (3.1 - 380) /System/Library/PrivateFrameworks/DisplayServices.framework/Versions/A/DisplayServices 0x7fff363bb000 - 0x7fff363ebfff libtidy.A.dylib (18.1) /usr/lib/libtidy.A.dylib 0x7fff363ec000 - 0x7fff3640dfff com.apple.MarkupUI (1.0 - 383.3) /System/Library/PrivateFrameworks/MarkupUI.framework/Versions/A/MarkupUI 0x7fff3640e000 - 0x7fff36421fff com.apple.Engram (1.0 - 1) /System/Library/PrivateFrameworks/Engram.framework/Versions/A/Engram 0x7fff36422000 - 0x7fff3643dfff com.apple.openscripting (1.7 - 190) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting 0x7fff3643e000 - 0x7fff36441fff com.apple.securityhi (9.0 - 55008) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI 0x7fff36442000 - 0x7fff36445fff com.apple.ink.framework (10.15 - 227) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink 0x7fff36446000 - 0x7fff36449fff com.apple.CommonPanels (1.2.6 - 101) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels 0x7fff3644a000 - 0x7fff36451fff com.apple.ImageCapture (1708 - 1708) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture 0x7fff36452000 - 0x7fff376fafff com.apple.JavaScriptCore (16610 - 16610.3.7.1.9) /System/Library/Frameworks/JavaScriptCore.framework/Versions/A/JavaScriptCore 0x7fff37765000 - 0x7fff3784cfff com.apple.audio.AVFAudio (1.0 - 477.9) /System/Library/Frameworks/AVFoundation.framework/Versions/A/Frameworks/AVFAudio.framework/Versions/A/AVFAudio 0x7fff3784d000 - 0x7fff37961fff com.apple.AVFCapture (1.0 - 80.17.1.1) /System/Library/PrivateFrameworks/AVFCapture.framework/Versions/A/AVFCapture 0x7fff37962000 - 0x7fff379f6fff com.apple.Quagga (47 - 47) /System/Library/PrivateFrameworks/Quagga.framework/Versions/A/Quagga 0x7fff379f7000 - 0x7fff37c52fff com.apple.CMCapture (1.0 - 80.17.1.1) /System/Library/PrivateFrameworks/CMCapture.framework/Versions/A/CMCapture 0x7fff37ff4000 - 0x7fff380a2fff com.apple.accounts.AccountsDaemon (113 - 113) /System/Library/PrivateFrameworks/AccountsDaemon.framework/Versions/A/AccountsDaemon 0x7fff380a3000 - 0x7fff380a5fff com.apple.OAuth (25 - 25) /System/Library/PrivateFrameworks/OAuth.framework/Versions/A/OAuth 0x7fff38639000 - 0x7fff38663fff com.apple.CloudServices (1.0 - 460.60.3) /System/Library/PrivateFrameworks/CloudServices.framework/Versions/A/CloudServices 0x7fff38664000 - 0x7fff38673fff com.apple.HID (1.0 - 1) /System/Library/PrivateFrameworks/HID.framework/Versions/A/HID 0x7fff38674000 - 0x7fff3879bfff com.apple.QuickLookUIFramework (5.0 - 928.1) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuickLookUI.framework/Versions/A/QuickLookUI 0x7fff38b70000 - 0x7fff38bfafff com.apple.coredav (1.0.1 - 889) /System/Library/PrivateFrameworks/CoreDAV.framework/Versions/A/CoreDAV 0x7fff38bfb000 - 0x7fff38c56fff com.apple.ExchangeWebServices (8.0 - 814) /System/Library/PrivateFrameworks/ExchangeWebServices.framework/Versions/A/ExchangeWebServices 0x7fff38c57000 - 0x7fff38c92fff com.apple.MediaServices (1.0 - 1) /System/Library/PrivateFrameworks/MediaServices.framework/Versions/A/MediaServices 0x7fff38d88000 - 0x7fff38d88fff com.apple.marco (10.0 - 1000) /System/Library/PrivateFrameworks/Marco.framework/Versions/A/Marco 0x7fff38f83000 - 0x7fff38fbefff com.apple.contacts.ContactsAutocomplete (1.0 - 1152.2) /System/Library/PrivateFrameworks/ContactsAutocomplete.framework/Versions/A/ContactsAutocomplete 0x7fff38fbf000 - 0x7fff38fcbfff com.apple.KerberosHelper (4.0 - 1.0) /System/Library/PrivateFrameworks/KerberosHelper.framework/Versions/A/KerberosHelper 0x7fff38fcc000 - 0x7fff39010fff com.apple.ResponseKit (1.0 - 164.1) /System/Library/PrivateFrameworks/ResponseKit.framework/Versions/A/ResponseKit 0x7fff39011000 - 0x7fff39030fff com.apple.proactive.support.ProactiveEventTracker (1.0 - 294.4) /System/Library/PrivateFrameworks/ProactiveEventTracker.framework/Versions/A/ProactiveEventTracker 0x7fff39437000 - 0x7fff3943afff com.apple.OSAServicesClient (1.0 - 1) /System/Library/PrivateFrameworks/OSAServicesClient.framework/Versions/A/OSAServicesClient 0x7fff3946d000 - 0x7fff3946dfff com.apple.PhoneNumbers (1.0 - 1) /System/Library/PrivateFrameworks/PhoneNumbers.framework/Versions/A/PhoneNumbers 0x7fff3946e000 - 0x7fff39475fff com.apple.URLFormatting (146 - 146.8) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting 0x7fff39476000 - 0x7fff39485fff com.apple.accessibility.AXCoreUtilities (1.0 - 1) /System/Library/PrivateFrameworks/AXCoreUtilities.framework/Versions/A/AXCoreUtilities 0x7fff39486000 - 0x7fff3949dfff libAccessibility.dylib (2885.13) /usr/lib/libAccessibility.dylib 0x7fff3c1e0000 - 0x7fff3c204fff com.apple.quicklook.QuickLookSupport (1.0 - 135.1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport 0x7fff3c205000 - 0x7fff3c29cfff com.apple.AirPlaySync (1.0 - 2760.6.4.6) /System/Library/PrivateFrameworks/AirPlaySync.framework/Versions/A/AirPlaySync 0x7fff3d0b8000 - 0x7fff3d13bfff com.apple.CorePDF (4.0 - 529) /System/Library/PrivateFrameworks/CorePDF.framework/Versions/A/CorePDF 0x7fff3d13c000 - 0x7fff3d13ffff com.apple.print.framework.Print (15 - 271) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print 0x7fff3d140000 - 0x7fff3d143fff com.apple.Carbon (160 - 164) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 0x7fff3d23d000 - 0x7fff3d23dfff com.apple.avfoundation (2.0 - 2000.5.4.2) /System/Library/Frameworks/AVFoundation.framework/Versions/A/AVFoundation 0x7fff3d3c8000 - 0x7fff3d3e7fff com.apple.private.SystemPolicy (1.0 - 1) /System/Library/PrivateFrameworks/SystemPolicy.framework/Versions/A/SystemPolicy 0x7fff3d539000 - 0x7fff3d593fff com.apple.AccessibilitySharedSupport (1.0 - 1) /System/Library/PrivateFrameworks/AccessibilitySharedSupport.framework/Versions/A/AccessibilitySharedSupport 0x7fff3d594000 - 0x7fff3d5b1fff com.apple.sidecar-core (1.0 - 228) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore 0x7fff3d5b2000 - 0x7fff3d5b9fff com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem 0x7fff3d9e2000 - 0x7fff3d9e8fff com.apple.FeatureFlagsSupport (1.0 - 28.60.1) /System/Library/PrivateFrameworks/FeatureFlagsSupport.framework/Versions/A/FeatureFlagsSupport 0x7fff3db60000 - 0x7fff3db77fff com.apple.SafariServices.framework (16610 - 16610.3.7.1.9) /System/Library/Frameworks/SafariServices.framework/Versions/A/SafariServices 0x7fff3dd11000 - 0x7fff3dd1cfff com.apple.MallocStackLogging (1.0 - 1) /System/Library/PrivateFrameworks/MallocStackLogging.framework/Versions/A/MallocStackLogging 0x7fff3dd32000 - 0x7fff3dd44fff libmis.dylib (274.60.2) /usr/lib/libmis.dylib 0x7fff3dd45000 - 0x7fff3dd48fff com.apple.gpusw.GPURawCounter (12.25 - 12.0) /System/Library/PrivateFrameworks/GPURawCounter.framework/Versions/A/GPURawCounter 0x7fff3dd61000 - 0x7fff3ded3fff com.apple.CoreHandwriting (161 - 1.2) /System/Library/PrivateFrameworks/CoreHandwriting.framework/Versions/A/CoreHandwriting 0x7fff3ded4000 - 0x7fff3e133fff com.apple.imageKit (3.0 - 1100) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/ImageKit 0x7fff3e134000 - 0x7fff3e253fff com.apple.PencilKit (1.0 - 1) /System/Library/Frameworks/PencilKit.framework/Versions/A/PencilKit 0x7fff3e254000 - 0x7fff3e265fff com.apple.sidecar-ui (1.0 - 228) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI 0x7fff3e84f000 - 0x7fff3e8b1fff com.apple.ImageCaptureCore (1708 - 1708) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore 0x7fff3e8b2000 - 0x7fff3e8d8fff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters 0x7fff3eb23000 - 0x7fff3ec7afff com.apple.MediaPlayer (1.0 - 1.0) /System/Library/Frameworks/MediaPlayer.framework/Versions/A/MediaPlayer 0x7fff3ec7b000 - 0x7fff3f051fff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud 0x7fff3f07e000 - 0x7fff3f1affff com.apple.AnnotationKit (1.0 - 383.3) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit 0x7fff3f1b0000 - 0x7fff3f651fff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer 0x7fff3f652000 - 0x7fff3f73ffff com.apple.PDFKit (1.0 - 950.10.3) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit 0x7fff40464000 - 0x7fff404e7fff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput 0x7fff41559000 - 0x7fff4155cfff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz 0x7fff41938000 - 0x7fff41956fff libCGInterfaces.dylib (544) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff43073000 - 0x7fff43d9cfff libfaceCore.dylib (4.1.2) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib 0x7fff43d9d000 - 0x7fff43eb4fff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition 0x7fff43eb5000 - 0x7fff43ecefff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark 0x7fff43f46000 - 0x7fff441bffff com.apple.RawCamera.bundle (9.10.0 - 1420.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera 0x7fff44b0f000 - 0x7fff44b13fff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit 0x7fff46532000 - 0x7fff46535fff libpmenergy.dylib (227.60.1) /usr/lib/libpmenergy.dylib 0x7fff46c3e000 - 0x7fff46c49fff libGPUSupportMercury.dylib (18.1.1) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib 0x7fff482aa000 - 0x7fff482f8fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics 0x7fff48b60000 - 0x7fff48b7bfff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics 0x7fff5221e000 - 0x7fff5224cfff com.apple.HelpData (2.3 - 200) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData 0x7fff5224d000 - 0x7fff52267fff com.apple.shortcut (2.16 - 117) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut 0x7fff52268000 - 0x7fff522fafff com.apple.Symbolication (12.2 - 64541.7.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication 0x7fff52474000 - 0x7fff52477fff libpmsample.dylib (227.60.1) /usr/lib/libpmsample.dylib 0x7fff54dd9000 - 0x7fff54e10fff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit 0x7fff56430000 - 0x7fff56433fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback 0x7fff6294d000 - 0x7fff62a30fff com.apple.driver.AppleIntelBDWGraphicsMTLDriver (16.1.7.1 - 16.0.1) /System/Library/Extensions/AppleIntelBDWGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsMTLDriver 0x7fff64446000 - 0x7fff6494dfff com.apple.driver.AppleIntelBDWGraphicsGLDriver (16.1.7.1 - 16.0.1) /System/Library/Extensions/AppleIntelBDWGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelBDWGraphicsGLDriver 0x7fff6c83c000 - 0x7fff6c842fff libCoreFSCache.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib 0x7fff6c843000 - 0x7fff6c847fff libCoreVMClient.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib 0x7fff6c848000 - 0x7fff6c857fff com.apple.opengl (18.1.1 - 18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff6c858000 - 0x7fff6c85afff libCVMSPluginSupport.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib 0x7fff6c85b000 - 0x7fff6c863fff libGFXShared.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff6c864000 - 0x7fff6c897fff libGLImage.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6c898000 - 0x7fff6c8d4fff libGLU.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6c8d5000 - 0x7fff6ca69fff libGLProgrammability.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x7fff6ca6a000 - 0x7fff6ca74fff libGL.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6ca75000 - 0x7fff6cbf0fff GLEngine (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine 0x7fff6cbf1000 - 0x7fff6cc1afff GLRendererFloat (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x7fff6deab000 - 0x7fff6df03fff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6ef82000 - 0x7fff6ef89fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff742fb000 - 0x7fff74306fff com.apple.SymptomAnalytics (1.0 - 1431.60.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics 0x7fff74524000 - 0x7fff7453cfff com.apple.SymptomPresentationFeed (1.0 - 1431.60.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed 0x7fff783c3000 - 0x7fff783cafff libRosetta.dylib (203.13.2) /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 4 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: 6997 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%) Writable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 816K 6 CG image 184K 29 CoreAnimation 84K 17 CoreGraphics 12K 2 CoreServices 764K 3 CoreUI image data 1608K 28 Foundation 36K 2 Kernel Alloc Once 8K 1 MALLOC 534.9M 787 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) Mach message 16K 2 OpenGL GLSL 384K 4 STACK GUARD 120K 30 Stack 173.7M 31 Stack Guard 56.0M 1 VM_ALLOCATE 86.8M 116 VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated) __CTF 759 1 __DATA 42.6M 793 __DATA_CONST 25.7M 313 __DATA_DIRTY 1707K 210 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 537.8M 368 __OBJC_RO 60.5M 1 __OBJC_RW 2452K 2 __TEXT 747.7M 750 __UNICODE 588K 1 mapped file 274.8M 59 shared memory 2240K 13 =========== ======= ======= TOTAL 2.8G 3587 TOTAL, minus reserved VM space 2.5G 3587 ===== Log before crash start ===== UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6ysz format mmcif fromDatabase pdb 6ysz title: Cryo-EM structure of T7 bacteriophage DNA translocation gp15 core protein intermediate assembly [more info...] Chain information for 6ysz #1 --- Chain | Description | UniProt A B C D E F | Internal virion protein gp15 | GP15_BPT7 > save ""/Users/simone/Documents/UT/marcotte/chimerax > sessions/6ysz_crosslinks.cxs"" > select /E:374@O 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 3 residues, 1 model selected > select up 2532 atoms, 2569 bonds, 316 residues, 1 model selected > ribbon sel > clear sel Unknown command: clear sel > clear select Unknown command: clear select > select clear > select /F:374@O 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 3 residues, 1 model selected > select up 2532 atoms, 2569 bonds, 316 residues, 1 model selected > ribbon sel > select clear > select /C:373@C 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 3 residues, 1 model selected > select up 2532 atoms, 2569 bonds, 316 residues, 1 model selected > ribbon sel > select clear > hide > save ""/Users/simone/Documents/UT/marcotte/chimerax > sessions/6ysz_crosslinks.cxs"" > ui tool show XMAS Peptide pair mapping of XlinkX evidence file: /Volumes/Marcotte/project/Simone/T7_xlink/2021_08_17_T7_DSSO_Crosslinks.csv Unique peptide pairs: 280 out of 281 Unique peptide pairs with pseudobonds: 12 Pseudobonds are stored in /Volumes/Marcotte/project/Simone/T7_xlink/2021_08_17_T7_DSSO_Crosslinks_1.pb Mapping information is stored in /Volumes/Marcotte/project/Simone/T7_xlink/2021_08_17_T7_DSSO_Crosslinks_1.tsv Please select pseudobonds Please select pseudobonds Please select pseudobonds Please select pseudobonds > select subtract #2 Nothing selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-16.1.7 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.8 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 425.0.0.0.0 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 11.1 (20C69) Kernel Version: Darwin 20.2.0 Time since boot: 4:44 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: LCD Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus) UI Looks like: 1440 x 900 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 et-xmlfile: 1.1.0 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openpyxl: 3.0.10 openvr: 1.16.802 packaging: 21.0 pandas: 1.4.3 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 QtRangeSlider: 0.1.5 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 seaborn: 0.11.2 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit fixed Tom Goddard Eric Pettersen all ChimeraX