id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5303 Crash in garbage collection p.drougkas@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.3.dev202109272116 (2021-09-27 21:16:30 UTC) Description This script consistently crashes ChimeraX. Every statement in the script is needed for the crash, including the x2 loop. import gc from chimerax.core.commands import run for i in range(2): run(session, ""open emdb:1043"") run(session, ""open 7ahc"") run(session, ""close session"") gc.collect() Fatal Python error: Segmentation fault Thread 0x0000700018702000 (most recent call first): File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 562 in select File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py"", line 1854 in _run_once File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py"", line 596 in run_forever File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tornado/platform/asyncio.py"", line 199 in start File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/iostream.py"", line 76 in _thread_main File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000176ff000 (most recent call first): File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 312 in wait File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/history.py"", line 829 in run File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/history.py"", line 58 in needs_sqlite File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/decorator.py"", line 232 in fun File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000011aa8adc0 (most recent call first): File """", line 5 in File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/interactiveshell.py"", line 3441 in run_code File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/interactiveshell.py"", line 3361 in run_ast_nodes File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/interactiveshell.py"", line 3169 in run_cell_async File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/async_helpers.py"", line 68 in _pseudo_sync_runner File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/interactiveshell.py"", line 2944 in _run_cell File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/interactiveshell.py"", line 2898 in run_cell File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/zmqshell.py"", line 539 in run_cell File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/ipkernel.py"", line 302 in do_execute File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tornado/gen.py"", line 234 in wrapper File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/kernelbase.py"", line 536 in execute_request File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tornado/gen.py"", line 234 in wrapper File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/inprocess/ipkernel.py"", line 80 in execute_request File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/kernelbase.py"", line 261 in dispatch_shell File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tornado/gen.py"", line 234 in wrapper File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/inprocess/client.py"", line 177 in _dispatch_to_kernel File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/inprocess/client.py"", line 109 in execute File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/frontend_widget.py"", line 285 in _execute File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/console_widget.py"", line 663 in do_execute File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/history_console_widget.py"", line 42 in do_execute File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/console_widget.py"", line 588 in _trigger_is_complete_callback File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/console_widget.py"", line 583 in _handle_is_complete_reply File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/base_frontend_mixin.py"", line 138 in _dispatch File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/inprocess.py"", line 46 in call_handlers File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/inprocess.py"", line 42 in File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 880 in init File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1029 in File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main Process: ChimeraX [4901] Path: /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.3.0 (1.3.0.0) Code Type: X86-64 (Native) Parent Process: tcsh [616] Responsible: Terminal [509] User ID: 501 Date/Time: 2021-09-28 13:11:14.540 -0700 OS Version: Mac OS X 10.15.7 (19H1419) Report Version: 12 Anonymous UUID: 1001EC17-01AB-23EF-FBAF-2E1668FB0851 Time Awake Since Boot: 19000 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 0x0000000000000018 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0x18: --> __TEXT 000000010e252000-000000010e256000 [ 16K] r-x/r-x SM=COW /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff69abc33a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff69b78e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff699d393e raise + 26 3 libsystem_platform.dylib 0x00007fff69b6d5fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 QtCore.abi3.so 0x0000000119771a47 PyQtSlot::call(_object*, _object*) const + 39 6 QtCore.abi3.so 0x0000000119771956 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374 7 QtCore.abi3.so 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0x000000010f44321f blas_thread_server + 207 3 libsystem_pthread.dylib 0x00007fff69b79109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff69b74b8b thread_start + 15 Thread 26:: ThreadPoolForegroundWorker 0 libsystem_kernel.dylib 0x00007fff69ab5dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff69ab6170 mach_msg + 60 2 QtWebEngineCore 0x0000000122671492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434 3 QtWebEngineCore 0x0000000122619778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56 4 QtWebEngineCore 0x0000000122619e3d base::internal::WorkerThread::RunWorker() + 237 5 QtWebEngineCore 0x0000000122619cd4 base::internal::WorkerThread::RunPooledWorker() + 20 6 QtWebEngineCore 0x000000012266ce07 base::(anonymous namespace)::ThreadFunc(void*) + 87 7 libsystem_pthread.dylib 0x00007fff69b79109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff69b74b8b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000011aa8adc0 rcx: 0x00007fd89c855a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fd89c855a80 rsp: 0x00007fd89c855a58 r8: 0x00007fd89c855f48 r9: 0xb1395366cd49d7cf r10: 0x000000011aa8adc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff69abc33a rfl: 0x0000000000000246 cr2: 0x00007fd89cbb8030 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10e252000 - 0x10e255ff3 +edu.ucsf.cgl.ChimeraX (1.3.0 - 1.3.0.0) /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX 0x10e268000 - 0x10e4ccfff +org.python.python (3.9.6, [c] 2001-2019 Python Software Foundation. - 3.9.6) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python 0x10e662000 - 0x10e664fff +_heapq.cpython-39-darwin.so (0) 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1.0) /System/Library/PrivateFrameworks/PersistentConnection.framework/Versions/A/PersistentConnection 0x7fff5a61a000 - 0x7fff5a64aff7 com.apple.pluginkit.framework (1.0 - 1) /System/Library/PrivateFrameworks/PlugInKit.framework/Versions/A/PlugInKit 0x7fff5a675000 - 0x7fff5a688ffc com.apple.PowerLog (1.0 - 1) /System/Library/PrivateFrameworks/PowerLog.framework/Versions/A/PowerLog 0x7fff5b504000 - 0x7fff5b55eff6 com.apple.ProtectedCloudStorage (1.0 - 1) /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage 0x7fff5b55f000 - 0x7fff5b578ffb com.apple.ProtocolBuffer (1 - 274.24.9.16.3) /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer 0x7fff5b68a000 - 0x7fff5b68dff4 com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem 0x7fff5b68e000 - 0x7fff5b6b1ff0 com.apple.quicklook.QuickLookSupport (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport 0x7fff5b6f8000 - 0x7fff5b771ff3 com.apple.Rapport (1.9.5 - 195.2) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport 0x7fff5b9d8000 - 0x7fff5ba01ff1 com.apple.RemoteViewServices (2.0 - 148) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices 0x7fff5bb66000 - 0x7fff5bba1ff0 com.apple.RunningBoardServices (1.0 - 223.140.2) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices 0x7fff5d482000 - 0x7fff5d485ff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper 0x7fff5d5f8000 - 0x7fff5d71ffff com.apple.Sharing (1526.37 - 1526.37) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing 0x7fff5d778000 - 0x7fff5d796ff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut 0x7fff5d797000 - 0x7fff5d7b7ff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore 0x7fff5d7b8000 - 0x7fff5d7caff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI 0x7fff5eb34000 - 0x7fff5ee2afff com.apple.SkyLight (1.600.0 - 451.6) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight 0x7fff5f677000 - 0x7fff5f685ffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore 0x7fff5fd61000 - 0x7fff5fda2ff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip 0x7fff5feb9000 - 0x7fff5fec2ff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.2) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter 0x7fff5ff33000 - 0x7fff5ff5dffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration 0x7fff60179000 - 0x7fff60189ff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC 0x7fff606ae000 - 0x7fff60774ff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO 0x7fff6090b000 - 0x7fff6090cfff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent 0x7fff60944000 - 0x7fff60b9cff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation 0x7fff60c33000 - 0x7fff60c39ffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting 0x7fff61839000 - 0x7fff61859ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement 0x7fff62605000 - 0x7fff626f0ff2 com.apple.ViewBridge (468 - 468) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge 0x7fff62896000 - 0x7fff62897fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient 0x7fff634c7000 - 0x7fff634caffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap 0x7fff63544000 - 0x7fff63552ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk 0x7fff63894000 - 0x7fff63896ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport 0x7fff63897000 - 0x7fff638aaffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login 0x7fff638dc000 - 0x7fff638e8ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata 0x7fff6636d000 - 0x7fff66379ff9 libAudioStatistics.dylib (1104.100) /usr/lib/libAudioStatistics.dylib 0x7fff6637a000 - 0x7fff663adffa libAudioToolboxUtility.dylib (1104.100) /usr/lib/libAudioToolboxUtility.dylib 0x7fff663b4000 - 0x7fff663e8fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib 0x7fff663eb000 - 0x7fff663f5fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib 0x7fff663f6000 - 0x7fff6647efff libCoreStorage.dylib (551.0.1) /usr/lib/libCoreStorage.dylib 0x7fff66481000 - 0x7fff66483ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff664c9000 - 0x7fff66680ffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib 0x7fff666a7000 - 0x7fff666adff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib 0x7fff6678f000 - 0x7fff66796fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib 0x7fff667c5000 - 0x7fff667e5ff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib 0x7fff66865000 - 0x7fff66942ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib 0x7fff66957000 - 0x7fff66958fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib 0x7fff66959000 - 0x7fff669e4ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib 0x7fff669e5000 - 0x7fff669e6fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib 0x7fff669fe000 - 0x7fff66a14fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib 0x7fff66a49000 - 0x7fff66abbff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib 0x7fff66abc000 - 0x7fff66b55fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib 0x7fff66b59000 - 0x7fff66b59ff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff66b5a000 - 0x7fff66c1effe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib 0x7fff66c1f000 - 0x7fff66c2fffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib 0x7fff66c30000 - 0x7fff66c3cfff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib 0x7fff66c3d000 - 0x7fff66c8ffff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib 0x7fff66c90000 - 0x7fff66ca5ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib 0x7fff66ca6000 - 0x7fff66ca6fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib 0x7fff66ca7000 - 0x7fff66cb8fff libcmph.dylib (8) /usr/lib/libcmph.dylib 0x7fff66cb9000 - 0x7fff66cd0fd7 libcompression.dylib (87.1) /usr/lib/libcompression.dylib 0x7fff66faa000 - 0x7fff66fc0ff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib 0x7fff66fc1000 - 0x7fff66fc2fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff67465000 - 0x7fff67569fef libcrypto.44.dylib (47.140.1) /usr/lib/libcrypto.44.dylib 0x7fff6756c000 - 0x7fff67577fff libcsfde.dylib (551.0.1) /usr/lib/libcsfde.dylib 0x7fff6757f000 - 0x7fff675deff7 libcups.2.dylib (483.8) /usr/lib/libcups.2.dylib 0x7fff675e0000 - 0x7fff67645ff7 libcurl.4.dylib (118.120.6) /usr/lib/libcurl.4.dylib 0x7fff676e8000 - 0x7fff676e8fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib 0x7fff676e9000 - 0x7fff67703ff7 libexpat.1.dylib (19.60.3) /usr/lib/libexpat.1.dylib 0x7fff67704000 - 0x7fff67710ffb libexslt.0.dylib (16.12) /usr/lib/libexslt.0.dylib 0x7fff67711000 - 0x7fff67713fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib 0x7fff67714000 - 0x7fff67719f57 libffi.dylib (26) /usr/lib/libffi.dylib 0x7fff67722000 - 0x7fff67727fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib 0x7fff67728000 - 0x7fff67731ff7 libheimdal-asn1.dylib (564.140.7) /usr/lib/libheimdal-asn1.dylib 0x7fff67732000 - 0x7fff67822fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib 0x7fff67823000 - 0x7fff67a7afff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib 0x7fff67a94000 - 0x7fff67a95fff liblangid.dylib (133) /usr/lib/liblangid.dylib 0x7fff67a96000 - 0x7fff67aaeff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib 0x7fff67ac6000 - 0x7fff67b6dff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib 0x7fff67b6e000 - 0x7fff67dd0ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib 0x7fff6813d000 - 0x7fff6816cfff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib 0x7fff6829c000 - 0x7fff68718ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib 0x7fff68719000 - 0x7fff68730fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib 0x7fff687b9000 - 0x7fff687ecfde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib 0x7fff687ed000 - 0x7fff687eeff7 libodfde.dylib (26) /usr/lib/libodfde.dylib 0x7fff687ff000 - 0x7fff68803fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib 0x7fff68806000 - 0x7fff6883cfff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib 0x7fff6887c000 - 0x7fff6888aff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib 0x7fff6888b000 - 0x7fff6888eff3 libpmenergy.dylib (214.120.2) /usr/lib/libpmenergy.dylib 0x7fff6888f000 - 0x7fff68891fff libpmsample.dylib (214.120.2) /usr/lib/libpmsample.dylib 0x7fff688c0000 - 0x7fff688d8fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff688da000 - 0x7fff6891eff7 libsandbox.1.dylib (1217.141.6) /usr/lib/libsandbox.1.dylib 0x7fff6891f000 - 0x7fff68931ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib 0x7fff68932000 - 0x7fff68933ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib 0x7fff68934000 - 0x7fff68b1eff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib 0x7fff68c12000 - 0x7fff68c3fffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib 0x7fff68d14000 - 0x7fff68d6eff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib 0x7fff68d6f000 - 0x7fff68d72ffb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff68d73000 - 0x7fff68d80ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib 0x7fff68d86000 - 0x7fff68e68fff libxml2.2.dylib (33.9) /usr/lib/libxml2.2.dylib 0x7fff68e6c000 - 0x7fff68e94fff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib 0x7fff68e95000 - 0x7fff68ea7ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff69756000 - 0x7fff6975bff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff6975c000 - 0x7fff69767fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff69768000 - 0x7fff6976ffff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff69770000 - 0x7fff69779ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff6977a000 - 0x7fff6980cfdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib 0x7fff69919000 - 0x7fff69959ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff6995a000 - 0x7fff69990fff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib 0x7fff69991000 - 0x7fff69991ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff69992000 - 0x7fff6999eff3 libkxld.dylib (6153.141.40.1) /usr/lib/system/libkxld.dylib 0x7fff6999f000 - 0x7fff6999fff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib 0x7fff699a0000 - 0x7fff699a5ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff699a6000 - 0x7fff699a8ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff699a9000 - 0x7fff699aaff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff699ab000 - 0x7fff699c2ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff699c3000 - 0x7fff699c3ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff699c4000 - 0x7fff69a4bfff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib 0x7fff69a4c000 - 0x7fff69a4fffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib 0x7fff69a50000 - 0x7fff69a53fff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib 0x7fff69a54000 - 0x7fff69a5cfff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib 0x7fff69a5d000 - 0x7fff69a64fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff69a65000 - 0x7fff69a66ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff69a67000 - 0x7fff69ab4ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff69ab5000 - 0x7fff69ae1ff7 libsystem_kernel.dylib (6153.141.40.1) /usr/lib/system/libsystem_kernel.dylib 0x7fff69ae2000 - 0x7fff69b29fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff69b2a000 - 0x7fff69b51fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff69b52000 - 0x7fff69b5fffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff69b60000 - 0x7fff69b69ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff69b6a000 - 0x7fff69b72fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff69b73000 - 0x7fff69b7dfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff69b7e000 - 0x7fff69b82ff3 libsystem_sandbox.dylib (1217.141.6) /usr/lib/system/libsystem_sandbox.dylib 0x7fff69b83000 - 0x7fff69b85fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff69b86000 - 0x7fff69b8dffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib 0x7fff69b8e000 - 0x7fff69ba4ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib 0x7fff69ba6000 - 0x7fff69babff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff69bac000 - 0x7fff69be1ffe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 11874 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%) Writable regions: Total=550.1M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=550.1M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 512K 4 Activity Tracing 256K 1 CG backing stores 336K 2 CG image 72K 13 CoreAnimation 80K 16 CoreGraphics 8K 1 CoreImage 8K 2 CoreUI image data 992K 16 Dispatch continuations 8192K 1 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 226.5M 575 MALLOC guard page 32K 7 MALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated) Mach message 24K 3 OpenGL GLSL 384K 4 STACK GUARD 104K 26 Stack 172.2M 27 Stack Guard 56.0M 1 VM_ALLOCATE 138.1M 69 __DATA 52.7M 567 __DATA_CONST 616K 37 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 479.8M 217 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 530.4M 540 __UNICODE 564K 1 mapped file 400.5M 53 shared memory 2840K 24 =========== ======= ======= TOTAL 2.1G 2215 TOTAL, minus reserved VM space 2.1G 2215 ===== Log before crash start ===== UCSF ChimeraX version: 1.3.dev202109272116 (2021-09-27) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Shell > open emdb:1043 Opened emdb 1043 as #1, grid size 128,128,128, pixel 1.6, shown at level 0.0738, step 1, values float32 > open 7ahc 7ahc title: OpuA apo inward-facing [more info...] Chain information for 7ahc #2 --- Chain | Description | UniProt A B | ABC transporter permease subunit | A0A0V8ETW8_LACLL C D | ABC-type proline/glycine betaine transport system ATPase component | A0A0R2NIU5_LACLL > close session > open emdb:1043 Opened emdb 1043 as #1, grid size 128,128,128, pixel 1.6, shown at level 0.0738, step 1, values float32 > open 7ahc 7ahc title: OpuA apo inward-facing [more info...] Chain information for 7ahc #2 --- Chain | Description | UniProt A B | ABC transporter permease subunit | A0A0V8ETW8_LACLL C D | ABC-type proline/glycine betaine transport system ATPase component | A0A0R2NIU5_LACLL > close session ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3.dev202109272116 (2021-09-27) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Shell OpenGL version: 4.1 INTEL-14.7.18 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB Boot ROM Version: 427.140.8.0.0 SMC Version (system): 2.32f21 Software: System Software Overview: System Version: macOS 10.15.7 (19H1419) Kernel Version: Darwin 19.6.0 Time since boot: 5:33 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.0 chardet: 4.0.0 charset-normalizer: 2.0.3 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.1 ChimeraX-AtomicLibrary: 4.1.4 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 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: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202109272116 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-GaudiViewX: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.1 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 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.1 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2 ChimeraX-ModelPanel: 1.2 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: 1.7 ChimeraX-PDB: 2.6.3 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.4 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: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.10.0 Cython: 0.29.23 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.3.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 2.11.3 jupyter-client: 6.1.12 jupyter-core: 4.7.1 kiwisolver: 1.3.1 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 1.1.1 matplotlib: 3.4.2 matplotlib-inline: 0.1.2 MolecularDynamicsViewer: 1.2 msgpack: 1.0.2 netCDF4: 1.5.6 networkx: 2.6.2 numexpr: 2.7.3 numpy: 1.21.0 numpydoc: 1.1.0 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.2.0 pip: 21.1.1 pkginfo: 1.7.0 prompt-toolkit: 3.0.19 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.9.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 PyYAML: 5.4.1 pyzmq: 22.2.0 qtconsole: 5.1.0 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.6.3 Send2Trash: 1.5.0 setuptools: 57.0.0 sfftk-rw: 0.7.0.post1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.0.1 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.2 wheel-filename: 1.3.0 }}} " defect closed normal Core fixed chimera-programmers all ChimeraX