The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
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 0x0000000204c61e00 (most recent call first):
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 [47471]
Path: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.5.0 (1.5.0.0)
Code Type: X86-64 (Translated)
Parent Process: ??? [1]
Responsible: ChimeraX [47471]
User ID: 502
Date/Time: 2023-06-30 18:26:04.005 +0800
OS Version: macOS 11.5.2 (20G95)
Report Version: 12
Anonymous UUID: F7EB6F8F-F324-6D49-4E0A-05990147C151
Sleep/Wake UUID: 46785B81-2128-4729-B6F9-E452542FFE22
Time Awake Since Boot: 2500000 seconds
Time Since Wake: 28000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0:
-->
__TEXT 1047ff000-104800000 [ 4K] 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 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203bb92e __pthread_kill + 10
2 libsystem_c.dylib 0x00007fff202cebd5 raise + 26
3 libsystem_platform.dylib 0x00007fff2042fd7d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 com.apple.AppKit 0x00007fff22c30532 -[NSThemeFrame _distanceFromToolbarBaseToTitlebar] + 275
6 com.apple.AppKit 0x00007fff22c5c6ae -[NSThemeFrame contentRectForFrameRect:styleMask:] + 179
7 com.apple.AppKit 0x00007fff22c5c566 -[NSWindow contentRectForFrameRect:styleMask:] + 86
8 com.apple.AppKit 0x00007fff22e084bd -[NSWindow contentRectForFrameRect:] + 82
9 libqcocoa.dylib 0x000000014ac95d24 0x14ac47000 + 322852
10 QtGui 0x000000012ac59511 QWindow::frameMargins() const + 65
11 libqcocoa.dylib 0x000000014acbfc2c 0x14ac47000 + 494636
12 com.apple.AppKit 0x00007fff234c84eb -[NSWindow _standardFrameForScreen:isMoveToiPad:] + 632
13 com.apple.AppKit 0x00007fff22f431cc -[NSWindow _standardFrame] + 34
14 com.apple.AppKit 0x00007fff22fedd73 -[NSWindow isZoomed] + 41
15 libqcocoa.dylib 0x000000014ac8e1a5 0x14ac47000 + 291237
16 libqcocoa.dylib 0x000000014ac9003b 0x14ac47000 + 299067
17 QtCore 0x000000012641c614 QMetaMethod::invoke(QObject*, Qt::ConnectionType, QGenericReturnArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument) const + 1284
18 libqcocoa.dylib 0x000000014ac96a6c 0x14ac47000 + 326252
19 com.apple.Foundation 0x00007fff2117101a -[__NSObserver _doit:] + 287
20 com.apple.CoreFoundation 0x00007fff204d8d09 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
21 com.apple.CoreFoundation 0x00007fff205746f8 ___CFXRegistrationPost_block_invoke + 49
22 com.apple.CoreFoundation 0x00007fff20574675 _CFXRegistrationPost + 454
23 com.apple.CoreFoundation 0x00007fff204a9fb4 _CFXNotificationPost + 795
24 com.apple.Foundation 0x00007fff21144bb8 -[NSNotificationCenter postNotificationName:object:userInfo:] + 59
25 com.apple.AppKit 0x00007fff22c67071 -[NSWindow _setFrameCommon:display:fromServer:] + 1610
26 com.apple.AppKit 0x00007fff22fc7f5f -[NSWindow _adjustWindowToScreen] + 1340
27 com.apple.AppKit 0x00007fff22ff05c2 -[NSWindow _displayChangedSoAdjustWindows:] + 105
28 com.apple.AppKit 0x00007fff237442fd ___NSApplicationPerformScreenInvalidationReactions_block_invoke + 72
29 com.apple.AppKit 0x00007fff22c0d3ce -[NSApplication enumerateWindowsWithOptions:usingBlock:] + 293
30 com.apple.AppKit 0x00007fff23743c78 ___NSApplicationReactToScreenInvalidation_block_invoke + 709
31 com.apple.AppKit 0x00007fff23743712 _NSApplicationReactToScreenInvalidation + 129
32 com.apple.AppKit 0x00007fff23743933 -[NSApplication(ScreenHandling) _reactToDisplayChanges:] + 366
33 com.apple.AppKit 0x00007fff23305cea _NSCGSDisplayConfigurationUpdateAndInvokeObservers + 441
34 com.apple.AppKit 0x00007fff23306007 _NSCGSDisplayConfigurationDidReconfigureNotificationHandler + 287
35 com.apple.SkyLight 0x00007fff24bbbf35 (anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*) + 1071
36 com.apple.SkyLight 0x00007fff24e5dde8 CGSDatagramReadStream::dispatchMainQueueDatagrams() + 202
37 com.apple.SkyLight 0x00007fff24e5dd0f invocation function for block in CGSDatagramReadStream::mainQueueWakeup() + 18
38 libdispatch.dylib 0x00007fff2023f623 _dispatch_call_block_and_release + 12
39 libdispatch.dylib 0x00007fff20240806 _dispatch_client_callout + 8
40 libdispatch.dylib 0x00007fff2024cb4f _dispatch_main_queue_callback_4CF + 940
41 com.apple.CoreFoundation 0x00007fff2052049e __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
42 com.apple.CoreFoundation 0x00007fff204e24a8 __CFRunLoopRun + 2769
43 com.apple.CoreFoundation 0x00007fff204e1310 CFRunLoopRunSpecific + 567
44 com.apple.HIToolbox 0x00007fff28989a83 RunCurrentEventLoopInMode + 292
45 com.apple.HIToolbox 0x00007fff289897e5 ReceiveNextEventCommon + 587
46 com.apple.HIToolbox 0x00007fff28989583 _BlockUntilNextEventMatchingListInModeWithFilter + 70
47 com.apple.AppKit 0x00007fff22c13172 _DPSNextEvent + 864
48 com.apple.AppKit 0x00007fff22c11945 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364
49 com.apple.AppKit 0x00007fff22c03c69 -[NSApplication run] + 586
50 libqcocoa.dylib 0x000000014ac600ac 0x14ac47000 + 102572
51 QtCore 0x0000000126416326 QEventLoop::exec(QFlags) + 486
52 QtCore 0x000000012640d235 QCoreApplication::exec() + 133
53 QtWidgets.abi3.so 0x00000001291ecd9a meth_QApplication_exec(_object*, _object*) + 90
54 org.python.python 0x000000010cda871d cfunction_call + 125
55 org.python.python 0x000000010cd695b7 _PyObject_MakeTpCall + 359
56 org.python.python 0x000000010ce41e9c call_function + 876
57 org.python.python 0x000000010ce3f2a2 _PyEval_EvalFrameDefault + 25554
58 org.python.python 0x000000010cd69d28 function_code_fastcall + 104
59 org.python.python 0x000000010cd6bd6a method_vectorcall + 202
60 org.python.python 0x000000010ce41e0c call_function + 732
61 org.python.python 0x000000010ce3f2a2 _PyEval_EvalFrameDefault + 25554
62 org.python.python 0x000000010ce42b03 _PyEval_EvalCode + 2611
63 org.python.python 0x000000010cd69cb1 _PyFunction_Vectorcall + 289
64 org.python.python 0x000000010ce41e0c call_function + 732
65 org.python.python 0x000000010ce3f34b _PyEval_EvalFrameDefault + 25723
66 org.python.python 0x000000010ce42b03 _PyEval_EvalCode + 2611
67 org.python.python 0x000000010ce38dab PyEval_EvalCode + 139
68 org.python.python 0x000000010ce35c12 builtin_exec + 626
69 org.python.python 0x000000010cda8023 cfunction_vectorcall_FASTCALL + 195
70 org.python.python 0x000000010ce41e0c call_function + 732
71 org.python.python 0x000000010ce3f34b _PyEval_EvalFrameDefault + 25723
72 org.python.python 0x000000010ce42b03 _PyEval_EvalCode + 2611
73 org.python.python 0x000000010cd69cb1 _PyFunction_Vectorcall + 289
74 org.python.python 0x000000010ce41e0c call_function + 732
75 org.python.python 0x000000010ce3f34b _PyEval_EvalFrameDefault + 25723
76 org.python.python 0x000000010ce42b03 _PyEval_EvalCode + 2611
77 org.python.python 0x000000010cd69cb1 _PyFunction_Vectorcall + 289
78 org.python.python 0x000000010cea8870 pymain_run_module + 208
79 org.python.python 0x000000010cea7f87 Py_RunMain + 1431
80 org.python.python 0x000000010cea858f pymain_main + 223
81 org.python.python 0x000000010cea849b Py_Main + 43
82 edu.ucsf.cgl.ChimeraX 0x00000001047ffdc8 main + 120
83 libdyld.dylib 0x00007fff20405f3d start + 1
Thread 1:: com.apple.rosetta.exceptionserver
0 runtime 0x00007ffdffe87a28 0x7ffdffe83000 + 18984
1 runtime 0x00007ffdffe8ceec 0x7ffdffe83000 + 40684
2 runtime 0x00007ffdffe8e2c0 0x7ffdffe83000 + 45760
Thread 2:: ThreadPoolServiceThread
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203be1d2 kevent64 + 10
2 QtWebEngineCore 0x00000001307e0927 0x12c880000 + 66455847
3 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
4 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
5 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
6 QtWebEngineCore 0x00000001307672ad 0x12c880000 + 65958573
7 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
8 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 3:: ThreadPoolForegroundWorker
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307737bf 0x12c880000 + 66009023
4 QtWebEngineCore 0x000000013077426c 0x12c880000 + 66011756
5 QtWebEngineCore 0x0000000130773e6d 0x12c880000 + 66010733
6 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 4:: ThreadPoolBackgroundWorker
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307737bf 0x12c880000 + 66009023
4 QtWebEngineCore 0x000000013077426c 0x12c880000 + 66011756
5 QtWebEngineCore 0x0000000130773ddd 0x12c880000 + 66010589
6 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 5:: Chrome_IOThread
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203be1d2 kevent64 + 10
2 QtWebEngineCore 0x00000001307e0927 0x12c880000 + 66455847
3 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
4 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
5 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
6 QtWebEngineCore 0x000000012f6a53a2 0x12c880000 + 48386978
7 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
8 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 6:: NetworkConfigWatcher
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307aebef 0x12c880000 + 66251759
4 QtWebEngineCore 0x00000001306e41c9 0x12c880000 + 65421769
5 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
6 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
7 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
8 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
9 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 7:: CompositorTileWorker1
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 QtWebEngineCore 0x00000001307a6d1b 0x12c880000 + 66219291
3 QtWebEngineCore 0x000000013287492d 0x12c880000 + 100616493
4 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
5 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
6 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 8:: Chrome_InProcGpuThread
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307aebef 0x12c880000 + 66251759
4 QtWebEngineCore 0x00000001306e41c9 0x12c880000 + 65421769
5 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
6 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
7 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
8 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
9 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 9:: Chrome_ChildIOThread
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203be1d2 kevent64 + 10
2 QtWebEngineCore 0x00000001307e0927 0x12c880000 + 66455847
3 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
4 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
5 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
6 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
7 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
8 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 10:: VizCompositorThread
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001306e4168 0x12c880000 + 65421672
4 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
5 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
6 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
7 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
8 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
9 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 11:: NetworkConfigWatcher
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307aebef 0x12c880000 + 66251759
4 QtWebEngineCore 0x00000001306e41c9 0x12c880000 + 65421769
5 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
6 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
7 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
8 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
9 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 12:: NetworkService
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203be1d2 kevent64 + 10
2 QtWebEngineCore 0x00000001307e0927 0x12c880000 + 66455847
3 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
4 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
5 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
6 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
7 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
8 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 13:: NetworkConfigWatcher
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307aebef 0x12c880000 + 66251759
4 QtWebEngineCore 0x00000001306e41c9 0x12c880000 + 65421769
5 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
6 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
7 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
8 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
9 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 14:: ThreadPoolSingleThreadForegroundBlocking0
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307737bf 0x12c880000 + 66009023
4 QtWebEngineCore 0x000000013077426c 0x12c880000 + 66011756
5 QtWebEngineCore 0x0000000130773ecd 0x12c880000 + 66010829
6 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 15:: NetworkConfigWatcher
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307aebef 0x12c880000 + 66251759
4 QtWebEngineCore 0x00000001306e41c9 0x12c880000 + 65421769
5 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
6 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
7 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
8 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
9 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 16:: MemoryInfra
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307aebef 0x12c880000 + 66251759
4 QtWebEngineCore 0x00000001306e41c9 0x12c880000 + 65421769
5 QtWebEngineCore 0x000000013075da5c 0x12c880000 + 65919580
6 QtWebEngineCore 0x0000000130715998 0x12c880000 + 65624472
7 QtWebEngineCore 0x000000013077feb8 0x12c880000 + 66059960
8 QtWebEngineCore 0x000000013078004a 0x12c880000 + 66060362
9 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
10 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 QtWebEngineCore 0x00000001307aee26 0x12c880000 + 66252326
3 QtWebEngineCore 0x00000001307737bf 0x12c880000 + 66009023
4 QtWebEngineCore 0x0000000130773f9a 0x12c880000 + 66011034
5 QtWebEngineCore 0x0000000130773e0d 0x12c880000 + 66010637
6 QtWebEngineCore 0x00000001307a7908 0x12c880000 + 66222344
7 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 18:: com.apple.NSEventThread
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b52ba mach_msg_trap + 10
2 com.apple.CoreFoundation 0x00007fff204e3855 __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff204e1f0b __CFRunLoopRun + 1332
4 com.apple.CoreFoundation 0x00007fff204e1310 CFRunLoopRunSpecific + 567
5 com.apple.AppKit 0x00007fff22d9923a _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 19:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 20:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 21:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 22:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 23:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 24:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 25:
0 ??? 0x00007ffe946228f4 ???
1 libsystem_kernel.dylib 0x00007fff203b7cde __psynch_cvwait + 10
2 libopenblas64_.0.dylib 0x000000010e84823f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff203ea8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff203e6443 thread_start + 15
Thread 26:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 27:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 28:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 29:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 30:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 31:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 32:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 33:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 34:
0 runtime 0x00007ffdffea57c8 0x7ffdffe83000 + 141256
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000204c61e00 rcx: 0x0000000000000000 rdx: 0x0000000000000000
rdi: 0x03a3d302f702b68f rsi: 0x00000001526a2088 rbp: 0x03a3d302f702b68f rsp: 0x00000001526a2088
r8: 0x000000000000000b r9: 0x03a3d302f702b68f r10: 0x0000000204c61e00 r11: 0x00007fff202cebbb
r12: 0x0000000000000103 r13: 0x0000000000000000 r14: 0x000000000000000b r15: 0x0000000000000016
rip: rfl: 0x0000000000000283
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0x7fff6be34000 - 0x7fff6bfc7fff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6bfc8000 - 0x7fff6bfd2fff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6bfd3000 - 0x7fff6c150fff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6c151000 - 0x7fff6c179fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6d412000 - 0x7fff6d46afff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6e514000 - 0x7fff6e51bfff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff6e51c000 - 0x7fff6e603fff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x7fff6fb81000 - 0x7fff6fb93fff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging
0x7fff73e95000 - 0x7fff73ea0fff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff740b6000 - 0x7fff740cefff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff77c46000 - 0x7fff77c4dfff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib
Translated Code Information:
tmp0: 0xffffffffffffffff tmp1: 0x00007ffe946228c8 tmp2: 0x00007fff203bb924
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
CG backing stores 4416K 12
CG image 208K 19
CoreAnimation 72K 10
CoreGraphics 16K 3
CoreServices 624K 2
CoreUI image data 2708K 21
Foundation 16K 1
Kernel Alloc Once 8K 1
MALLOC 422.3M 134
MALLOC guard page 192K 8
MALLOC_MEDIUM (reserved) 848.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Mach message 16K 4
OpenGL GLSL 384K 4
Rosetta Arena 4096K 2
Rosetta Generic 1392K 345
Rosetta IndirectBranch 2048K 1
Rosetta JIT 128.0M 1
Rosetta Return Stack 680K 68
Rosetta Thread Context 680K 68
STACK GUARD 36K 9
Stack 144.6M 34
Stack Guard 56.1M 25
VM_ALLOCATE 139.3M 331
VM_ALLOCATE (reserved) 128.1M 15 reserved VM address space (unallocated)
__DATA 35.5M 629
__DATA_CONST 25.3M 303
__DATA_DIRTY 1695K 206
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 535.6M 190
__OBJC_RO 70.3M 1
__OBJC_RW 2480K 2
__TEXT 647.9M 612
__UNICODE 588K 1
mapped file 4.3G 1043
shared memory 3020K 26
unshared pmap 10.4M 6
=========== ======= =======
TOTAL 7.8G 4150
TOTAL, minus reserved VM space 6.5G 4150
System Profile:
Network Service: Wi-Fi, AirPort, en0
Boot Volume File System Type: apfs
Memory Module: LPDDR4
USB Device: USB 3.1 Bus
USB Device: USB 3.1 Bus
USB Device: USB3.0 Hub
USB Device: USB2.0 Hub
USB Device: USB Type-C VGA Adapter
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Model: MacBookPro17,1, BootROM 6723.140.2, proc 8:4:4 processors, 16 GB, SMC
Graphics: kHW_AppleM1Item, Apple M1, spdisplays_builtin
AirPort: spairport_wireless_card_type_airport_extreme, wl0: Jul 7 2021 00:48:27 version 18.50.40.10.7.8.121 FWID 01-f5ad2691
Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Updating list of available bundles failed: Internal Server Error
> open /Users/xueyang02/Downloads/interface/1a1a_C_B.pdb
Chain information for 1a1a_C_B.pdb #1
---
Chain | Description
B | No description available
C | No description available
> select /B:155-164
50 atoms, 47 bonds, 2 pseudobonds, 5 residues, 2 models selected
> select /C:101-103
41 atoms, 41 bonds, 3 residues, 1 model selected
> select /B:155-164
50 atoms, 47 bonds, 2 pseudobonds, 5 residues, 2 models selected
> select /C:101-103
41 atoms, 41 bonds, 3 residues, 1 model selected
> select /B:155-164
50 atoms, 47 bonds, 2 pseudobonds, 5 residues, 2 models selected
> select /C:101-103
41 atoms, 41 bonds, 3 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select clear
> hbonds reveal true
3 hydrogen bonds found
> open 1a1a
Summary of feedback from opening 1a1a fetched from pdb
---
notes | Fetching compressed mmCIF 1a1a from
http://files.rcsb.org/download/1a1a.cif
Fetching CCD PTH from http://ligand-expo.rcsb.org/reports/P/PTH/PTH.cif
Fetching CCD DIP from http://ligand-expo.rcsb.org/reports/D/DIP/DIP.cif
1a1a title:
C-SRC (SH2 domain with C188A mutation) complexed with ace-formyl phosphotyr-
glu-(N,N-dipentyl amine) [more info...]
Chain information for 1a1a #2
---
Chain | Description | UniProt
A B | C-SRC TYROSINE KINASE | SRC_HUMAN
C D | ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE) |
Non-standard residues in 1a1a #2
---
ACE — acetyl group
DIP — dipentylamine
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1a1a, chain A (#2) with 1a1a_C_B.pdb, chain B (#1), sequence
alignment score = 12.3
RMSD between 4 pruned atom pairs is 0.840 angstroms; (across all 5 pairs:
1.614)
> select #2/C:100-103
44 atoms, 44 bonds, 4 residues, 1 model selected
> select #2/C:100-103
44 atoms, 44 bonds, 4 residues, 1 model selected
> select #2/A:144-249
1048 atoms, 1065 bonds, 106 residues, 1 model selected
> select #2/A:144-249
1048 atoms, 1065 bonds, 106 residues, 1 model selected
> select #2/C:100-103
44 atoms, 44 bonds, 4 residues, 1 model selected
> select #2/B:148-249
1016 atoms, 1033 bonds, 102 residues, 1 model selected
> select #2/D:100-103
44 atoms, 44 bonds, 4 residues, 1 model selected
> select add #2
2734 atoms, 2574 bonds, 410 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> show #2 models
> color bychain
> select add #1
91 atoms, 88 bonds, 5 pseudobonds, 8 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
91 atoms, 88 bonds, 5 pseudobonds, 8 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1
91 atoms, 88 bonds, 5 pseudobonds, 8 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> coulombic #!1
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTH (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/q8/v0t7tw_j0j7fc2pm639b29m80000gp/T/tmpx6vlkwv1/ante.in.mol2 -fi
mol2 -o
/var/folders/q8/v0t7tw_j0j7fc2pm639b29m80000gp/T/tmpx6vlkwv1/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(PTH) ``
(PTH) `Welcome to antechamber 20.0: molecular input file processor.`
(PTH) ``
(PTH) `Info: Finished reading file
(/var/folders/q8/v0t7tw_j0j7fc2pm639b29m80000gp/T/tmpx6vlkwv1/ante.in.mol2);
atoms read (35), bonds read (35).`
(PTH) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTH) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTH) ``
(PTH) ``
(PTH) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PTH) `Info: Total number of electrons: 160; net charge: -2`
(PTH) ``
(PTH) `Running: /Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(PTH) ``
(PTH) `Running: /Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PTH) ``
(PTH) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTH) ``
Charges for residue PTH determined
Assigning partial charges to residue DIP (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/q8/v0t7tw_j0j7fc2pm639b29m80000gp/T/tmpndcr3h49/ante.in.mol2 -fi
mol2 -o
/var/folders/q8/v0t7tw_j0j7fc2pm639b29m80000gp/T/tmpndcr3h49/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(DIP) ``
(DIP) `Welcome to antechamber 20.0: molecular input file processor.`
(DIP) ``
(DIP) `Info: Finished reading file
(/var/folders/q8/v0t7tw_j0j7fc2pm639b29m80000gp/T/tmpndcr3h49/ante.in.mol2);
atoms read (39), bonds read (38).`
(DIP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(DIP) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(DIP) ``
(DIP) ``
(DIP) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(DIP) `Info: Total number of electrons: 112; net charge: 0`
(DIP) ``
(DIP) `Running: /Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(DIP) ``
(DIP) `Running: /Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(DIP) ``
(DIP) `Running:
/Applications/ChimeraX-1.5.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(DIP) ``
Charges for residue DIP determined
Coulombic values for 1a1a_C_B.pdb_B SES surface #1.3: minimum, -8.48, mean
-0.39, maximum 8.68
Coulombic values for 1a1a_C_B.pdb_C SES surface #1.4: minimum, -16.50, mean
-6.86, maximum -1.09
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!1
Map values for surface "1a1a_C_B.pdb_B SES surface": minimum -18.29, mean
-2.508, maximum 19.71
Map values for surface "1a1a_C_B.pdb_C SES surface": minimum -16.26, mean
76.2, maximum 173.4
To also show corresponding color key, enter the above mlp command and add key
true
> color #!1 bypolymer
> rainbow #!1
> coulombic #!1
Coulombic values for 1a1a_C_B.pdb_B SES surface #1.3: minimum, -8.48, mean
-0.39, maximum 8.68
Coulombic values for 1a1a_C_B.pdb_C SES surface #1.4: minimum, -16.50, mean
-6.86, maximum -1.09
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor #!1
91 atoms, 8 residues, 2 surfaces, atom bfactor range 0 to 59.7
> color #!1 bynucleotide
> coulombic #!1
Coulombic values for 1a1a_C_B.pdb_B SES surface #1.3: minimum, -8.48, mean
-0.39, maximum 8.68
Coulombic values for 1a1a_C_B.pdb_C SES surface #1.4: minimum, -16.50, mean
-6.86, maximum -1.09
To also show corresponding color key, enter the above coulombic command and
add key true
QQuickWidget: Failed to make context current when creating FBO
QQuickWidget: Cannot render due to failing makeCurrent()
QQuickWidget: Failed to make context current when creating FBO
QQuickWidget: Cannot render due to failing makeCurrent()
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
2023-07-04 14:31:09,493 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fb273349a30>: Failed to establish a new connection: [Errno 61] Connection
refused')':
/cxservices/api/v1/chimerax/updates?uuid=484ff201-7e7e-5693-a209-14ed1b1afad3&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.5
2023-07-04 14:31:09,672 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fb2613ad220>: Failed to establish a new connection: [Errno 61] Connection
refused')':
/cxservices/api/v1/chimerax/updates?uuid=484ff201-7e7e-5693-a209-14ed1b1afad3&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.5
2023-07-04 14:31:09,851 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7fb2613ad490>: Failed to establish a new connection: [Errno 61] Connection
refused')':
/cxservices/api/v1/chimerax/updates?uuid=484ff201-7e7e-5693-a209-14ed1b1afad3&OS=macosx&OSVersion=10.16&ChimeraXVersion=1.5
> open /Users/xueyang02/Downloads/designed_relaxed_pose1.pdb
Summary of feedback from opening
/Users/xueyang02/Downloads/designed_relaxed_pose1.pdb
---
warnings | Ignored bad PDB record found on line 3684
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 3685
#BEGIN_POSE_ENERGIES_TABLE expected_outputs/designed_relaxed_pose1.pdb
Ignored bad PDB record found on line 3686
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13
coordinate_constraint omega fa_dun p_aa_pp yhh_planarity ref rama_prepro
cart_bonded total
Ignored bad PDB record found on line 3687
weights 1 0.55 1 0.005 1 1 1 1 1 1 1 1.25 1 0.4 0.7 0.6 0.625 1 0.45 0.5 NA
Ignored bad PDB record found on line 3688
pose -1391.54 113.86 995.327 3.0392 58.5124 -32.1235 -410.162 -157.968 0
-3.47917 -69.1176 0 0 26.1662 360.78 -21.0192 0.16276 -20.0796 -15.2446
542.833 -20.0579
212 messages similar to the above omitted
Chain information for designed_relaxed_pose1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
> select /A:1-70
1263 atoms, 1278 bonds, 70 residues, 1 model selected
Alignment identifier is 1/A
> select /B:71-139
1186 atoms, 1187 bonds, 69 residues, 1 model selected
Alignment identifier is 1/B
> select /C:140-210
1222 atoms, 1223 bonds, 71 residues, 1 model selected
Alignment identifier is 1/C
> show sel atoms
> hide sel atoms
> select add #1
3671 atoms, 3688 bonds, 210 residues, 1 model selected
> select subtract #1
Nothing selected
> hbonds reveal true
252 hydrogen bonds found
> hbonds reveal true
252 hydrogen bonds found
> ~hbonds
> hide atoms
> select /A:1-70
1263 atoms, 1278 bonds, 70 residues, 1 model selected
> hbonds sel reveal true
98 hydrogen bonds found
> ~hbonds
[Repeated 1 time(s)]
> hide sel atoms
> select add #1
3671 atoms, 3688 bonds, 210 residues, 1 model selected
> select subtract #1
Nothing selected
> hbonds reveal true
252 hydrogen bonds found
> ~hbonds
> hide atoms
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for designed_relaxed_pose1.pdb_A SES surface #1.1: minimum,
-14.59, mean 1.05, maximum 36.78
Coulombic values for designed_relaxed_pose1.pdb_B SES surface #1.2: minimum,
-12.22, mean 0.06, maximum 14.15
Coulombic values for designed_relaxed_pose1.pdb_C SES surface #1.3: minimum,
-13.35, mean 0.42, maximum 17.89
To also show corresponding color key, enter the above coulombic command and
add key true
> color bypolymer
[Repeated 1 time(s)]
> color byhetero
> rainbow
> coulombic
Coulombic values for designed_relaxed_pose1.pdb_A SES surface #1.1: minimum,
-14.59, mean 1.05, maximum 36.78
Coulombic values for designed_relaxed_pose1.pdb_B SES surface #1.2: minimum,
-12.22, mean 0.06, maximum 14.15
Coulombic values for designed_relaxed_pose1.pdb_C SES surface #1.3: minimum,
-13.35, mean 0.42, maximum 17.89
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow
[Repeated 1 time(s)]
> mlp
Map values for surface "designed_relaxed_pose1.pdb_A SES surface": minimum
-25.16, mean -2.988, maximum 23.64
Map values for surface "designed_relaxed_pose1.pdb_B SES surface": minimum
-22.37, mean -1.242, maximum 24.44
Map values for surface "designed_relaxed_pose1.pdb_C SES surface": minimum
-23.67, mean -1.459, maximum 22.59
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 5J0J
Summary of feedback from opening 5J0J fetched from pdb
---
note | Fetching compressed mmCIF 5j0j from
http://files.rcsb.org/download/5j0j.cif
5j0j title:
De novo design of protein homo-oligomers with modular hydrogen bond network-
mediated specificity [more info...]
Chain information for 5j0j #2
---
Chain | Description
A B C | designed protein 2L6HC3_6
> select #2/A:2-71
1204 atoms, 1205 bonds, 70 residues, 1 model selected
> select #2/A:2-71
1204 atoms, 1205 bonds, 70 residues, 1 model selected
Alignment identifier is 2/A
> select clear
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
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 4 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 11.5.2 (20G95)
Kernel Version: Darwin 20.6.0
Time since boot: 118 days 22:49
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
HP E223:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
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-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-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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Two displays. I wonder if this is another flavor of the common QTabBar Mac crash.