![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8455 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-20.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [1656]
Path: /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.1.1 (1.1.1.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [1656]
User ID: 502
Date/Time: 2023-02-07 15:01:15.978 -0800
OS Version: macOS 11.2.3 (20D91)
Report Version: 12
Anonymous UUID: B79D706D-003A-84DD-775C-D1F559EF1D49
Time Awake Since Boot: 450000 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 0x00000000000000a9
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0xa9:
-->
__TEXT 103d90000-103d91000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff20471462 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff2049f610 pthread_kill + 263
2 libsystem_c.dylib 0x00007fff20381ba3 raise + 26
3 libsystem_platform.dylib 0x00007fff204e3d7d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x0000000103e08980 tupletraverse + 64
6 org.python.python 0x0000000103eee9a3 collect + 2083
7 org.python.python 0x0000000103eef14e _PyObject_GC_Alloc + 286
8 org.python.python 0x0000000103eef224 _PyObject_GC_New + 20
9 org.python.python 0x0000000103dd6900 PyList_New + 96
10 _cmsgpack.cpython-37m-darwin.so 0x000000010bb47725 int unpack_execute(unpack_context*, char const*, long, long*) + 437
11 _cmsgpack.cpython-37m-darwin.so 0x000000010bb4b69f __pyx_pw_7msgpack_9_cmsgpack_3unpackb(_object*, _object*, _object*) + 1711
12 org.python.python 0x0000000103dbdb34 PyCFunction_Call + 148
13 _serialize.cpython-37m-darwin.so 0x000000010bb10da1 __Pyx_PyObject_Call(_object*, _object*, _object*) + 97
14 _serialize.cpython-37m-darwin.so 0x000000010bb134c7 __pyx_f_4core_10_serialize__decode_bytes(_object*) + 247
15 _serialize.cpython-37m-darwin.so 0x000000010bb0825f __pyx_f_4core_10_serialize__decode_ext(int, _object*) + 671
16 _serialize.cpython-37m-darwin.so 0x000000010bb12f06 __pyx_pw_11cfunc_dot_to_py_42__Pyx_CFunc_object____int____bytes___to_py_1wrap(_object*, _object*, _object*) + 134
17 org.python.python 0x0000000103dbd112 _PyObject_FastCallDict + 354
18 org.python.python 0x0000000103dbea90 _PyObject_CallFunctionVa + 272
19 org.python.python 0x0000000103dbec4e _PyObject_CallFunction_SizeT + 142
20 _cmsgpack.cpython-37m-darwin.so 0x000000010bb47f97 int unpack_execute(unpack_context*, char const*, long, long*) + 2599
21 _cmsgpack.cpython-37m-darwin.so 0x000000010bb41050 __pyx_f_7msgpack_9_cmsgpack_8Unpacker__unpack(__pyx_obj_7msgpack_9_cmsgpack_Unpacker*, int (*)(unpack_context*, char const*, long, long*), __pyx_opt_args_7msgpack_9_cmsgpack_8Unpacker__unpack*) + 176
22 _cmsgpack.cpython-37m-darwin.so 0x000000010bb45f26 __pyx_pw_7msgpack_9_cmsgpack_8Unpacker_23__next__(_object*) + 38
23 org.python.python 0x0000000103e871a4 builtin_next + 100
24 org.python.python 0x0000000103dbe52d _PyMethodDef_RawFastCallKeywords + 653
25 org.python.python 0x0000000103dbd8b9 _PyCFunction_FastCallKeywords + 41
26 org.python.python 0x0000000103e92b60 call_function + 656
27 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
28 org.python.python 0x0000000103dbdd61 function_code_fastcall + 177
29 org.python.python 0x0000000103e92bd4 call_function + 772
30 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
31 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
32 org.python.python 0x0000000103dbd879 _PyFunction_FastCallKeywords + 217
33 org.python.python 0x0000000103e92bd4 call_function + 772
34 org.python.python 0x0000000103e895c4 _PyEval_EvalFrameDefault + 1396
35 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
36 org.python.python 0x0000000103dbd377 _PyFunction_FastCallDict + 455
37 org.python.python 0x0000000103e8fa3a _PyEval_EvalFrameDefault + 27114
38 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
39 org.python.python 0x0000000103dbd377 _PyFunction_FastCallDict + 455
40 org.python.python 0x0000000103dbe873 _PyObject_Call_Prepend + 131
41 org.python.python 0x0000000103dbd9d8 PyObject_Call + 136
42 org.python.python 0x0000000103e8fa3a _PyEval_EvalFrameDefault + 27114
43 org.python.python 0x0000000103dbdd61 function_code_fastcall + 177
44 org.python.python 0x0000000103e92bd4 call_function + 772
45 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
46 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
47 org.python.python 0x0000000103dbd377 _PyFunction_FastCallDict + 455
48 org.python.python 0x0000000103e8fa3a _PyEval_EvalFrameDefault + 27114
49 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
50 org.python.python 0x0000000103dbd879 _PyFunction_FastCallKeywords + 217
51 org.python.python 0x0000000103e92bd4 call_function + 772
52 org.python.python 0x0000000103e895c4 _PyEval_EvalFrameDefault + 1396
53 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
54 org.python.python 0x0000000103dbd377 _PyFunction_FastCallDict + 455
55 org.python.python 0x0000000103e8fa3a _PyEval_EvalFrameDefault + 27114
56 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
57 org.python.python 0x0000000103dbd879 _PyFunction_FastCallKeywords + 217
58 org.python.python 0x0000000103e92bd4 call_function + 772
59 org.python.python 0x0000000103e895c4 _PyEval_EvalFrameDefault + 1396
60 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
61 org.python.python 0x0000000103dbd879 _PyFunction_FastCallKeywords + 217
62 org.python.python 0x0000000103e92bd4 call_function + 772
63 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
64 org.python.python 0x0000000103dbdd61 function_code_fastcall + 177
65 org.python.python 0x0000000103e92bd4 call_function + 772
66 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
67 org.python.python 0x0000000103dbdd61 function_code_fastcall + 177
68 org.python.python 0x0000000103dbe873 _PyObject_Call_Prepend + 131
69 org.python.python 0x0000000103dbd9d8 PyObject_Call + 136
70 sip.so 0x0000000113b51f7a call_method + 76
71 sip.so 0x0000000113b4dc40 sip_api_call_method + 136
72 QtWidgets.so 0x00000001109dc45b sipQApplication::event(QEvent*) + 123
73 QtWidgets 0x0000000110e1c67d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
74 QtWidgets 0x0000000110e1da82 QApplication::notify(QObject*, QEvent*) + 594
75 QtWidgets.so 0x00000001109dc3ca sipQApplication::notify(QObject*, QEvent*) + 234
76 QtCore 0x0000000111b08324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
77 QtGui 0x00000001113eff7e QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*) + 414
78 QtGui 0x00000001113d7061 QWindowSystemInterface::handleFileOpenEvent(QString const&) + 65
79 libqcocoa.dylib 0x000000011b9eca10 0x11b9b4000 + 231952
80 com.apple.AppKit 0x00007fff23221f59 withWindowOrderingObserverHeuristic + 473
81 com.apple.AppKit 0x00007fff23221ad2 -[NSApplication(NSAppleEventHandling) _openURLs:withCompletionHandler:] + 1279
82 com.apple.AppKit 0x00007fff230c9149 __69-[NSApplication(NSAppleEventHandling) _handleAEOpenDocumentsForURLs:]_block_invoke + 887
83 com.apple.AppKit 0x00007fff230c8d47 -[NSApplication(NSAppleEventHandling) _handleAEOpenDocumentsForURLs:] + 236
84 com.apple.AppKit 0x00007fff22dbb713 -[NSApplication(NSAppleEventHandling) _handleCoreEvent:withReplyEvent:] + 741
85 com.apple.Foundation 0x00007fff212f8056 -[NSAppleEventManager dispatchRawAppleEvent:withRawReply:handlerRefCon:] + 308
86 com.apple.Foundation 0x00007fff212f7ec6 _NSAppleEventManagerGenericHandler + 80
87 com.apple.AE 0x00007fff26375ed9 0x7fff26369000 + 52953
88 com.apple.AE 0x00007fff263755f4 0x7fff26369000 + 50676
89 com.apple.AE 0x00007fff2636e260 aeProcessAppleEvent + 452
90 com.apple.HIToolbox 0x00007fff2882f5a2 AEProcessAppleEvent + 54
91 com.apple.AppKit 0x00007fff22db5e3e _DPSNextEvent + 2048
92 com.apple.AppKit 0x00007fff22db4177 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366
93 com.apple.AppKit 0x00007fff22da668a -[NSApplication run] + 586
94 libqcocoa.dylib 0x000000011b9e9de3 0x11b9b4000 + 220643
95 QtCore 0x0000000111b0393f QEventLoop::exec(QFlags) + 431
96 QtCore 0x0000000111b08932 QCoreApplication::exec() + 130
97 QtWidgets.so 0x0000000110acb7d2 meth_QApplication_exec_(_object*, _object*) + 82
98 org.python.python 0x0000000103dbe382 _PyMethodDef_RawFastCallKeywords + 226
99 org.python.python 0x0000000103dbd8b9 _PyCFunction_FastCallKeywords + 41
100 org.python.python 0x0000000103e92b60 call_function + 656
101 org.python.python 0x0000000103e8f817 _PyEval_EvalFrameDefault + 26567
102 org.python.python 0x0000000103dbdd61 function_code_fastcall + 177
103 org.python.python 0x0000000103e92bd4 call_function + 772
104 org.python.python 0x0000000103e8f817 _PyEval_EvalFrameDefault + 26567
105 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
106 org.python.python 0x0000000103dbd879 _PyFunction_FastCallKeywords + 217
107 org.python.python 0x0000000103e92bd4 call_function + 772
108 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
109 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
110 org.python.python 0x0000000103e88fb0 PyEval_EvalCode + 48
111 org.python.python 0x0000000103e86547 builtin_exec + 583
112 org.python.python 0x0000000103dbe52d _PyMethodDef_RawFastCallKeywords + 653
113 org.python.python 0x0000000103dbd8b9 _PyCFunction_FastCallKeywords + 41
114 org.python.python 0x0000000103e92b60 call_function + 656
115 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
116 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
117 org.python.python 0x0000000103dbd879 _PyFunction_FastCallKeywords + 217
118 org.python.python 0x0000000103e92bd4 call_function + 772
119 org.python.python 0x0000000103e8f8ae _PyEval_EvalFrameDefault + 26718
120 org.python.python 0x0000000103e93a2c _PyEval_EvalCodeWithName + 3276
121 org.python.python 0x0000000103dbd377 _PyFunction_FastCallDict + 455
122 org.python.python 0x0000000103eedaf3 pymain_run_module + 147
123 org.python.python 0x0000000103eecbdc pymain_main + 5900
124 org.python.python 0x0000000103eeb4c3 Py_Main + 51
125 edu.ucsf.cgl.ChimeraX 0x0000000103d90dc8 main + 120
126 libdyld.dylib 0x00007fff204ba621 start + 1
Thread 1:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff20597bf7 __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff205962ca __CFRunLoopRun + 1315
4 com.apple.CoreFoundation 0x00007fff205956ce CFRunLoopRunSpecific + 563
5 com.apple.AppKit 0x00007fff22f3b7c6 _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 2:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e22f 0x1143bc000 + 35267119
4 QtWebEngineCore 0x000000011651205d 0x1143bc000 + 34955357
5 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
6 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 3:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff2046f7e2 kevent + 10
1 QtWebEngineCore 0x000000011681f9a9 0x1143bc000 + 38156713
2 QtWebEngineCore 0x000000011681ccbd 0x1143bc000 + 38145213
3 QtWebEngineCore 0x00000001165d3cdc 0x1143bc000 + 35749084
4 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
5 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
6 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
7 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 4:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff2046f7e2 kevent + 10
1 QtWebEngineCore 0x000000011681f9a9 0x1143bc000 + 38156713
2 QtWebEngineCore 0x000000011681ccbd 0x1143bc000 + 38145213
3 QtWebEngineCore 0x00000001165d3cc4 0x1143bc000 + 35749060
4 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
5 QtWebEngineCore 0x000000011657ca74 0x1143bc000 + 35392116
6 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 5:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x00000001165762c4 0x1143bc000 + 35365572
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 6:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x00000001165762c4 0x1143bc000 + 35365572
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 7:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 8:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff2046f7e2 kevent + 10
1 QtWebEngineCore 0x000000011681f9a9 0x1143bc000 + 38156713
2 QtWebEngineCore 0x000000011681ccbd 0x1143bc000 + 38145213
3 QtWebEngineCore 0x00000001165d3cc4 0x1143bc000 + 35749060
4 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
5 QtWebEngineCore 0x0000000115ea9fe4 0x1143bc000 + 28237796
6 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 9:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e22f 0x1143bc000 + 35267119
4 QtWebEngineCore 0x0000000116575d1a 0x1143bc000 + 35364122
5 QtWebEngineCore 0x00000001165763bf 0x1143bc000 + 35365823
6 QtWebEngineCore 0x0000000116576264 0x1143bc000 + 35365476
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 10:: CompositorTileWorker1/57091
0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254
2 QtWebEngineCore 0x00000001165cbfa8 0x1143bc000 + 35717032
3 QtWebEngineCore 0x00000001175524c8 0x1143bc000 + 51995848
4 QtWebEngineCore 0x000000011658c694 0x1143bc000 + 35456660
5 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
6 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 11:: AudioThread
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e22f 0x1143bc000 + 35267119
4 QtWebEngineCore 0x000000011651205d 0x1143bc000 + 34955357
5 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
6 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e22f 0x1143bc000 + 35267119
4 QtWebEngineCore 0x000000011651205d 0x1143bc000 + 34955357
5 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
6 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 13:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x0000000116512052 0x1143bc000 + 34955346
4 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
5 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
6 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
7 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 14:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff2046f7e2 kevent + 10
1 QtWebEngineCore 0x000000011681f9a9 0x1143bc000 + 38156713
2 QtWebEngineCore 0x000000011681ccbd 0x1143bc000 + 38145213
3 QtWebEngineCore 0x00000001165d3cdc 0x1143bc000 + 35749084
4 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
5 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
6 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
7 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 15:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e22f 0x1143bc000 + 35267119
4 QtWebEngineCore 0x0000000116575d1a 0x1143bc000 + 35364122
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x0000000116576324 0x1143bc000 + 35365668
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e22f 0x1143bc000 + 35267119
4 QtWebEngineCore 0x000000011651205d 0x1143bc000 + 34955357
5 QtWebEngineCore 0x000000011653b085 0x1143bc000 + 35123333
6 QtWebEngineCore 0x000000011658d9bc 0x1143bc000 + 35461564
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 17:
0 libsystem_kernel.dylib 0x00007fff2046af86 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff2049d07c cthread_yield + 11
2 libopenblasp-r0.3.7.dylib 0x00000001056bac05 blas_thread_server + 565
3 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 18:
0 libsystem_kernel.dylib 0x00007fff2046af86 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff2049d07c cthread_yield + 11
2 libopenblasp-r0.3.7.dylib 0x00000001056bac05 blas_thread_server + 565
3 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254
2 libopenblasp-r0.3.7.dylib 0x00000001056bac3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 20:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 21:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254
2 QtCore 0x00000001119488ab 0x11191e000 + 174251
3 QtCore 0x000000011194880c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x0000000111047762 0x110e0c000 + 2340706
5 QtCore 0x00000001119400b3 0x11191e000 + 139443
6 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 22:
0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0
Thread 23:
0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0
Thread 24:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254
2 QtCore 0x00000001119488ab 0x11191e000 + 174251
3 QtCore 0x000000011194880c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x0000000111047762 0x110e0c000 + 2340706
5 QtCore 0x00000001119400b3 0x11191e000 + 139443
6 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 25:
0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0
Thread 26:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 27:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x00000001165763bf 0x1143bc000 + 35365823
6 QtWebEngineCore 0x00000001165762c4 0x1143bc000 + 35365572
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 28:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60
2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373
3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617
4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136
5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491
6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428
7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031
8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15
Thread 29:
0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0
Thread 30:
0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010bf51e00 rcx: 0x00007fbdd805fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fbdd805fa80 rsp: 0x00007fbdd805fa58
r8: 0x00007fbdd805ff48 r9: 0xc19c27be4b361c66 r10: 0x000000010bf51e00 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x000000012bc61320 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff20471462 rfl: 0x0000000000000246 cr2: 0x0000000103ff8fa4
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream:
48 8b 40 18 4a 8b 1c e8-48 ff 03 48 89 df 4c 89 H.@.J...H..H..L.
fe 4c 89 f2 4c 89 e1 31-c0 e8 72 e9 ec ff 48 85 .L..L..1..r...H.
c0 74 9d 48 ff 08 74 b8-48 ff 0b 74 a0 49 ff c5 .t.H..t.H..t.I..
48 8d 05 39 a0 12 00 48-8b 80 88 02 00 00 4c 3b H..9...H......L;
68 10 7c bc 49 ff 0c 24-74 24 48 83 c4 08 5b 41 h.|.I..$t$H...[A
5c 41 5d 41 5e 41 5f 5d-c3 31 ff 48 83 c4 08 5b \A]A^A_].1.H...[
41 5c 41 5d 41 5e 41 5f-5d e9 f2 8e fb ff 49 8b A\A]A^A_].....I.
44 24 08 4c 89 e7 48 83-c4 08 5b 41 5c 41 5d 41 D$.L..H...[A\A]A
5e 41 5f 5d ff 60 30 66-0f 1f 84 00 00 00 00 00 ^A_].`0f........
55 48 89 e5 53 50 48 8b-47 08[f6]80 a9 00 00 00 UH..SPH.G....... /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
0x103d9a000 - 0x103f95fff +org.python.python (3.7.8, [c] 2001-2019 Python Software Foundation. - 3.7.8) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/Python
0x104317000 - 0x104318fff +_heapq.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_heapq.cpython-37m-darwin.so
0x1043e1000 - 0x1043e4fff +zlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/zlib.cpython-37m-darwin.so
0x1043ee000 - 0x104402fff +libz.1.2.11.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libz.1.2.11.dylib
0x10444c000 - 0x10444dfff +_bz2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bz2.cpython-37m-darwin.so
0x104456000 - 0x104459fff +_lzma.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_lzma.cpython-37m-darwin.so
0x104464000 - 0x104464fff +grp.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/grp.cpython-37m-darwin.so
0x1044ac000 - 0x1044b1fff +math.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/math.cpython-37m-darwin.so
0x1044bd000 - 0x1044bffff +_hashlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_hashlib.cpython-37m-darwin.so
0x1044c9000 - 0x104526fff +libssl.1.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libssl.1.1.dylib
0x104555000 - 0x10471cfff +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libcrypto.1.1.dylib
0x1047b5000 - 0x1047bafff +_blake2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_blake2.cpython-37m-darwin.so
0x1047c4000 - 0x1047d4fff +_sha3.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_sha3.cpython-37m-darwin.so
0x1047df000 - 0x1047dffff +_bisect.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bisect.cpython-37m-darwin.so
0x1047e7000 - 0x1047e8fff +_random.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_random.cpython-37m-darwin.so
0x1048b0000 - 0x1048b6fff +_json.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_json.cpython-37m-darwin.so
0x1048ff000 - 0x10490cfff +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so
0x104922000 - 0x10492bfff +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so
0x10497d000 - 0x104980fff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so
0x10498b000 - 0x10498ffff +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so
0x10499d000 - 0x1049a1fff +binascii.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/binascii.cpython-37m-darwin.so
0x104aaa000 - 0x104ab8fff +_datetime.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_datetime.cpython-37m-darwin.so
0x104b08000 - 0x104b08fff +_scproxy.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_scproxy.cpython-37m-darwin.so
0x104b10000 - 0x104b4efff +_decimal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_decimal.cpython-37m-darwin.so
0x104bb2000 - 0x104bdffff +pyexpat.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/pyexpat.cpython-37m-darwin.so
0x104bf7000 - 0x104bf8fff +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so
0x104cc1000 - 0x104cc2fff +_posixsubprocess.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_posixsubprocess.cpython-37m-darwin.so
0x104d0a000 - 0x104d1cfff +_pickle.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_pickle.cpython-37m-darwin.so
0x104d6d000 - 0x104d70fff +_csv.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_csv.cpython-37m-darwin.so
0x104efb000 - 0x10525efff +_multiarray_umath.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so
0x105384000 - 0x108deffff +libopenblasp-r0.3.7.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libopenblasp-r0.3.7.dylib
0x1090f9000 - 0x109210fff +libgfortran.3.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x10927e000 - 0x1092b4fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x1092c8000 - 0x1092ddfff +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x10b46d000 - 0x10b47afff +_multiarray_tests.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_tests.cpython-37m-darwin.so
0x10b490000 - 0x10b4a2fff +_ctypes.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so
0x10b539000 - 0x10b53afff +lapack_lite.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/lapack_lite.cpython-37m-darwin.so
0x10b542000 - 0x10b55bfff +_umath_linalg.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/_umath_linalg.cpython-37m-darwin.so
0x10b62f000 - 0x10b640fff +_pocketfft_internal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/fft/_pocketfft_internal.cpython-37m-darwin.so
0x10b6c9000 - 0x10b734fff +mtrand.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/mtrand.cpython-37m-darwin.so
0x10b78f000 - 0x10b7acfff +_bit_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bit_generator.cpython-37m-darwin.so
0x10b7cd000 - 0x10b7fcfff +_common.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_common.cpython-37m-darwin.so
0x10b817000 - 0x10b86bfff +_bounded_integers.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bounded_integers.cpython-37m-darwin.so
0x10b893000 - 0x10b8a5fff +_mt19937.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_mt19937.cpython-37m-darwin.so
0x10b8b6000 - 0x10b8c2fff +_philox.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_philox.cpython-37m-darwin.so
0x10b8d2000 - 0x10b8dcfff +_pcg64.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_pcg64.cpython-37m-darwin.so
0x10b8ec000 - 0x10b8f3fff +_sfc64.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_sfc64.cpython-37m-darwin.so
0x10b902000 - 0x10b984fff +_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_generator.cpython-37m-darwin.so
0x10bae4000 - 0x10bae5fff +_appdirs.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/_appdirs.so
0x10baed000 - 0x10baeefff +libappdirs.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libappdirs.dylib
0x10baf6000 - 0x10bb17fff +_serialize.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/_serialize.cpython-37m-darwin.so
0x10bb37000 - 0x10bb4ffff +_cmsgpack.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/msgpack/_cmsgpack.cpython-37m-darwin.so
0x10bba8000 - 0x10bc03fff +_imaging.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PIL/_imaging.cpython-37m-darwin.so
0x10bc32000 - 0x10bc6afff +libjpeg.9.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/PIL/.dylibs/libjpeg.9.dylib
0x10bc80000 - 0x10bcf6fff +libopenjp2.2.3.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/PIL/.dylibs/libopenjp2.2.3.1.dylib
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0x7fff31abb000 - 0x7fff31ae8fff com.apple.CoreAuthentication.SharedUtils (1.0 - 827.80.7) /System/Library/Frameworks/LocalAuthentication.framework/Support/SharedUtils.framework/Versions/A/SharedUtils
0x7fff31b61000 - 0x7fff31ba2fff com.apple.CoreHaptics (1.0 - 1) /System/Library/Frameworks/CoreHaptics.framework/Versions/A/CoreHaptics
0x7fff31bb0000 - 0x7fff31beffff com.apple.AppleVPAFramework (3.21.1 - 3.21.1) /System/Library/PrivateFrameworks/AppleVPA.framework/Versions/A/AppleVPA
0x7fff31cc0000 - 0x7fff31cfcfff com.apple.DebugSymbols (195.1 - 195.1) /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
0x7fff31cfd000 - 0x7fff31dbafff com.apple.CoreSymbolication (12.2 - 64541.4) /System/Library/PrivateFrameworks/CoreSymbolication.framework/Versions/A/CoreSymbolication
0x7fff31dbb000 - 0x7fff31dc4fff com.apple.CoreTime (284) /System/Library/PrivateFrameworks/CoreTime.framework/Versions/A/CoreTime
0x7fff31dc5000 - 0x7fff31e3cfff com.apple.Rapport (2.3.0 - 230.1) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport
0x7fff32685000 - 0x7fff326d2fff com.apple.coreduetcontext (1.0 - 1) /System/Library/PrivateFrameworks/CoreDuetContext.framework/Versions/A/CoreDuetContext
0x7fff326d3000 - 0x7fff32c50fff com.apple.Intents (1.0 - 1) /System/Library/Frameworks/Intents.framework/Versions/A/Intents
0x7fff32c51000 - 0x7fff32cb4fff com.apple.framework.Apple80211 (17.0 - 1728) /System/Library/PrivateFrameworks/Apple80211.framework/Versions/A/Apple80211
0x7fff32cb5000 - 0x7fff32e07fff com.apple.CoreWiFi (3.0 - 341) /System/Library/PrivateFrameworks/CoreWiFi.framework/Versions/A/CoreWiFi
0x7fff32e08000 - 0x7fff32e20fff com.apple.BackBoardServices (1.0 - 1.0) /System/Library/PrivateFrameworks/BackBoardServices.framework/Versions/A/BackBoardServices
0x7fff32e21000 - 0x7fff32e58fff com.apple.LDAPFramework (2.4.28 - 194.5) /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
0x7fff32e59000 - 0x7fff32e5afff com.apple.TrustEvaluationAgent (2.0 - 35) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff32e5b000 - 0x7fff32f5efff libcrypto.44.dylib (56.60.2) /usr/lib/libcrypto.44.dylib
0x7fff32f5f000 - 0x7fff32f8cfff libssl.46.dylib (56.60.2) /usr/lib/libssl.46.dylib
0x7fff32f8d000 - 0x7fff3303cfff com.apple.DiskImagesFramework (595.40.1 - 595.40.1) /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages
0x7fff33074000 - 0x7fff33083fff com.apple.xpc.RemoteServiceDiscovery (1.0 - 2038.80.3) /System/Library/PrivateFrameworks/RemoteServiceDiscovery.framework/Versions/A/RemoteServiceDiscovery
0x7fff33084000 - 0x7fff3309bfff com.apple.xpc.RemoteXPC (1.0 - 2038.80.3) /System/Library/PrivateFrameworks/RemoteXPC.framework/Versions/A/RemoteXPC
0x7fff330e3000 - 0x7fff330e6fff com.apple.help (1.3.8 - 71) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
0x7fff330e7000 - 0x7fff330eefff com.apple.EFILogin (2.0 - 2) /System/Library/PrivateFrameworks/EFILogin.framework/Versions/A/EFILogin
0x7fff330ef000 - 0x7fff330fafff libcsfde.dylib (554) /usr/lib/libcsfde.dylib
0x7fff330fb000 - 0x7fff33160fff libcurl.4.dylib (121.40.2) /usr/lib/libcurl.4.dylib
0x7fff33161000 - 0x7fff33168fff com.apple.LoginUICore (4.0 - 4.0) /System/Library/PrivateFrameworks/LoginUIKit.framework/Versions/A/Frameworks/LoginUICore.framework/Versions/A/LoginUICore
0x7fff33169000 - 0x7fff331ccfff com.apple.AppSupport (1.0.0 - 29) /System/Library/PrivateFrameworks/AppSupport.framework/Versions/A/AppSupport
0x7fff3326d000 - 0x7fff3331ffff com.apple.GameController (1.0 - 1) /System/Library/Frameworks/GameController.framework/Versions/A/GameController
0x7fff33328000 - 0x7fff33328fff com.apple.ApplicationServices (48 - 50) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x7fff334e5000 - 0x7fff33524fff com.apple.AppleIDSSOAuthentication (1.0 - 1) /System/Library/PrivateFrameworks/AppleIDSSOAuthentication.framework/Versions/A/AppleIDSSOAuthentication
0x7fff33629000 - 0x7fff33629fff libHeimdalProxy.dylib (79) /System/Library/Frameworks/Kerberos.framework/Versions/A/Libraries/libHeimdalProxy.dylib
0x7fff336dc000 - 0x7fff336dcfff com.apple.audio.units.AudioUnit (1.14 - 1.14) /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
0x7fff33701000 - 0x7fff33743fff com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff33744000 - 0x7fff33764fff com.apple.DuetActivityScheduler (1.0 - 1) /System/Library/PrivateFrameworks/DuetActivityScheduler.framework/Versions/A/DuetActivityScheduler
0x7fff33778000 - 0x7fff33785fff com.apple.IntentsFoundation (1.0 - 1) /System/Library/PrivateFrameworks/IntentsFoundation.framework/Versions/A/IntentsFoundation
0x7fff33786000 - 0x7fff3378bfff com.apple.PushKit (1.0 - 1) /System/Library/Frameworks/PushKit.framework/Versions/A/PushKit
0x7fff3378c000 - 0x7fff337c2fff com.apple.C2 (1.3 - 569) /System/Library/PrivateFrameworks/C2.framework/Versions/A/C2
0x7fff337c3000 - 0x7fff337f4fff com.apple.QuickLookThumbnailing (1.0 - 135.1) /System/Library/Frameworks/QuickLookThumbnailing.framework/Versions/A/QuickLookThumbnailing
0x7fff337f5000 - 0x7fff34002fff com.apple.vision.EspressoFramework (1.0 - 256.2.2) /System/Library/PrivateFrameworks/Espresso.framework/Versions/A/Espresso
0x7fff34003000 - 0x7fff3401afff com.apple.ANEServices (4.52 - 4.52) /System/Library/PrivateFrameworks/ANEServices.framework/Versions/A/ANEServices
0x7fff34137000 - 0x7fff34139fff com.apple.CoreDuetDebugLogging (1.0 - 1) /System/Library/PrivateFrameworks/CoreDuetDebugLogging.framework/Versions/A/CoreDuetDebugLogging
0x7fff3413a000 - 0x7fff34147fff com.apple.CoreDuetDaemonProtocol (1.0 - 1) /System/Library/PrivateFrameworks/CoreDuetDaemonProtocol.framework/Versions/A/CoreDuetDaemonProtocol
0x7fff34693000 - 0x7fff346e3fff com.apple.ChunkingLibrary (334 - 334) /System/Library/PrivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary
0x7fff34f95000 - 0x7fff34f97fff com.apple.ConstantClasses (1.0 - 1) /System/Library/PrivateFrameworks/ConstantClasses.framework/Versions/A/ConstantClasses
0x7fff34faf000 - 0x7fff34fc5fff com.apple.CoreML.AppleNeuralEngine (1.0 - 1) /System/Library/PrivateFrameworks/AppleNeuralEngine.framework/Versions/A/AppleNeuralEngine
0x7fff35019000 - 0x7fff35085fff com.apple.audio.midi.CoreMIDI (2.0 - 88) /System/Library/Frameworks/CoreMIDI.framework/Versions/A/CoreMIDI
0x7fff3512b000 - 0x7fff3512efff com.apple.Cocoa (6.11 - 23) /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
0x7fff35179000 - 0x7fff35557fff com.apple.AppleMediaServices (1.0 - 1) /System/Library/PrivateFrameworks/AppleMediaServices.framework/Versions/A/AppleMediaServices
0x7fff35ca3000 - 0x7fff35caafff com.apple.DisplayServicesFW (3.1 - 380) /System/Library/PrivateFrameworks/DisplayServices.framework/Versions/A/DisplayServices
0x7fff3650b000 - 0x7fff3653bfff libtidy.A.dylib (18.1) /usr/lib/libtidy.A.dylib
0x7fff3653c000 - 0x7fff3655dfff com.apple.MarkupUI (1.0 - 383.3) /System/Library/PrivateFrameworks/MarkupUI.framework/Versions/A/MarkupUI
0x7fff3655e000 - 0x7fff36571fff com.apple.Engram (1.0 - 1) /System/Library/PrivateFrameworks/Engram.framework/Versions/A/Engram
0x7fff36572000 - 0x7fff3658dfff com.apple.openscripting (1.7 - 190) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x7fff3658e000 - 0x7fff36591fff com.apple.securityhi (9.0 - 55008) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x7fff36592000 - 0x7fff36595fff com.apple.ink.framework (10.15 - 227) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x7fff36596000 - 0x7fff36599fff com.apple.CommonPanels (1.2.6 - 101) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
0x7fff3659a000 - 0x7fff365a1fff com.apple.ImageCapture (1708.1 - 1708.1) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x7fff365a2000 - 0x7fff3784afff com.apple.JavaScriptCore (16610 - 16610.4.3.1.7) /System/Library/Frameworks/JavaScriptCore.framework/Versions/A/JavaScriptCore
0x7fff378b5000 - 0x7fff3799cfff com.apple.audio.AVFAudio (1.0 - 477.11) /System/Library/Frameworks/AVFoundation.framework/Versions/A/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x7fff3799d000 - 0x7fff37ab0fff com.apple.AVFCapture (1.0 - 80.20.5) /System/Library/PrivateFrameworks/AVFCapture.framework/Versions/A/AVFCapture
0x7fff37ab1000 - 0x7fff37b45fff com.apple.Quagga (47 - 47) /System/Library/PrivateFrameworks/Quagga.framework/Versions/A/Quagga
0x7fff37b46000 - 0x7fff37da1fff com.apple.CMCapture (1.0 - 80.20.5) /System/Library/PrivateFrameworks/CMCapture.framework/Versions/A/CMCapture
0x7fff387b4000 - 0x7fff387c3fff com.apple.HID (1.0 - 1) /System/Library/PrivateFrameworks/HID.framework/Versions/A/HID
0x7fff387c4000 - 0x7fff388ebfff com.apple.QuickLookUIFramework (5.0 - 928.2) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuickLookUI.framework/Versions/A/QuickLookUI
0x7fff38ee0000 - 0x7fff38ee0fff com.apple.marco (10.0 - 1000) /System/Library/PrivateFrameworks/Marco.framework/Versions/A/Marco
0x7fff39117000 - 0x7fff39123fff com.apple.KerberosHelper (4.0 - 1.0) /System/Library/PrivateFrameworks/KerberosHelper.framework/Versions/A/KerberosHelper
0x7fff3958f000 - 0x7fff39592fff com.apple.OSAServicesClient (1.0 - 1) /System/Library/PrivateFrameworks/OSAServicesClient.framework/Versions/A/OSAServicesClient
0x7fff395c6000 - 0x7fff395cdfff com.apple.URLFormatting (146 - 146.8) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff395ce000 - 0x7fff395ddfff com.apple.accessibility.AXCoreUtilities (1.0 - 1) /System/Library/PrivateFrameworks/AXCoreUtilities.framework/Versions/A/AXCoreUtilities
0x7fff395de000 - 0x7fff395f5fff libAccessibility.dylib (2885.15.7) /usr/lib/libAccessibility.dylib
0x7fff3c10c000 - 0x7fff3c11bfff com.apple.NetFS (6.0 - 4.0) /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
0x7fff3c33c000 - 0x7fff3c360fff com.apple.quicklook.QuickLookSupport (1.0 - 135.1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport
0x7fff3c361000 - 0x7fff3c3f8fff com.apple.AirPlaySync (1.0 - 2765.6.4.2) /System/Library/PrivateFrameworks/AirPlaySync.framework/Versions/A/AirPlaySync
0x7fff3d214000 - 0x7fff3d297fff com.apple.CorePDF (4.0 - 529) /System/Library/PrivateFrameworks/CorePDF.framework/Versions/A/CorePDF
0x7fff3d298000 - 0x7fff3d29bfff com.apple.print.framework.Print (15 - 271) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x7fff3d29c000 - 0x7fff3d29ffff com.apple.Carbon (160 - 164) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
0x7fff3d399000 - 0x7fff3d399fff com.apple.avfoundation (2.0 - 2005.3.4.1) /System/Library/Frameworks/AVFoundation.framework/Versions/A/AVFoundation
0x7fff3d524000 - 0x7fff3d543fff com.apple.private.SystemPolicy (1.0 - 1) /System/Library/PrivateFrameworks/SystemPolicy.framework/Versions/A/SystemPolicy
0x7fff3d695000 - 0x7fff3d6effff com.apple.AccessibilitySharedSupport (1.0 - 1) /System/Library/PrivateFrameworks/AccessibilitySharedSupport.framework/Versions/A/AccessibilitySharedSupport
0x7fff3d6f0000 - 0x7fff3d70dfff com.apple.sidecar-core (1.0 - 228) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff3d70e000 - 0x7fff3d715fff com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x7fff3db3e000 - 0x7fff3db44fff com.apple.FeatureFlagsSupport (1.0 - 28.60.1) /System/Library/PrivateFrameworks/FeatureFlagsSupport.framework/Versions/A/FeatureFlagsSupport
0x7fff3dcbc000 - 0x7fff3dcd3fff com.apple.SafariServices.framework (16610 - 16610.4.3.1.7) /System/Library/Frameworks/SafariServices.framework/Versions/A/SafariServices
0x7fff3de6d000 - 0x7fff3de78fff com.apple.MallocStackLogging (1.0 - 1) /System/Library/PrivateFrameworks/MallocStackLogging.framework/Versions/A/MallocStackLogging
0x7fff3de8e000 - 0x7fff3dea0fff libmis.dylib (274.60.2) /usr/lib/libmis.dylib
0x7fff3debd000 - 0x7fff3e02ffff com.apple.CoreHandwriting (161 - 1.2) /System/Library/PrivateFrameworks/CoreHandwriting.framework/Versions/A/CoreHandwriting
0x7fff3e030000 - 0x7fff3e28ffff com.apple.imageKit (3.0 - 1100) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/ImageKit
0x7fff3e290000 - 0x7fff3e3affff com.apple.PencilKit (1.0 - 1) /System/Library/Frameworks/PencilKit.framework/Versions/A/PencilKit
0x7fff3e3b0000 - 0x7fff3e3c1fff com.apple.sidecar-ui (1.0 - 228) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff3e9ab000 - 0x7fff3ea0dfff com.apple.ImageCaptureCore (1708.1 - 1708.1) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
0x7fff3ea0e000 - 0x7fff3ea34fff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters
0x7fff3f1db000 - 0x7fff3f30cfff com.apple.AnnotationKit (1.0 - 383.3) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit
0x7fff3f30d000 - 0x7fff3f7aefff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
0x7fff3f7af000 - 0x7fff3f89cfff com.apple.PDFKit (1.0 - 950.20.2) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit
0x7fff405c1000 - 0x7fff40644fff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput
0x7fff4165a000 - 0x7fff41663fff com.apple.IOAccelMemoryInfo (1.0 - 1) /System/Library/PrivateFrameworks/IOAccelMemoryInfo.framework/Versions/A/IOAccelMemoryInfo
0x7fff416bb000 - 0x7fff416befff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz
0x7fff41a9a000 - 0x7fff41ab8fff libCGInterfaces.dylib (544.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x7fff440a8000 - 0x7fff44321fff com.apple.RawCamera.bundle (9.10.0 - 1430) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x7fff46da9000 - 0x7fff46db4fff libGPUSupportMercury.dylib (18.1.1) /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
0x7fff48417000 - 0x7fff48466fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x7fff48734000 - 0x7fff48757fff com.apple.SMBClient (3.4 - 3.4) /System/Library/PrivateFrameworks/SMBClient.framework/Versions/A/SMBClient
0x7fff4f7e3000 - 0x7fff4f852fff com.apple.DCERPC (2.0 - 71) /System/Library/PrivateFrameworks/DCERPC.framework/Versions/A/DCERPC
0x7fff523a5000 - 0x7fff523d3fff com.apple.HelpData (2.3 - 200) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
0x7fff523d4000 - 0x7fff523eefff com.apple.shortcut (2.16 - 117) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff523ef000 - 0x7fff52481fff com.apple.Symbolication (12.2 - 64541.7.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x7fff54f6a000 - 0x7fff54fa1fff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x7fff565c5000 - 0x7fff565c8fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x7fff5f05b000 - 0x7fff5fa6efff libSC.dylib (4.2.15) /System/Library/Extensions/AMDShared.bundle/Contents/PlugIns/libSC.dylib
0x7fff6a580000 - 0x7fff6a584fff libmetal_timestamp.dylib (31001.161) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x7fff6c9ee000 - 0x7fff6c9f4fff libCoreFSCache.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6c9f5000 - 0x7fff6c9f9fff libCoreVMClient.dylib (177.22) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6c9fa000 - 0x7fff6ca09fff com.apple.opengl (18.1.1 - 18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6ca0a000 - 0x7fff6ca0cfff libCVMSPluginSupport.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6ca0d000 - 0x7fff6ca15fff libGFXShared.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6ca16000 - 0x7fff6ca49fff libGLImage.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6ca4a000 - 0x7fff6ca86fff libGLU.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6ca87000 - 0x7fff6cc1bfff libGLProgrammability.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6cc1c000 - 0x7fff6cc26fff libGL.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6cc27000 - 0x7fff6cda2fff GLEngine (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6cda3000 - 0x7fff6cdccfff GLRendererFloat (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6e05d000 - 0x7fff6e0b5fff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6ebff000 - 0x7fff6edbffff com.apple.AMDMTLBronzeDriver (4.2.15 - 4.0.2) /System/Library/Extensions/AMDMTLBronzeDriver.bundle/Contents/MacOS/AMDMTLBronzeDriver
0x7fff6ef38000 - 0x7fff6ef87fff ATIRadeonX4000SCLib.dylib (4.2.15) /System/Library/Extensions/AMDRadeonX4000GLDriver.bundle/Contents/MacOS/ATIRadeonX4000SCLib.dylib
0x7fff6f134000 - 0x7fff6f13bfff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff744ca000 - 0x7fff744d5fff com.apple.SymptomAnalytics (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff746f3000 - 0x7fff7470bfff com.apple.SymptomPresentationFeed (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff78222000 - 0x7fff78229fff libRosetta.dylib (203.30) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 11
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: 354607
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=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG backing stores 4608K 6
CG image 700K 33
CG raster data 316K 1
CoreAnimation 2060K 27
CoreGraphics 12K 2
CoreServices 624K 2
CoreUI image data 4220K 33
Foundation 36K 2
Kernel Alloc Once 8K 1
MALLOC 1.3G 132
MALLOC guard page 48K 10
MALLOC_LARGE (reserved) 24.6M 2 reserved VM address space (unallocated)
MALLOC_MEDIUM (reserved) 336.0M 4 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 120K 30
Stack 165.7M 31
Stack Guard 56.0M 1
VM_ALLOCATE 234.3M 500
__CTF 759 1
__DATA 41.3M 596
__DATA_CONST 21.0M 268
__DATA_DIRTY 1191K 165
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 513.9M 145
__OBJC_RO 60.5M 1
__OBJC_RW 2449K 2
__TEXT 537.1M 571
__UNICODE 588K 1
mapped file 261.6M 45
shared memory 48K 6
=========== ======= =======
TOTAL 3.8G 2631
TOTAL, minus reserved VM space 3.2G 2631
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/NativeGP_April15_2022_glycans_2510C.cxs
Log from Wed May 25 10:47:48 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs"
Log from Thu Apr 14 17:05:32 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs
Log from Tue Apr 12 22:31:49 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSEM.cxs" format session
Log from Tue Apr 12 22:19:12 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/haoyangli/Downloads/cryosparc_P34_J338_003_volume_map.mrc
Opened cryosparc_P34_J338_003_volume_map.mrc, grid size 256,256,256, pixel
1.7, shown at level 0.0358, step 1, values float32
> volume #1 level 0.132
> lighting soft
> vop gaussian #1 sdev 5.1
> lighting simple
> set bgColor white
> graphics silhouettes true
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting simple
> volume #2 level 0.1463
> volume #2 level 0.1738
> close session
> open /Users/haoyangli/Downloads/cryosparc_P34_J338_004_volume_map.mrc
Opened cryosparc_P34_J338_004_volume_map.mrc, grid size 256,256,256, pixel
1.7, shown at level 0.0334, step 1, values float32
> volume #1 level 0.1693
> vop flip #1 axis Z
> open "/Users/haoyangli/Google
> Drive/Phenix/20210626_LASV_LIV_FL_372DscFv_89FscFv_27A/RealSpaceRefine_37/GP_89F_035_real_space_refined_037.pdb"
> format pdb
Chain information for GP_89F_035_real_space_refined_037.pdb #3
---
Chain | Description
A B C | No description available
H | No description available
L | No description available
O Q S | No description available
P R T | No description available
a b c | No description available
> select #3
16782 atoms, 17250 bonds, 2086 residues, 1 model selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected atoms"
> volume #2 color #b2b2b287
> ui tool show "Fit in Map"
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
cryosparc_P34_J338_004_volume_map.mrc (#1) using 16782 atoms
average map value = 0.3944, steps = 144
shifted from previous position = 23.4
rotated from previous position = 29.2 degrees
atoms outside contour = 2799, contour level = 0.16929
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
cryosparc_P34_J338_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.69067126 -0.72237609 0.03385264 384.18231999
-0.65805864 0.60838594 -0.44365006 215.46441868
0.29988673 -0.32869336 -0.89556051 297.38624159
Axis 0.38724200 -0.89615983 0.21665915
Axis point 226.44252262 0.00000000 190.41112465
Rotation angle (degrees) 171.46404372
Shift along axis 20.11242331
> select /H:2-136
1048 atoms, 1077 bonds, 135 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /L:2-109
794 atoms, 811 bonds, 108 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "translate selected models"
> select #3
14940 atoms, 15362 bonds, 1843 residues, 1 model selected
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
cryosparc_P34_J338_004_volume_map.mrc (#1) using 14940 atoms
average map value = 0.4023, steps = 128
shifted from previous position = 29.5
rotated from previous position = 11.1 degrees
atoms outside contour = 2471, contour level = 0.16929
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
cryosparc_P34_J338_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.69705133 -0.70756218 0.11608274 375.00662146
-0.62124709 0.51514232 -0.59049170 238.64293114
0.35801046 -0.48371909 -0.79865158 304.49585974
Axis 0.38383654 -0.86970526 0.31029386
Axis point 228.31622372 0.00000000 209.40965166
Rotation angle (degrees) 172.00503731
Shift along axis 30.87542576
> ui mousemode right "rotate selected models"
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
cryosparc_P34_J338_004_volume_map.mrc (#1) using 14940 atoms
average map value = 0.405, steps = 268
shifted from previous position = 30.7
rotated from previous position = 44.3 degrees
atoms outside contour = 2480, contour level = 0.16929
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
cryosparc_P34_J338_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.49913481 -0.33264473 -0.80013245 369.11913823
-0.80043264 0.53069610 0.27869203 189.56109972
0.33192173 0.77955701 -0.53114859 98.81139685
Axis 0.37848450 -0.85545001 -0.35348942
Axis point 209.13813889 0.00000000 96.62329565
Rotation angle (degrees) 138.57250641
Shift along axis -57.38295523
> ui mousemode right "translate selected models"
> volume #1 level 0.1365
> close #1
> volume #2 level 0.04382
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
cryosparc_P34_J338_004_volume_map.mrc z flip (#2) using 14940 atoms
average map value = 0.5177, steps = 96
shifted from previous position = 2.41
rotated from previous position = 12.3 degrees
atoms outside contour = 14, contour level = 0.043823
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
cryosparc_P34_J338_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.70237571 -0.68484180 0.19406202 366.27148750
-0.71159044 0.68227881 -0.16773392 191.62360549
-0.01753320 -0.25590491 -0.96654294 341.83502139
Axis -0.38204662 0.91684624 -0.11590235
Axis point 233.83781508 0.00000000 171.51284623
Rotation angle (degrees) 173.37370831
Shift along axis -3.86288335
> volume #2 level 0.1371
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
cryosparc_P34_J338_004_volume_map.mrc z flip (#2) using 14940 atoms
average map value = 0.5177, steps = 40
shifted from previous position = 0.0312
rotated from previous position = 0.00331 degrees
atoms outside contour = 77, contour level = 0.13712
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
cryosparc_P34_J338_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.70241137 -0.68480229 0.19407241 366.25922596
-0.71155455 0.68231861 -0.16772431 191.61265797
-0.01756122 -0.25590456 -0.96654253 341.86731742
Axis -0.38202193 0.91685703 -0.11589839
Axis point 233.82910121 0.00000000 171.52625749
Rotation angle (degrees) 173.37257867
Shift along axis -3.85951704
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
cryosparc_P34_J338_004_volume_map.mrc z flip (#2) using 14940 atoms
average map value = 0.5177, steps = 44
shifted from previous position = 0.00948
rotated from previous position = 0.017 degrees
atoms outside contour = 77, contour level = 0.13712
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
cryosparc_P34_J338_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.70233399 -0.68495040 0.19382961 366.28538947
-0.71163610 0.68223226 -0.16772959 191.63622780
-0.01735036 -0.25573834 -0.96659033 341.82242339
Axis -0.38208865 0.91683464 -0.11585554
Axis point 233.83090473 0.00000000 171.52456066
Rotation angle (degrees) 173.38668645
Shift along axis -3.85677781
> sequence chain #3/A#3/B#3/C
Alignment identifier is 1
> color sel cornflower blue
> sequence chain #3/a#3/b#3/c
Alignment identifier is 2
> color sel hot pink
> color sel cornflower blue
> color sel hot pink
> color zone #2 near #1 distance 12
> color zone #3 near #2 distance 12
> color zone #2 near #3 distance 12
> select ::name="BMA"::name="FUC"::name="MAN"::name="NAG"
1062 atoms, 1111 bonds, 82 residues, 1 model selected
> color sel cornflower blue
> sequence chain #3/a#3/b#3/c
Alignment identifier is 1
> color sel cornflower blue
> sequence chain #3/O#3/Q#3/S
Alignment identifier is 2
> color sel orange
> sequence chain #3/P#3/R#3/T
Alignment identifier is 3
> color sel orange
> color zone #2 near #3 distance 12
> color zone #2 near #3 distance 15
> color zone #2 near #3 distance 10
> color zone #2 near #3 distance 13
> hide #3 models
> select #3
14940 atoms, 15362 bonds, 1843 residues, 1 model selected
> ~select #3
Nothing selected
> volume #2 level 0.3115
> color zone #2 near #3 distance 12
> color zone #2 near #3 distance 10
> volume #2 level 0.35
> lighting soft
> graphics silhouettes false
> vop gaussian #2 sdev 5.1
> color zone #1 near #3 distance 10
> volume #1 level 0.2347
> color zone #1 near #3 distance 12
> color zone #1 near #3 distance 12
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSEM.cxs" includeMaps true
opened ChimeraX session
> show #!2 models
> hide #!1 models
> color zone #2 near #3 distance 10
> color zone #2 near #3 distance 12
> color zone #2 near #3 distance 15
> color zone #2 near #3 distance 13
> volume #2 level 0.2514
> color zone #2 near #3 distance 15
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSEM.cxs" includeMaps true
opened ChimeraX session
> close #1-2
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain /O /Q /S
Alignment identifier is 1
> sequence chain /P /R /T
Alignment identifier is 2
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
> save
> /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs
> open
> /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc
Opened WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc, grid size 256,256,256, pixel
1.7, shown at level 0.0376, step 1, values float32
> volume #1 level 0.2164
> volume #1 color #b2b2b2fb
> volume #1 color #b2b2b2e9
> volume #1 color #b2b2b2bd
> volume #1 color #b2b2b274
> volume #1 color #b2b2b271
> volume #1 color #b2b2b26f
> volume #1 color #b2b2b26e
> volume #1 color #b2b2b26d
> volume #1 color #b2b2b26c
> volume #1 color #b2b2b26b
> volume #1 color #b2b2b26a
> volume #1 color #b2b2b268
> volume #1 color #b2b2b267
> volume #1 color #b2b2b262
> volume #1 color #b2b2b260
> volume #1 color #b2b2b261
> volume #1 color #b2b2b263
> volume #1 color #b2b2b265
> volume #1 color #b2b2b26b
> volume #1 color #b2b2b271
> volume #1 color #b2b2b276
> volume #1 color #b2b2b277
> volume #1 color #b2b2b278
> volume #1 color #b2b2b27d
> volume #1 color #b2b2b281
> volume #1 color #b2b2b284
> volume #1 color #b2b2b285
> volume #1 color #b2b2b287
> volume #1 color #b2b2b289
> volume #1 color #b2b2b28a
> volume #1 color #b2b2b28b
> volume #1 color #b2b2b28d
> volume #1 color #b2b2b28f
> volume #1 color #b2b2b294
> volume #1 color #b2b2b297
> volume #1 color #b2b2b29d
> volume #1 color #b2b2b2a1
> volume #1 color #b2b2b2a4
> select #3
9645 atoms, 9932 bonds, 1156 residues, 1 model selected
> select #1
2 models selected
> select #3
9645 atoms, 9932 bonds, 1156 residues, 1 model selected
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc (#1) using 9645 atoms
average map value = 0.5301, steps = 168
shifted from previous position = 14.6
rotated from previous position = 48.8 degrees
atoms outside contour = 762, contour level = 0.21641
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc (#1) coordinates:
Matrix rotation and translation
-0.98048923 -0.17332729 -0.09272815 336.81000333
0.18581598 -0.97114052 -0.14952759 356.22342895
-0.06413485 -0.16384056 0.98439981 166.19874474
Axis -0.03969608 -0.07930160 0.99605998
Axis point 155.01660267 200.31825196 0.00000000
Rotation angle (degrees) 169.61381710
Shift along axis 123.92479216
> ui mousemode right "rotate selected models"
> vop flip #1 axis Z
> select #2
2 models selected
> ui mousemode right "translate selected models"
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) using 9645 atoms
average map value = 0.5452, steps = 160
shifted from previous position = 7.36
rotated from previous position = 40.4 degrees
atoms outside contour = 660, contour level = 0.21641
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.64139211 0.75631872 -0.12883376 56.87855910
0.70209586 -0.64632118 -0.29888178 274.34396971
-0.30931788 0.10124677 -0.94555356 307.42004625
Axis 0.90468148 0.40807045 -0.12259665
Axis point 0.00000000 104.36813840 171.36502302
Rotation angle (degrees) 167.22380457
Shift along axis 125.71997824
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) using 9645 atoms
average map value = 0.5452, steps = 44
shifted from previous position = 0.00164
rotated from previous position = 0.00431 degrees
atoms outside contour = 660, contour level = 0.21641
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.64137799 0.75631940 -0.12890010 56.88582627
0.70207968 -0.64632504 -0.29891144 274.34784440
-0.30938388 0.10121708 -0.94553514 307.42941901
Axis 0.90467751 0.40806794 -0.12263423
Axis point 0.00000000 104.36745270 171.37191875
Rotation angle (degrees) 167.22374860
Shift along axis 125.71451854
> ~select #2
Nothing selected
> volume #1 color #b2b2b2a5
> volume #1 color #b2b2b2af
> volume #1 color #b2b2b2bf
> volume #1 color #b2b2b2d2
> volume #1 color #b2b2b2eb
> volume #1 color #b2b2b2
> select #2
2 models selected
> volume #2 color #b2b2b2a6
> volume #2 color #b2b2b2ad
> volume #2 color #b2b2b2c0
> volume #2 color #b2b2b2dc
> volume #2 color #b2b2b2fd
> volume #2 color #b2b2b2
> color zone #2 near #3 distance 10
> color zone #2 near #3 distance 15
> color zone #2 near #3 distance 13
> color zone #2 near #3 distance 15
> hide #3 models
> select clear
> vop gaussian #2 sdev 5.1
> volume #4 level 0.1778
> volume #4 color #b3b3b3
> color zone #4 near #3 distance 15
> color zone #4 near #3 distance 13
> color zone #4 near #3 distance 10
> color zone #4 near #3 distance 12
> color zone #4 near #3 distance 13
> volume #4 color #b3b3b3fc
> volume #4 color #b3b3b3f5
> volume #4 color #b3b3b3f1
> volume #4 color #b3b3b3e6
> volume #4 color #b3b3b3e0
> volume #4 color #b3b3b3da
> volume #4 color #b3b3b3d6
> volume #4 color #b3b3b3d5
> volume #4 color #b3b3b3d2
> volume #4 color #b3b3b3ce
> volume #4 color #b3b3b3c7
> volume #4 color #b3b3b3c2
> volume #4 color #b3b3b3bc
> volume #4 color #b3b3b3b9
> volume #4 color #b3b3b3b8
> volume #4 color #b3b3b3b7
> volume #4 color #b3b3b3ac
> volume #4 color #b3b3b3a5
> volume #4 color #b3b3b3a1
> volume #4 color #b3b3b3a0
> show #3 models
> select #3
9645 atoms, 9932 bonds, 1156 residues, 1 model selected
> volume #4 color #b3b3b3a1
> volume #4 color #b3b3b3a3
> volume #4 color #b3b3b3a9
> volume #4 color #b3b3b3b4
> volume #4 color #b3b3b3bd
> volume #4 color #b3b3b3d1
> volume #4 color #b3b3b3e4
> volume #4 color #b3b3b3f5
> volume #4 color #b3b3b3
> color zone #4 near #3 distance 13
> hide #3 models
> ~select #3
Nothing selected
> show #3 models
> volume #4 color #b3b3b3fe
> volume #4 color #b3b3b3f8
> volume #4 color #b3b3b3ef
> volume #4 color #b3b3b3e6
> volume #4 color #b3b3b3dd
> volume #4 color #b3b3b3cc
> volume #4 color #b3b3b3c4
> volume #4 color #b3b3b3bf
> volume #4 color #b3b3b3b8
> volume #4 color #b3b3b3b4
> volume #4 color #b3b3b3b1
> volume #4 color #b3b3b3ab
> volume #4 color #b3b3b3a7
> volume #4 color #b3b3b3a6
> volume #4 color #b3b3b3a4
> volume #4 color #b3b3b3a2
> volume #4 color #b3b3b39e
> color zone #4 near #3 distance 15
> select #3
9645 atoms, 9932 bonds, 1156 residues, 1 model selected
> color zone #4 near #3 distance 15
> hide #3 models
> color zone #4 near #3 distance 13
> color zone #4 near #3 distance 14
> color zone #4 near #3 distance 15
> volume #4 color #b3b3b3a8
> volume #4 color #b3b3b3be
> volume #4 color #b3b3b3d9
> volume #4 color #b3b3b3
> color zone #4 near #3 distance 15
> save
> /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs
> includeMaps true
opened ChimeraX session
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"
> close #1-2
> show #3 models
> hide #!4 models
> show #!4 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/5vk2_377H.pdb"
5vk2_377H.pdb title:
Structural basis for antibody-mediated neutralization of lassa virus [more
info...]
Chain information for 5vk2_377H.pdb #1
---
Chain | Description
A B C | pre-glycoprotein polyprotein GP complex
D F H | fab 37.7H heavy chain
E G L | fab 37.7H light chain
a b c | pre-glycoprotein polyprotein GP complex
Non-standard residues in 5vk2_377H.pdb #1
---
BMA — β-D-mannopyranose
FUC — α-L-fucopyranose
MAN — α-D-mannopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> mmaker #1/A to #3/A showAlignment true
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 GP_89F_035_real_space_refined_037.pdb, chain A (#3) with
5vk2_377H.pdb, chain A (#1), sequence alignment score = 1006.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 5vk2_377H.pdb #1/A,
GP_89F_035_real_space_refined_037.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 180 pruned atom pairs is 0.540 angstroms; (across all 186 pairs:
0.910)
> select #4
2 models selected
> select #3
9645 atoms, 9932 bonds, 1156 residues, 1 model selected
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc"
Opened WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc, grid size 256,256,256, pixel
1.7, shown at level 0.127, step 1, values float32
> select #2
2 models selected
> hide #!4 models
> hide #3 models
> ui mousemode right "rotate selected models"
> ui tool show "Fit in Map"
Fit map WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc in map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 167760 points
correlation = 0.663, correlation about mean = 0.2592, overlap = 1.605e+04
steps = 160, shift = 29.6, angle = 15.3 degrees
Position of WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc (#2) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates:
Matrix rotation and translation
0.70576768 -0.70799007 -0.02533847 223.08775843
-0.70843650 -0.70515209 -0.02963510 531.45132478
0.00311388 0.03886619 -0.99923957 421.83274303
Axis 0.92348968 -0.38357605 -0.00601857
Axis point 0.00000000 307.81922727 216.97963673
Rotation angle (degrees) 177.87451049
Shift along axis -0.37159010
> show #3 models
> hide #3 models
> show #!4 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> volume #4 level 0.1812
> volume #2 level 0.2904
> volume #2 color #b3b3b387
> vop flip #2 axis Z
> hide #!4 models
> select #4
2 models selected
> ~select #4
Nothing selected
> select #5
2 models selected
> vop gaussian #5 sdev 5.1
> select #6
2 models selected
> ui mousemode right "translate selected models"
Fit molecule 5vk2_377H.pdb (#1) to map
WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian (#6) using 18672
atoms
average map value = 0.4481, steps = 136
shifted from previous position = 22.8
rotated from previous position = 21.5 degrees
atoms outside contour = 618, contour level = 0.12427
Position of 5vk2_377H.pdb (#1) relative to
WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian (#6) coordinates:
Matrix rotation and translation
-0.46173942 -0.88060213 -0.10647345 226.76312435
-0.88456595 0.46604971 -0.01845904 132.15488486
0.06587699 0.08565952 -0.99414418 233.97249263
Axis 0.51697972 -0.85577135 -0.01968158
Axis point 146.39941073 -0.00000000 122.16150024
Rotation angle (degrees) 174.22058307
Shift along axis -0.46737797
> show #!5 models
Fit map WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip in map
WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian using 117889 points
correlation = 0.9917, correlation about mean = 0.8723, overlap = 2.621e+04
steps = 180, shift = 20.5, angle = 29.4 degrees
Position of WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip (#5) relative to
WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian (#6) coordinates:
Matrix rotation and translation
0.99999944 0.00105727 0.00007889 -0.23280697
-0.00105715 0.99999820 -0.00157322 0.56981858
-0.00008055 0.00157314 0.99999876 -0.09383230
Axis 0.82926089 0.04202061 -0.55727969
Axis point 0.00000000 101.31860533 365.20261645
Rotation angle (degrees) 0.10869527
Shift along axis -0.11682275
> ~select #6
Nothing selected
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> volume #5 level 0.1854
> close #6
> color zone #5 near #2 distance 12
> color zone #5 near #1 distance 12
> volume #5 level 0.2935
> color zone #5 near #1 distance 12
> volume #5 level 0.2661
> color zone #5 near #1 distance 15
> sequence chain #1/D#1/F#1/H
Alignment identifier is 1
> color sel orange red
> select #1/E#1/G#1/L
4749 atoms, 4875 bonds, 634 residues, 1 model selected
> color sel orange red
> color zone #5 near #1 distance 15
> color zone #5 near #1 distance 14
> hide #!1 models
> color zone #5 near #1 distance 12
> volume #5 level 0.3828
> color zone #5 near #1 distance 13
> color zone #5 near #1 distance 13
> volume #5 level 0.35
> volume #5 level 0.3
> color zone #5 near #1 distance 15
> volume #5 level 0.25
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"
> includeMaps true
> color zone #5 near #1 distance 16
> save /Users/haoyangli/Desktop/image5.png supersample 3
> color zone #5 near #1 distance 16
> color zone #5 near #1 distance 14
> color zone #5 near #1 distance 15
> save /Users/haoyangli/Desktop/image6.png supersample 3
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"
> includeMaps true
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_197E.cxs"
> includeMaps true
> close #1-2,5
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc"
Opened WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc, grid size 256,256,256, pixel
1.7, shown at level 0.138, step 1, values float32
> show #3 models
> ui tool show "Fit in Map"
Fit map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc in map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 167722 points
correlation = 0.6062, correlation about mean = 0.4046, overlap = 1.116e+04
steps = 808, shift = 45.9, angle = 84.1 degrees
Position of WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates:
Matrix rotation and translation
-0.99021450 -0.13955195 -0.00069218 462.65938569
0.13953390 -0.99014554 0.01192009 397.56536334
-0.00234883 0.01170687 0.99992871 -51.44987377
Axis -0.00076400 0.00593589 0.99998209
Axis point 217.36170723 215.15420106 0.00000000
Rotation angle (degrees) 171.97845737
Shift along axis -49.44251938
> show #!4 models
> volume #1 level 0.1842
> ui mousemode right "rotate selected models"
> select #1
2 models selected
Fit map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc in map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 147086 points
correlation = 0.6461, correlation about mean = 0.2283, overlap = 1.379e+04
steps = 416, shift = 30.3, angle = 44.2 degrees
Position of WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates:
Matrix rotation and translation
0.55459277 0.83209463 -0.00673578 -82.77771676
0.83039376 -0.55394428 -0.05993266 171.68729837
-0.05360089 0.02764487 -0.99817969 439.90905021
Axis 0.88156614 0.47174993 -0.01712122
Axis point 0.00000000 101.79137113 221.56736430
Rotation angle (degrees) 177.15285770
Shift along axis 0.48766077
> volume #1 color #999999
> volume #1 color #b3b3b3
> volume #1 level 0.2
> volume #1 color #b3b3b37f
> volume #1 color #b3b3b380
> hide #!4 models
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/12.1F_Fab.pdb"
Chain information for 12.1F_Fab.pdb #2
---
Chain | Description
H | No description available
L | No description available
> select #2
3344 atoms, 3296 bonds, 2 pseudobonds, 546 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 9645 atoms
average map value = 0.3369, steps = 84
shifted from previous position = 2.79
rotated from previous position = 12.1 degrees
atoms outside contour = 1593, contour level = 0.2
Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates:
Matrix rotation and translation
0.99011269 -0.12634234 -0.06094662 154.13611387
0.12777199 0.99159897 0.02014451 56.71830280
0.05788950 -0.02773261 0.99793773 131.98613278
Axis -0.16823518 -0.41757764 0.89293104
Axis point -577.75617756 1356.06792412 0.00000000
Rotation angle (degrees) 8.18051056
Shift along axis 68.23910360
Fit molecule 12.1F_Fab.pdb (#2) to map
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms
average map value = 0.4006, steps = 200
shifted from previous position = 46.4
rotated from previous position = 13.9 degrees
atoms outside contour = 325, contour level = 0.2
Position of 12.1F_Fab.pdb (#2) relative to
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates:
Matrix rotation and translation
-0.82175967 0.43583550 -0.36709466 -28.04937749
0.12218975 0.76400188 0.63353833 440.21967352
0.55657950 0.47576104 -0.68108055 -66.50171599
Axis -0.15966930 -0.93475055 -0.31740689
Axis point -24.90473847 0.00000000 -120.66840638
Rotation angle (degrees) 150.39121272
Shift along axis -385.90885256
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/12.1F_Fab.pdb"
Chain information for 12.1F_Fab.pdb #5
---
Chain | Description
H | No description available
L | No description available
> select #5
3344 atoms, 3296 bonds, 2 pseudobonds, 546 residues, 2 models selected
> ui mousemode right "translate selected models"
Fit molecule 12.1F_Fab.pdb (#5) to map
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms
average map value = 0.4019, steps = 304
shifted from previous position = 22.3
rotated from previous position = 108 degrees
atoms outside contour = 162, contour level = 0.2
Position of 12.1F_Fab.pdb (#5) relative to
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates:
Matrix rotation and translation
-0.77732189 -0.37326612 -0.50640209 25.97470394
0.03377099 0.77903999 -0.62606407 -8.51748442
0.62819599 -0.50375501 -0.59295927 5.69004618
Axis 0.10094918 -0.93645344 0.33595271
Axis point 12.26034921 0.00000000 5.76863493
Rotation angle (degrees) 142.71391108
Shift along axis 12.50993905
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecule 12.1F_Fab.pdb (#5) to map
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms
average map value = 0.3904, steps = 100
shifted from previous position = 20.8
rotated from previous position = 14.5 degrees
atoms outside contour = 289, contour level = 0.2
Position of 12.1F_Fab.pdb (#5) relative to
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates:
Matrix rotation and translation
0.41107464 -0.82451862 -0.38882735 153.38537500
0.85318879 0.19775456 0.48266142 476.67588214
-0.32107094 -0.53015300 0.78476192 471.27459800
Axis -0.51650775 -0.03455392 0.85558505
Axis point -128.67321405 470.57837099 0.00000000
Rotation angle (degrees) 78.65036600
Shift along axis 307.51974417
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/12.1F_Fab.pdb"
Chain information for 12.1F_Fab.pdb #6
---
Chain | Description
H | No description available
L | No description available
> select #6
3344 atoms, 3296 bonds, 2 pseudobonds, 546 residues, 2 models selected
Fit molecule 12.1F_Fab.pdb (#6) to map
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms
average map value = 0.4068, steps = 204
shifted from previous position = 22.5
rotated from previous position = 82.8 degrees
atoms outside contour = 320, contour level = 0.2
Position of 12.1F_Fab.pdb (#6) relative to
WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates:
Matrix rotation and translation
0.30197533 -0.84840729 -0.43475967 120.13084230
-0.78237386 0.04002208 -0.62152183 -102.52211603
0.54470363 0.52782886 -0.65168601 -57.53517381
Axis 0.76039013 -0.64799563 0.04368655
Axis point 0.00000000 19.24108198 -32.79209306
Rotation angle (degrees) 130.90784484
Shift along axis 155.26667653
> color zone #1 near #2 #3 #5 #6 distance 15
> color zone #1 near #2 #3 #5 #6 distance 15
> hide #!2 models
> hide #3 models
> hide #!5 models
> hide #!6 models
> ~select #6
Nothing selected
> save /Users/haoyangli/Desktop/image7.png supersample 3
> save /Users/haoyangli/Desktop/image8.png supersample 3
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_197E.cxs"
> includeMaps true
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_197E.cxs"
> includeMaps true
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_2510C.cxs"
> includeMaps true
> close #1
> close #5
> close #6
> close #2
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc"
Opened WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc, grid size 256,256,256,
pixel 1.7, shown at level 0.0969, step 1, values float32
> open "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/2510C-LIV-LASV-12bGP.pdb"
Summary of feedback from opening /Users/haoyangli/Google
Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/2510C-LIV-LASV-12bGP.pdb
---
warnings | Start residue of secondary structure not found: HELIX 46 46 ASN 1
162 GLY 1 164 5 3
Start residue of secondary structure not found: HELIX 47 47 SER 1 193 GLY 1
197 5 5
Start residue of secondary structure not found: HELIX 48 48 ASN 2 162 GLY 2
164 5 3
Start residue of secondary structure not found: HELIX 49 49 SER 2 193 GLY 2
197 5 5
Start residue of secondary structure not found: HELIX 50 50 ASN 3 162 GLY 3
164 5 3
22 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (147 )
Cannot find LINK/SSBOND residue CYS (147 )
Cannot find LINK/SSBOND residue CYS (147 )
Chain information for 2510C-LIV-LASV-12bGP.pdb #2
---
Chain | Description
A B C | No description available
D G J | No description available
E H K | No description available
> volume #1 level 0.3562
Fit map WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc in map
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 106123 points
correlation = 0.6784, correlation about mean = -0.01018, overlap = 1.732e+04
steps = 408, shift = 30.3, angle = 66 degrees
Position of WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc (#1) relative to
WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates:
Matrix rotation and translation
-0.90718349 -0.16565403 -0.38675167 538.56945391
-0.39854732 0.04377414 0.91610253 100.12591732
-0.13482636 0.98521193 -0.10573215 64.46373715
Axis 0.19747014 -0.71984021 -0.66545895
Axis point 279.42151287 -0.00000000 19.04011409
Rotation angle (degrees) 169.92210037
Shift along axis -8.62124657
> show #!4 models
> close #3
> close #4
> select #1
2 models selected
> ~select #1
Nothing selected
> select #2
17148 atoms, 17550 bonds, 42 pseudobonds, 2166 residues, 2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecule 2510C-LIV-LASV-12bGP.pdb (#2) to map
WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc (#1) using 17148 atoms
average map value = 0.5426, steps = 180
shifted from previous position = 42
rotated from previous position = 24.8 degrees
atoms outside contour = 3712, contour level = 0.35616
Position of 2510C-LIV-LASV-12bGP.pdb (#2) relative to
WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc (#1) coordinates:
Matrix rotation and translation
0.79560198 0.60581577 0.00217737 -32.12655918
-0.60579072 0.79559395 -0.00691809 184.60555379
-0.00592339 0.00418501 0.99997370 44.28889132
Axis 0.00916336 0.00668553 -0.99993567
Axis point 258.15211222 139.47332906 0.00000000
Rotation angle (degrees) 37.28947192
Shift along axis -43.34624320
> select up
17148 atoms, 17550 bonds, 42 pseudobonds, 2166 residues, 2 models selected
> ~select #2
Nothing selected
> select #2
17148 atoms, 17550 bonds, 42 pseudobonds, 2166 residues, 2 models selected
> vop flip #1 axis Z
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Fit molecule 2510C-LIV-LASV-12bGP.pdb (#2) to map
WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc z flip (#3) using 17148 atoms
average map value = 0.6296, steps = 160
shifted from previous position = 8.65
rotated from previous position = 24.7 degrees
atoms outside contour = 1632, contour level = 0.35616
Position of 2510C-LIV-LASV-12bGP.pdb (#2) relative to
WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99422172 0.10732870 0.00193569 21.66191515
0.10733834 -0.99420526 -0.00586441 376.14651114
0.00129506 0.00603830 -0.99998094 387.14059424
Axis 0.99855439 0.05374452 0.00080883
Axis point 0.00000000 186.91268192 194.11941524
Rotation angle (degrees) 179.65851662
Shift along axis 42.15954571
> sequence chain #2/D#2/G#2/J
Alignment identifier is 1
> color sel #808003ff
> sequence chain #2/E#2/H#2/K
Alignment identifier is 2
> color sel #408002ff
> color sel #808003ff
> color zone #3 near #2 distance 15
> hide #!2 models
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_2510C.cxs"
> includeMaps true
> save /Users/haoyangli/Desktop/image9.png supersample 3
> save /Users/haoyangli/Desktop/image10.png supersample 3
> save "/Users/haoyangli/Google
> Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_2510C.cxs"
> includeMaps true
opened ChimeraX session
OpenGL version: 4.1 ATI-4.2.15
OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
System Firmware Version: 429.80.1.0.0
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 11.2.3 (20D91)
Kernel Version: Darwin 20.3.0
Time since boot: 5 days 6:03
Graphics/Displays:
Radeon Pro 575:
Chipset Model: Radeon Pro 575
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c4
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1P-025
EFI Driver Version: 01.00.931
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Haoyang,
--Eric