![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 5 years ago
#3794 closed defect (can't reproduce)
Crash during session save
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
The crash happened while trying to save a session. The session wasn't particularly large or otherwise unusual that I know of, and maps were not being saved. This is the first time this happened.
Process: ChimeraX [12117]
Path: /Applications/ChimeraX-1.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.1.0 (1.1.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [12117]
User ID: 504
Date/Time: 2020-10-04 17:31:30.827 +0200
OS Version: Mac OS X 10.15.7 (19H2)
Report Version: 12
Anonymous UUID: DB56B5AD-0CD9-2D16-8E96-8D112F6D657A
Sleep/Wake UUID: 650AE370-4240-4019-A26C-DE91319E7FD0
Time Awake Since Boot: 780000 seconds
Time Since Wake: 780000 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 0x0000000000000020
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x20:
-->
__TEXT 000000010fcac000-000000010fcad000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.1.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff7069833a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff70754e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff705af93e raise + 26
3 libsystem_platform.dylib 0x00007fff707495fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 sip.so 0x00000001239bd4ff sip_api_convert_from_type + 225
6 QtCore.so 0x0000000123af9d98 Chimera::toPyObject(void*) const + 760
7 QtCore.so 0x0000000123b02de3 PyQtSlot::invoke(void**, _object*, void*, bool) const + 307
8 QtCore.so 0x0000000123b03925 PyQtSlotProxy::unislot(void**) + 85
9 QtCore.so 0x0000000123b0389a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
10 QtCore 0x0000000121a3a13d QMetaObject::activate(QObject*, int, int, void**) + 1773
11 QtCore 0x0000000121a322ca QObject::destroyed(QObject*) + 74
12 QtWidgets 0x0000000120d482f2 QWidget::~QWidget() + 946
13 QtWidgets.so 0x00000001208bec77 sipQPushButton::~sipQPushButton() + 55
14 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
15 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
16 QtWidgets.so 0x00000001208e46e7 sipQFrame::~sipQFrame() + 55
17 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
18 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
19 QtWidgets.so 0x00000001208e46e7 sipQFrame::~sipQFrame() + 55
20 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
21 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
22 QtWidgets.so 0x00000001208e46e7 sipQFrame::~sipQFrame() + 55
23 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
24 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
25 QtWidgets 0x0000000120d48c3e QWidget::~QWidget() + 14
26 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
27 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
28 QtWidgets.so 0x000000012080d517 sipQScrollArea::~sipQScrollArea() + 55
29 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
30 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
31 QtWidgets.so 0x00000001208f1da7 sipQWidget::~sipQWidget() + 55
32 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
33 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
34 QtWidgets.so 0x00000001208f1da7 sipQWidget::~sipQWidget() + 55
35 QtCore 0x0000000121a323d0 QObjectPrivate::deleteChildren() + 224
36 QtWidgets 0x0000000120d48363 QWidget::~QWidget() + 1059
37 QtWidgets.so 0x00000001208a00f7 sipQDockWidget::~sipQDockWidget() + 55
38 sip.so 0x00000001239bf21c forgetObject + 174
39 sip.so 0x00000001239befc6 sipWrapper_dealloc + 14
40 org.python.python 0x000000010fd24e5d subtype_dealloc + 1085
41 org.python.python 0x000000010fd06c27 dict_dealloc + 151
42 org.python.python 0x000000010fd35481 subtype_clear + 289
43 org.python.python 0x000000010fe08a5c collect + 2252
44 org.python.python 0x000000010fe0915e _PyObject_GC_Alloc + 286
45 org.python.python 0x000000010fd240c1 PyType_GenericAlloc + 225
46 org.python.python 0x000000010fcdf49c PyDescr_NewWrapper + 44
47 org.python.python 0x000000010fd2521d PyType_Ready + 749
48 org.python.python 0x000000010fd28e5d type_new + 4509
49 org.python.python 0x000000010fd2745c type_call + 44
50 org.python.python 0x000000010fcd79f8 PyObject_Call + 136
51 sip.so 0x00000001239c6321 createContainerType + 238
52 sip.so 0x00000001239c5b7d createClassType + 658
53 sip.so 0x00000001239c0fc9 sip_api_init_module + 739
54 QtMultimedia.so 0x000000014ce78134 PyInit_QtMultimedia + 324
55 org.python.python 0x000000010fdce653 _PyImport_LoadDynamicModuleWithSpec + 579
56 org.python.python 0x000000010fdce0a0 _imp_create_dynamic + 352
57 org.python.python 0x000000010fcd8079 _PyMethodDef_RawFastCallDict + 601
58 org.python.python 0x000000010fcd7b88 PyCFunction_Call + 200
59 org.python.python 0x000000010fda9b4a _PyEval_EvalFrameDefault + 27370
60 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
61 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
62 org.python.python 0x000000010fdacbe4 call_function + 772
63 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
64 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
65 org.python.python 0x000000010fdacbe4 call_function + 772
66 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
67 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
68 org.python.python 0x000000010fdacbe4 call_function + 772
69 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
70 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
71 org.python.python 0x000000010fdacbe4 call_function + 772
72 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
73 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
74 org.python.python 0x000000010fdacbe4 call_function + 772
75 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
76 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
77 org.python.python 0x000000010fcd970b object_vacall + 619
78 org.python.python 0x000000010fcd97fd _PyObject_CallMethodIdObjArgs + 173
79 org.python.python 0x000000010fdccfec PyImport_ImportModuleLevelObject + 1788
80 org.python.python 0x000000010fda7fde _PyEval_EvalFrameDefault + 20350
81 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
82 org.python.python 0x000000010fda2fc0 PyEval_EvalCode + 48
83 org.python.python 0x000000010fda0557 builtin_exec + 583
84 org.python.python 0x000000010fcd8079 _PyMethodDef_RawFastCallDict + 601
85 org.python.python 0x000000010fcd7b88 PyCFunction_Call + 200
86 org.python.python 0x000000010fda9b4a _PyEval_EvalFrameDefault + 27370
87 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
88 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
89 org.python.python 0x000000010fdacbe4 call_function + 772
90 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
91 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
92 org.python.python 0x000000010fdacbe4 call_function + 772
93 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
94 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
95 org.python.python 0x000000010fdacbe4 call_function + 772
96 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
97 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
98 org.python.python 0x000000010fdacbe4 call_function + 772
99 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
100 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
101 org.python.python 0x000000010fcd970b object_vacall + 619
102 org.python.python 0x000000010fcd97fd _PyObject_CallMethodIdObjArgs + 173
103 org.python.python 0x000000010fdccfec PyImport_ImportModuleLevelObject + 1788
104 org.python.python 0x000000010fd9f9d9 builtin___import__ + 137
105 org.python.python 0x000000010fcd7b54 PyCFunction_Call + 148
106 org.python.python 0x000000010fda9b4a _PyEval_EvalFrameDefault + 27370
107 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
108 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
109 org.python.python 0x000000010fdacbe4 call_function + 772
110 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
111 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
112 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
113 org.python.python 0x000000010fcd970b object_vacall + 619
114 org.python.python 0x000000010fcd97fd _PyObject_CallMethodIdObjArgs + 173
115 org.python.python 0x000000010fdcd0d1 PyImport_ImportModuleLevelObject + 2017
116 org.python.python 0x000000010fda7fde _PyEval_EvalFrameDefault + 20350
117 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
118 org.python.python 0x000000010fdacbe4 call_function + 772
119 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
120 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
121 org.python.python 0x000000010fdacbe4 call_function + 772
122 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
123 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
124 org.python.python 0x000000010fdacbe4 call_function + 772
125 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
126 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
127 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
128 org.python.python 0x000000010fdacbe4 call_function + 772
129 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
130 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
131 org.python.python 0x000000010fdacbe4 call_function + 772
132 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
133 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
134 org.python.python 0x000000010fdacbe4 call_function + 772
135 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
136 org.python.python 0x000000010fce68d8 gen_send_ex + 248
137 org.python.python 0x000000010fda5b66 _PyEval_EvalFrameDefault + 11014
138 org.python.python 0x000000010fce68d8 gen_send_ex + 248
139 org.python.python 0x000000010fcf1739 list_extend + 505
140 org.python.python 0x000000010fcf30c4 list___init__ + 244
141 org.python.python 0x000000010fd27554 type_call + 292
142 org.python.python 0x000000010fcd76ff _PyObject_FastCallKeywords + 575
143 org.python.python 0x000000010fdacbdd call_function + 765
144 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
145 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
146 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
147 org.python.python 0x000000010fdacbe4 call_function + 772
148 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
149 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
150 org.python.python 0x000000010fdacbe4 call_function + 772
151 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
152 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
153 org.python.python 0x000000010fdacbe4 call_function + 772
154 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
155 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
156 org.python.python 0x000000010fdacbe4 call_function + 772
157 org.python.python 0x000000010fda980a _PyEval_EvalFrameDefault + 26538
158 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
159 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
160 org.python.python 0x000000010fdacbe4 call_function + 772
161 org.python.python 0x000000010fda35d4 _PyEval_EvalFrameDefault + 1396
162 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
163 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
164 org.python.python 0x000000010fda9a4a _PyEval_EvalFrameDefault + 27114
165 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
166 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
167 org.python.python 0x000000010fcd8893 _PyObject_Call_Prepend + 131
168 org.python.python 0x000000010fcd79f8 PyObject_Call + 136
169 org.python.python 0x000000010fda9a4a _PyEval_EvalFrameDefault + 27114
170 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
171 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
172 org.python.python 0x000000010fda9a4a _PyEval_EvalFrameDefault + 27114
173 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
174 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
175 org.python.python 0x000000010fdacbe4 call_function + 772
176 org.python.python 0x000000010fda35d4 _PyEval_EvalFrameDefault + 1396
177 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
178 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
179 org.python.python 0x000000010fda9a4a _PyEval_EvalFrameDefault + 27114
180 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
181 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
182 org.python.python 0x000000010fdacbe4 call_function + 772
183 org.python.python 0x000000010fda35d4 _PyEval_EvalFrameDefault + 1396
184 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
185 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
186 org.python.python 0x000000010fdacbe4 call_function + 772
187 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
188 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
189 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
190 org.python.python 0x000000010fcd8893 _PyObject_Call_Prepend + 131
191 org.python.python 0x000000010fcd79f8 PyObject_Call + 136
192 org.python.python 0x000000010fda9a4a _PyEval_EvalFrameDefault + 27114
193 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
194 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
195 org.python.python 0x000000010fdacbe4 call_function + 772
196 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
197 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
198 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
199 org.python.python 0x000000010fdacbe4 call_function + 772
200 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
201 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
202 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
203 QtCore.so 0x0000000123b02f17 PyQtSlot::call(_object*, _object*) const + 39
204 QtCore.so 0x0000000123b02e26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
205 QtCore.so 0x0000000123b03925 PyQtSlotProxy::unislot(void**) + 85
206 QtCore.so 0x0000000123b0389a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
207 QtCore 0x0000000121a3a13d QMetaObject::activate(QObject*, int, int, void**) + 1773
208 QtWidgets 0x0000000120d14075 QAction::activate(QAction::ActionEvent) + 309
209 QtCore 0x0000000121a32d41 QObject::event(QEvent*) + 753
210 QtWidgets.so 0x00000001208de810 sipQAction::event(QEvent*) + 192
211 QtWidgets 0x0000000120d1d67d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
212 QtWidgets 0x0000000120d1ea82 QApplication::notify(QObject*, QEvent*) + 594
213 QtWidgets.so 0x00000001208dd3ca sipQApplication::notify(QObject*, QEvent*) + 234
214 QtCore 0x0000000121a09324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
215 QtCore 0x0000000121a0a55e QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 878
216 libqcocoa.dylib 0x000000012b81d8f9 0x12b7e7000 + 223481
217 libqcocoa.dylib 0x000000012b81e068 0x12b7e7000 + 225384
218 com.apple.CoreFoundation 0x00007fff36679d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
219 com.apple.CoreFoundation 0x00007fff36679cf1 __CFRunLoopDoSource0 + 103
220 com.apple.CoreFoundation 0x00007fff36679b67 __CFRunLoopDoSources0 + 301
221 com.apple.CoreFoundation 0x00007fff3667883a __CFRunLoopRun + 927
222 com.apple.CoreFoundation 0x00007fff36677e3e CFRunLoopRunSpecific + 462
223 com.apple.HIToolbox 0x00007fff352a4abd RunCurrentEventLoopInMode + 292
224 com.apple.HIToolbox 0x00007fff352a46f4 ReceiveNextEventCommon + 359
225 com.apple.HIToolbox 0x00007fff352a4579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
226 com.apple.AppKit 0x00007fff338ea039 _DPSNextEvent + 883
227 com.apple.AppKit 0x00007fff338e8880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
228 com.apple.AppKit 0x00007fff338da58e -[NSApplication run] + 658
229 libqcocoa.dylib 0x000000012b81cde3 0x12b7e7000 + 220643
230 QtCore 0x0000000121a0493f QEventLoop::exec(QFlags) + 431
231 QtCore 0x0000000121a09932 QCoreApplication::exec() + 130
232 QtWidgets.so 0x00000001209cc7d2 meth_QApplication_exec_(_object*, _object*) + 82
233 org.python.python 0x000000010fcd83a2 _PyMethodDef_RawFastCallKeywords + 226
234 org.python.python 0x000000010fcd78d9 _PyCFunction_FastCallKeywords + 41
235 org.python.python 0x000000010fdacb70 call_function + 656
236 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
237 org.python.python 0x000000010fcd7d81 function_code_fastcall + 177
238 org.python.python 0x000000010fdacbe4 call_function + 772
239 org.python.python 0x000000010fda9827 _PyEval_EvalFrameDefault + 26567
240 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
241 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
242 org.python.python 0x000000010fdacbe4 call_function + 772
243 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
244 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
245 org.python.python 0x000000010fda2fc0 PyEval_EvalCode + 48
246 org.python.python 0x000000010fda0557 builtin_exec + 583
247 org.python.python 0x000000010fcd854d _PyMethodDef_RawFastCallKeywords + 653
248 org.python.python 0x000000010fcd78d9 _PyCFunction_FastCallKeywords + 41
249 org.python.python 0x000000010fdacb70 call_function + 656
250 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
251 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
252 org.python.python 0x000000010fcd7899 _PyFunction_FastCallKeywords + 217
253 org.python.python 0x000000010fdacbe4 call_function + 772
254 org.python.python 0x000000010fda98be _PyEval_EvalFrameDefault + 26718
255 org.python.python 0x000000010fdada3c _PyEval_EvalCodeWithName + 3276
256 org.python.python 0x000000010fcd7397 _PyFunction_FastCallDict + 455
257 org.python.python 0x000000010fe07b03 pymain_run_module + 147
258 org.python.python 0x000000010fe06bec pymain_main + 5900
259 org.python.python 0x000000010fe054d3 Py_Main + 51
260 edu.ucsf.cgl.ChimeraX 0x000000010fcacdc8 main + 120
261 libdyld.dylib 0x00007fff70550cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001115d2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001115d2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001115d2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001115d2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x00000001115d2c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 6:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff36679ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff366789c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff36677e3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff33a8b954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 7:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d022f 0x12422e000 + 35267119
4 QtWebEngineCore 0x000000012638405d 0x12422e000 + 34955357
5 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
6 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 8:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff70696766 kevent + 10
1 QtWebEngineCore 0x00000001266919a9 0x12422e000 + 38156713
2 QtWebEngineCore 0x000000012668ecbd 0x12422e000 + 38145213
3 QtWebEngineCore 0x0000000126445cdc 0x12422e000 + 35749084
4 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
5 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
6 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
7 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 9:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff70696766 kevent + 10
1 QtWebEngineCore 0x00000001266919a9 0x12422e000 + 38156713
2 QtWebEngineCore 0x000000012668ecbd 0x12422e000 + 38145213
3 QtWebEngineCore 0x0000000126445cc4 0x12422e000 + 35749060
4 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
5 QtWebEngineCore 0x00000001263eea74 0x12422e000 + 35392116
6 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 10:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d0421 0x12422e000 + 35267617
4 QtWebEngineCore 0x00000001263e7d28 0x12422e000 + 35364136
5 QtWebEngineCore 0x00000001263e865b 0x12422e000 + 35366491
6 QtWebEngineCore 0x00000001263e82c4 0x12422e000 + 35365572
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 11:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d0421 0x12422e000 + 35267617
4 QtWebEngineCore 0x00000001263e7d28 0x12422e000 + 35364136
5 QtWebEngineCore 0x00000001263e865b 0x12422e000 + 35366491
6 QtWebEngineCore 0x00000001263e82c4 0x12422e000 + 35365572
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 12:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d0421 0x12422e000 + 35267617
4 QtWebEngineCore 0x00000001263e7d28 0x12422e000 + 35364136
5 QtWebEngineCore 0x00000001263e865b 0x12422e000 + 35366491
6 QtWebEngineCore 0x00000001263e8234 0x12422e000 + 35365428
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 13:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff70696766 kevent + 10
1 QtWebEngineCore 0x00000001266919a9 0x12422e000 + 38156713
2 QtWebEngineCore 0x000000012668ecbd 0x12422e000 + 38145213
3 QtWebEngineCore 0x0000000126445cc4 0x12422e000 + 35749060
4 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
5 QtWebEngineCore 0x0000000125d1bfe4 0x12422e000 + 28237796
6 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 14:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d022f 0x12422e000 + 35267119
4 QtWebEngineCore 0x00000001263e7d1a 0x12422e000 + 35364122
5 QtWebEngineCore 0x00000001263e83bf 0x12422e000 + 35365823
6 QtWebEngineCore 0x00000001263e8264 0x12422e000 + 35365476
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 15:: CompositorTileWorker1/58627
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000012643dfa8 0x12422e000 + 35717032
3 QtWebEngineCore 0x00000001273c44c8 0x12422e000 + 51995848
4 QtWebEngineCore 0x00000001263fe694 0x12422e000 + 35456660
5 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
6 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 16:: AudioThread
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d022f 0x12422e000 + 35267119
4 QtWebEngineCore 0x000000012638405d 0x12422e000 + 34955357
5 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
6 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 17:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x0000000126384052 0x12422e000 + 34955346
4 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
5 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
6 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
7 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 18:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff70696766 kevent + 10
1 QtWebEngineCore 0x00000001266919a9 0x12422e000 + 38156713
2 QtWebEngineCore 0x000000012668ecbd 0x12422e000 + 38145213
3 QtWebEngineCore 0x0000000126445cdc 0x12422e000 + 35749084
4 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
5 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
6 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
7 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 19:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d022f 0x12422e000 + 35267119
4 QtWebEngineCore 0x000000012638405d 0x12422e000 + 34955357
5 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
6 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 20:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d022f 0x12422e000 + 35267119
4 QtWebEngineCore 0x00000001263e7d1a 0x12422e000 + 35364122
5 QtWebEngineCore 0x00000001263e865b 0x12422e000 + 35366491
6 QtWebEngineCore 0x00000001263e8324 0x12422e000 + 35365668
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 21:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d022f 0x12422e000 + 35267119
4 QtWebEngineCore 0x000000012638405d 0x12422e000 + 34955357
5 QtWebEngineCore 0x00000001263ad085 0x12422e000 + 35123333
6 QtWebEngineCore 0x00000001263ff9bc 0x12422e000 + 35461564
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 22:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff70691dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff70692170 mach_msg + 60
2 QtWebEngineCore 0x00000001263d032d 0x12422e000 + 35267373
3 QtWebEngineCore 0x00000001263d0421 0x12422e000 + 35267617
4 QtWebEngineCore 0x00000001263e7d28 0x12422e000 + 35364136
5 QtWebEngineCore 0x00000001263e865b 0x12422e000 + 35366491
6 QtWebEngineCore 0x00000001263e8234 0x12422e000 + 35365428
7 QtWebEngineCore 0x000000012643f717 0x12422e000 + 35723031
8 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 23:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff70694882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff70755425 _pthread_cond_wait + 698
2 QtCore 0x00000001218498ab 0x12181f000 + 174251
3 QtCore 0x000000012184980c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x0000000120f48762 0x120d0d000 + 2340706
5 QtCore 0x00000001218410b3 0x12181f000 + 139443
6 libsystem_pthread.dylib 0x00007fff70755109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff70750b8b thread_start + 15
Thread 24:
0 libsystem_pthread.dylib 0x00007fff70750b68 start_wqthread + 0
Thread 25:
0 libsystem_pthread.dylib 0x00007fff70750b68 start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x00007fff70750b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011d7f0dc0 rcx: 0x00007fe7b808fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fe7b808fa80 rsp: 0x00007fe7b808fa58
r8: 0x00007fe7b808ff48 r9: 0xa948fa4065e2fb04 r10: 0x000000011d7f0dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007fe7826501f0 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff7069833a rfl: 0x0000000000000246 cr2: 0x000000010ff12fa4
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x10fcb4000 - 0x10feaffff +org.python.python (3.7.8, [c] 2001-2019 Python Software Foundation. - 3.7.8) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/Python
0x11022f000 - 0x110230ff7 +_heapq.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_heapq.cpython-37m-darwin.so
0x1102f9000 - 0x1102fcff3 +zlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/zlib.cpython-37m-darwin.so
0x110306000 - 0x11031aff7 +libz.1.2.11.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/libz.1.2.11.dylib
0x110364000 - 0x110365ff7 +_bz2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bz2.cpython-37m-darwin.so
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0x11037c000 - 0x11037cffb +grp.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/grp.cpython-37m-darwin.so
0x1103c4000 - 0x1103c9ffb +math.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/math.cpython-37m-darwin.so
0x1103d5000 - 0x1103d7ff3 +_hashlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_hashlib.cpython-37m-darwin.so
0x1103e1000 - 0x11043eff7 +libssl.1.1.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/libssl.1.1.dylib
0x11046d000 - 0x110634af3 +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/libcrypto.1.1.dylib
0x1106cd000 - 0x1106d2ff3 +_blake2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_blake2.cpython-37m-darwin.so
0x1106dc000 - 0x1106ecff3 +_sha3.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_sha3.cpython-37m-darwin.so
0x1106f7000 - 0x1106f7ffb +_bisect.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bisect.cpython-37m-darwin.so
0x1106ff000 - 0x110700ffb +_random.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_random.cpython-37m-darwin.so
0x1107c8000 - 0x1107ceffb +_json.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_json.cpython-37m-darwin.so
0x110817000 - 0x110824ff7 +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so
0x11083a000 - 0x110843ffb +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so
0x110895000 - 0x110898fff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so
0x1108a3000 - 0x1108a7ffb +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so
0x1108b5000 - 0x1108b9ff7 +binascii.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/binascii.cpython-37m-darwin.so
0x1109c2000 - 0x1109d0ff3 +_datetime.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_datetime.cpython-37m-darwin.so
0x110a20000 - 0x110a20ff3 +_scproxy.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_scproxy.cpython-37m-darwin.so
0x110a28000 - 0x110a66fff +_decimal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_decimal.cpython-37m-darwin.so
0x110aca000 - 0x110af7ff3 +pyexpat.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/pyexpat.cpython-37m-darwin.so
0x110b0f000 - 0x110b10ff3 +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so
0x110bd9000 - 0x110bdafff +_posixsubprocess.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_posixsubprocess.cpython-37m-darwin.so
0x110c22000 - 0x110c34fff +_pickle.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_pickle.cpython-37m-darwin.so
0x110c85000 - 0x110c88ffb +_csv.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_csv.cpython-37m-darwin.so
0x110e13000 - 0x111176fe7 +_multiarray_umath.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so
0x11129c000 - 0x114d07ae7 +libopenblasp-r0.3.7.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libopenblasp-r0.3.7.dylib
0x115011000 - 0x115128ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x115196000 - 0x1151ccfff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x1151e0000 - 0x1151f5ff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgcc_s.1.dylib
0x11d385000 - 0x11d392ff3 +_multiarray_tests.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_tests.cpython-37m-darwin.so
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0x7fff622fe000 - 0x7fff62377ff3 com.apple.Rapport (1.9.5 - 195.2) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport
0x7fff625de000 - 0x7fff62607ff1 com.apple.RemoteViewServices (2.0 - 148) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
0x7fff6276c000 - 0x7fff627a7ff0 com.apple.RunningBoardServices (1.0 - 223.140.2) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices
0x7fff64088000 - 0x7fff6408bff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff641fe000 - 0x7fff64325fff com.apple.Sharing (1526.37 - 1526.37) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff6437e000 - 0x7fff6439cff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff6439d000 - 0x7fff643bdff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff643be000 - 0x7fff643d0ff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff6573a000 - 0x7fff65a30ff7 com.apple.SkyLight (1.600.0 - 451.4) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff6627d000 - 0x7fff6628bffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff66967000 - 0x7fff669a8ff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff66abf000 - 0x7fff66ac8ff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.1) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff66b39000 - 0x7fff66b63ffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff66d7f000 - 0x7fff66d8fff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff672b4000 - 0x7fff6737aff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff67511000 - 0x7fff67512fff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff6754a000 - 0x7fff677a2ff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff67839000 - 0x7fff6783fffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff68418000 - 0x7fff68438ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff691e4000 - 0x7fff692ceff8 com.apple.ViewBridge (464.1 - 464.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff69474000 - 0x7fff69475fff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff6a0a5000 - 0x7fff6a0a8ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff6a122000 - 0x7fff6a130ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff6a472000 - 0x7fff6a474ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff6a475000 - 0x7fff6a488ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff6a4ba000 - 0x7fff6a4c6ffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff6cf4b000 - 0x7fff6cf57ff9 libAudioStatistics.dylib (1104.93) /usr/lib/libAudioStatistics.dylib
0x7fff6cf58000 - 0x7fff6cf8bffa libAudioToolboxUtility.dylib (1104.93) /usr/lib/libAudioToolboxUtility.dylib
0x7fff6cf92000 - 0x7fff6cfc6fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff6cfc9000 - 0x7fff6cfd3fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff6cfd4000 - 0x7fff6d05cfff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib
0x7fff6d05f000 - 0x7fff6d061ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff6d0a7000 - 0x7fff6d25effb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff6d285000 - 0x7fff6d28bff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff6d36d000 - 0x7fff6d374fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff6d3a3000 - 0x7fff6d3c3ff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff6d443000 - 0x7fff6d520ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff6d535000 - 0x7fff6d536fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff6d537000 - 0x7fff6d5c2ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff6d5c3000 - 0x7fff6d5c4fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff6d5dc000 - 0x7fff6d5f2fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff6d627000 - 0x7fff6d699ff7 libarchive.2.dylib (72.140.1) /usr/lib/libarchive.2.dylib
0x7fff6d69a000 - 0x7fff6d733fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff6d737000 - 0x7fff6d737ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff6d738000 - 0x7fff6d7fcffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib
0x7fff6d7fd000 - 0x7fff6d80dffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff6d80e000 - 0x7fff6d81afff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff6d81b000 - 0x7fff6d86dfff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff6d86e000 - 0x7fff6d883ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff6d884000 - 0x7fff6d884fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff6d885000 - 0x7fff6d896fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff6d897000 - 0x7fff6d8aefd7 libcompression.dylib (87) /usr/lib/libcompression.dylib
0x7fff6db88000 - 0x7fff6db9eff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff6db9f000 - 0x7fff6dba0fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff6e043000 - 0x7fff6e147fef libcrypto.44.dylib (47.140.1) /usr/lib/libcrypto.44.dylib
0x7fff6e14a000 - 0x7fff6e155fff libcsfde.dylib (551) /usr/lib/libcsfde.dylib
0x7fff6e15d000 - 0x7fff6e1bcff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib
0x7fff6e1be000 - 0x7fff6e223ff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib
0x7fff6e2c6000 - 0x7fff6e2c6fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff6e2c7000 - 0x7fff6e2dffff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib
0x7fff6e2ed000 - 0x7fff6e2effff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff6e2fe000 - 0x7fff6e303fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff6e304000 - 0x7fff6e30dff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib
0x7fff6e30e000 - 0x7fff6e3fefff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6e3ff000 - 0x7fff6e656fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff6e670000 - 0x7fff6e671fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6e672000 - 0x7fff6e68aff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6e6a2000 - 0x7fff6e749ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6e74a000 - 0x7fff6e9acff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6ed19000 - 0x7fff6ed48fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6ee78000 - 0x7fff6f2f4ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff6f2f5000 - 0x7fff6f30cfff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6f395000 - 0x7fff6f3c8fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6f3c9000 - 0x7fff6f3caff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6f3db000 - 0x7fff6f3dffff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6f3e2000 - 0x7fff6f418ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff6f458000 - 0x7fff6f466ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6f49c000 - 0x7fff6f4b4fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6f4b6000 - 0x7fff6f4faff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff6f4fb000 - 0x7fff6f50dff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6f50e000 - 0x7fff6f50fff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6f510000 - 0x7fff6f6faff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff6f7ee000 - 0x7fff6f81bffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff6f8f0000 - 0x7fff6f94aff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff6f94b000 - 0x7fff6f94effb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff6f94f000 - 0x7fff6f95cff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff6f962000 - 0x7fff6fa44fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff6fa48000 - 0x7fff6fa70fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff6fa71000 - 0x7fff6fa83ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff70332000 - 0x7fff70337ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff70338000 - 0x7fff70343fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff70344000 - 0x7fff7034bfff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff7034c000 - 0x7fff70355ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff70356000 - 0x7fff703e8fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff704f5000 - 0x7fff70535ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff70536000 - 0x7fff7056cfff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff7056d000 - 0x7fff7056dffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff7056e000 - 0x7fff7057aff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib
0x7fff7057b000 - 0x7fff7057bff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff7057c000 - 0x7fff70581ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff70582000 - 0x7fff70584ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff70585000 - 0x7fff70586ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff70587000 - 0x7fff7059eff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff7059f000 - 0x7fff7059fff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff705a0000 - 0x7fff70627fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff70628000 - 0x7fff7062bffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff7062c000 - 0x7fff7062ffff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff70630000 - 0x7fff70638fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff70639000 - 0x7fff70640fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff70641000 - 0x7fff70642ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff70643000 - 0x7fff70690ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff70691000 - 0x7fff706bdff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff706be000 - 0x7fff70705fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff70706000 - 0x7fff7072dfff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff7072e000 - 0x7fff7073bffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff7073c000 - 0x7fff70745ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff70746000 - 0x7fff7074efef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff7074f000 - 0x7fff70759fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff7075a000 - 0x7fff7075eff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff7075f000 - 0x7fff70761fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff70762000 - 0x7fff70769ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff7076a000 - 0x7fff70780ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff70782000 - 0x7fff70787ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff70788000 - 0x7fff707bdffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 308
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: 33780863
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=932.7M resident=0K(0%) swapped_out_or_unallocated=932.7M(100%)
Writable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 768K 6
Activity Tracing 256K 1
CG backing stores 2096K 4
CG image 416K 32
CoreAnimation 1112K 100
CoreGraphics 8K 1
CoreImage 32K 4
CoreUI image data 3868K 42
Foundation 36K 2
Kernel Alloc Once 8K 1
MALLOC 2.3G 137
MALLOC guard page 48K 10
MALLOC_MEDIUM (reserved) 496.0M 6 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 104K 26
Stack 141.2M 27
Stack Guard 56.0M 1
VM_ALLOCATE 227.4M 457
VM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)
__DATA 61.8M 548
__DATA_CONST 128K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 414.0M 144
__OBJC_RO 32.3M 1
__OBJC_RW 1904K 1
__TEXT 518.8M 515
__UNICODE 564K 1
mapped file 127.4M 102
shared memory 652K 17
=========== ======= =======
TOTAL 4.5G 2203
TOTAL, minus reserved VM space 3.8G 2203
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/crowe/Dropbox/rqcH-project/rqcH-DR/200731_RqcH-DR-maps-
> comparison_04.cxs
Log from Fri Jul 31 19:27:15 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/crowe/Dropbox/rqcH-DR/200731_RqcH-DR-maps-comparison_03.cxs
Log from Fri Jul 31 16:00:57 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/crowe/Dropbox/rqcH-DR/200727_RqcH-DR-maps-comparison.cxs
Log from Mon Jul 27 17:08:40 2020UCSF ChimeraX version: 1.1.dev202007180211
(2020-07-18)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j035_APE-cl4_run_class001.mrc
> /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j058_APE-cl6-E-tRNA_run_class001.mrc
> /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j057_APE-cl3_run_class001.mrc
> /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j056_APE-cl1_run_class001.mrc
Opened j035_APE-cl4_run_class001.mrc, grid size 420,420,420, pixel 0.82, shown
at level 0.0136, step 2, values float32
> close #1.2
> close #1.3
> close #1.4
> open /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j056_APE-cl1_run_class001.mrc
Opened j056_APE-cl1_run_class001.mrc, grid size 420,420,420, pixel 0.82, shown
at level 0.0142, step 2, values float32
> open /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j057_APE-cl3_run_class001.mrc
Opened j057_APE-cl3_run_class001.mrc, grid size 420,420,420, pixel 0.82, shown
at level 0.0142, step 2, values float32
> open /Volumes/ccmdb/Dropbox/rqcH-DR/maps/j058_APE-
> cl6-E-tRNA_run_class001.mrc
Opened j058_APE-cl6-E-tRNA_run_class001.mrc, grid size 420,420,420, pixel
0.82, shown at level 0.0139, step 2, values float32
> fitmap #2 inMap #1
Fit map j056_APE-cl1_run_class001.mrc in map j035_APE-cl4_run_class001.mrc
using 92587 points
correlation = 0.9885, correlation about mean = 0.7732, overlap = 33.29
steps = 68, shift = 1.7, angle = 1.95 degrees
Position of j056_APE-cl1_run_class001.mrc (#2) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99950116 0.01215350 -0.02915011 1.74210922
-0.01178217 0.99984768 0.01287658 0.76864126
0.02930217 -0.01252670 0.99949210 -2.49686574
Axis -0.37313765 -0.85857984 -0.35158065
Axis point 91.30885329 0.00000000 52.66923317
Rotation angle (degrees) 1.95073057
Shift along axis -0.43213673
> fitmap #3 inMap #1
Fit map j057_APE-cl3_run_class001.mrc in map j035_APE-cl4_run_class001.mrc
using 92604 points
correlation = 0.9897, correlation about mean = 0.7898, overlap = 33.16
steps = 60, shift = 1.48, angle = 1.6 degrees
Position of j057_APE-cl3_run_class001.mrc (#3) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99962717 0.01501435 -0.02280541 0.35697902
-0.01488720 0.99987273 0.00573490 2.50601152
0.02288861 -0.00539325 0.99972347 -2.88107420
Axis -0.19967806 -0.81991139 -0.53653890
Axis point 139.57405095 0.00000000 8.29157261
Rotation angle (degrees) 1.59676603
Shift along axis -0.58017988
> fitmap #4 inMap #1
Fit map j058_APE-cl6-E-tRNA_run_class001.mrc in map j035_APE-
cl4_run_class001.mrc using 92571 points
correlation = 0.991, correlation about mean = 0.808, overlap = 32.08
steps = 64, shift = 1.03, angle = 2.3 degrees
Position of j058_APE-cl6-E-tRNA_run_class001.mrc (#4) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99928066 -0.02073120 -0.03175487 8.45371085
0.02115114 0.99969247 0.01294582 -5.28679291
0.03147672 -0.01360816 0.99941184 -3.03802358
Axis -0.33044424 -0.78686933 0.52119408
Axis point 97.81648029 0.00000000 261.74526018
Rotation angle (degrees) 2.30271947
Shift along axis -0.21686478
> volume step 1
> volume level 0.01
> set bgColor white
> volume #1.1 level 0.006236
> volume #1.1 level 0.007
> save /Volumes/ccmdb/Dropbox/rqcH-DR/200727_RqcH-DR-maps-comparison.cxs
opened ChimeraX session
> lighting soft
> lighting simple
> open /Users/crowe/Dropbox/rqcH-project/modelling/EPA-
> cl1_modelling/200616_cl1-RSR36_50S-only.pdb
Chain information for 200616_cl1-RSR36_50S-only.pdb #5
---
Chain | Description
A | No description available
B | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
K | No description available
L | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> volume #1.1 color #b2b2b2fe
> volume #1.1 color #b2b2b2f2
> volume #1.1 color #b2b2b2eb
> volume #1.1 color #b2b2b2e0
> volume #1.1 color #b2b2b2d2
> volume #1.1 color #b2b2b2c3
> volume #1.1 color #b2b2b2b3
> volume #1.1 color #b2b2b2a4
> volume #1.1 color #b2b2b293
> volume #1.1 color #b2b2b283
> volume #1.1 color #b2b2b278
> volume #1.1 color #b2b2b275
> volume #1.1 color #b2b2b274
> volume #1.1 color #b2b2b271
> volume #1.1 color #b2b2b26b
> volume #1.1 color #b2b2b267
> volume #1.1 color #b2b2b25f
> volume #1.1 color #b2b2b25d
> volume #1.1 color #b2b2b25b
> volume #1.1 color #b2b2b24f
> volume #1.1 color #b2b2b24a
> volume #1.1 color #b2b2b249
> volume #1.1 color #b2b2b248
> volume #1.1 color #b2b2b246
> volume #1.1 color #b2b2b247
> volume #1.1 color #b2b2b249
> volume #1.1 color #b2b2b24a
> open /Users/crowe/Dropbox/rqcH-project/modelling/EPA-
> cl1_modelling/200616_cl1-RSR36_P-tRNA-only.pdb /Users/crowe/Dropbox/rqcH-
> project/modelling/EPA-cl1_modelling/200616_cl1-RSR36_RqcH-only.pdb
Chain information for 200616_cl1-RSR36_P-tRNA-only.pdb #6
---
Chain | Description
2 | No description available
Chain information for 200616_cl1-RSR36_RqcH-only.pdb #7
---
Chain | Description
0 | No description available
> open /Users/crowe/Dropbox/rqcH-project/modelling/EPA-
> cl1_modelling/individual-parts/200313_cl1_YabO.pdb
Chain information for 200313_cl1_YabO.pdb #8
---
Chain | Description
1 | No description available
Drag select of 87588 atoms, 23 pseudobonds, 691 residues, 219 shapes
> 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"
> select clear
> fitmap #5 inMap #1.1
Fit molecule 200616_cl1-RSR36_50S-only.pdb (#5) to map j035_APE-
cl4_run_class001.mrc (#1.1) using 87588 atoms
average map value = 0.01569, steps = 92
shifted from previous position = 4.97
rotated from previous position = 4.44 degrees
atoms outside contour = 6126, contour level = 0.007
Position of 200616_cl1-RSR36_50S-only.pdb (#5) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.63234884 0.71639479 -0.29481088 -10.25846422
-0.20864912 -0.20899496 -0.95539869 408.88172169
-0.74605663 0.66565728 0.01731741 183.60528144
Axis 0.84421395 0.23499988 -0.48174460
Axis point 0.00000000 124.50066879 270.67410940
Rotation angle (degrees) 106.24017336
Shift along axis -1.02403765
> fitmap #6 inMap #1.1
Fit molecule 200616_cl1-RSR36_P-tRNA-only.pdb (#6) to map j035_APE-
cl4_run_class001.mrc (#1.1) using 1563 atoms
average map value = 0.01117, steps = 112
shifted from previous position = 2.49
rotated from previous position = 2.95 degrees
atoms outside contour = 391, contour level = 0.007
Position of 200616_cl1-RSR36_P-tRNA-only.pdb (#6) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.64982851 0.70608134 -0.28137530 -13.94106733
-0.17902070 -0.21759729 -0.95948059 405.48279492
-0.73869784 0.67386984 -0.01499775 187.12942015
Axis 0.85372126 0.23903381 -0.46262603
Axis point 0.00000000 123.81921700 265.86366466
Rotation angle (degrees) 106.94078823
Shift along axis -1.54862915
> hide #!1.1 models
> show #!1.1 models
> fitmap #7 inMap #1.1
Fit molecule 200616_cl1-RSR36_RqcH-only.pdb (#7) to map j035_APE-
cl4_run_class001.mrc (#1.1) using 3986 atoms
average map value = 0.005717, steps = 116
shifted from previous position = 7.95
rotated from previous position = 6.85 degrees
atoms outside contour = 2819, contour level = 0.007
Position of 200616_cl1-RSR36_RqcH-only.pdb (#7) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.61397241 0.74687690 -0.25536791 -21.02853540
-0.20997068 -0.15732877 -0.96496631 397.15129380
-0.76088777 0.64608246 0.06022672 184.37272194
Axis 0.83010830 0.26047395 -0.49302488
Axis point 0.00000000 116.21682620 273.51091239
Rotation angle (degrees) 103.97891567
Shift along axis -4.90873595
> fitmap #8 inMap #1.1
Fit molecule 200313_cl1_YabO.pdb (#8) to map j035_APE-cl4_run_class001.mrc
(#1.1) using 659 atoms
average map value = 0.008248, steps = 96
shifted from previous position = 7.24
rotated from previous position = 16.7 degrees
atoms outside contour = 256, contour level = 0.007
Position of 200313_cl1_YabO.pdb (#8) relative to j035_APE-cl4_run_class001.mrc
(#1.1) coordinates:
Matrix rotation and translation
0.61716421 0.69477744 -0.36931376 9.07152784
-0.40050406 -0.12662576 -0.90750340 430.04565595
-0.67727752 0.70799027 0.20011230 129.89320377
Axis 0.81758610 0.15585755 -0.55431163
Axis point 0.00000000 145.48197816 292.84894863
Rotation angle (degrees) 98.89792637
Shift along axis 2.44130503
> delete #7/0:279-565
> select up
Nothing selected
> select down
Nothing selected
> fitmap #7 inMap #1.1
Fit molecule 200616_cl1-RSR36_RqcH-only.pdb (#7) to map j035_APE-
cl4_run_class001.mrc (#1.1) using 2145 atoms
average map value = 0.00482, steps = 132
shifted from previous position = 4.47
rotated from previous position = 23.7 degrees
atoms outside contour = 1862, contour level = 0.007
Position of 200616_cl1-RSR36_RqcH-only.pdb (#7) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.63098868 0.77185081 0.07810005 -90.21122144
-0.18580863 0.24810052 -0.95074775 313.12165340
-0.75321208 0.58539940 0.29996516 149.07900403
Axis 0.77117030 0.41733192 -0.48076027
Axis point 0.00000000 78.83686463 271.63132828
Rotation angle (degrees) 84.86359331
Shift along axis -10.56381746
> open /Users/crowe/Dropbox/rqcH-project/modelling/EPA-
> cl1_modelling/200616_cl1-RSR36_RqcH-only.pdb
Chain information for 200616_cl1-RSR36_RqcH-only.pdb #9
---
Chain | Description
0 | No description available
> delete #9/0:2-278
> select #9/0:529
5 atoms, 4 bonds, 1 model selected
> select up
35 atoms, 34 bonds, 1 model selected
> select up
1841 atoms, 1856 bonds, 1 model selected
> ui mousemode right "translate selected atoms"
> volume #1.1 color #b2b2b250
> volume #1.1 color #b2b2b26f
> volume #1.1 color #b2b2b280
> volume #1.1 color #b2b2b285
> volume #1.1 color #b2b2b28a
> volume #1.1 color #b2b2b292
> volume #1.1 color #b2b2b298
> volume #1.1 color #b2b2b29b
> volume #1.1 color #b2b2b29c
> volume #1.1 color #b2b2b29f
> volume #1.1 color #b2b2b2a9
> volume #1.1 color #b2b2b2ac
> volume #1.1 color #b2b2b2ae
> volume #1.1 color #b2b2b2b0
> volume #1.1 color #b2b2b2b4
> volume #1.1 color #b2b2b2b5
> volume #1.1 color #b2b2b2b8
> volume #1.1 color #b2b2b2b9
> volume #1.1 color #b2b2b2b8
> volume #1.1 color #b2b2b2b7
> select clear
> fitmap #9 inMap #1.1
Fit molecule 200616_cl1-RSR36_RqcH-only.pdb (#9) to map j035_APE-
cl4_run_class001.mrc (#1.1) using 1841 atoms
average map value = 0.007793, steps = 144
shifted from previous position = 6.47
rotated from previous position = 20.2 degrees
atoms outside contour = 748, contour level = 0.007
Position of 200616_cl1-RSR36_RqcH-only.pdb (#9) relative to j035_APE-
cl4_run_class001.mrc (#1.1) coordinates:
Matrix rotation and translation
0.56939705 0.78307671 -0.25015570 -52.68593699
-0.16566800 -0.18875199 -0.96794979 473.86063673
-0.80519632 0.59259055 0.02225592 221.21684236
Axis 0.81755549 0.29078166 -0.49704030
Axis point 0.00000000 150.26883279 309.58115341
Rotation angle (degrees) 107.37050427
Shift along axis -15.23738120
> hide atoms
> show cartoons
> select #6/2:34
20 atoms, 21 bonds, 1 model selected
> select clear
> color #5 grey
> color #5/A lightgrey
> color #6 skyblue
> color #7 darkviolet
> color #9 darkviolet
> volume #1.1 level 0.006338
> cartoon style #7 modeHelix tube
> cartoon style modeHelix tube
> select clear
> open /Users/crowe/Dropbox/rqcH-project/modelling/EPA-
> cl7_modelling/200502_cl7_50S-PP-tRNA-YabO_RSR28_H69-full.pdb
Chain information for 200502_cl7_50S-PP-tRNA-YabO_RSR28_H69-full.pdb #10
---
Chain | Description
1 | No description available
2 | No description available
A | No description available
B | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> mmaker #10 to #5
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 200616_cl1-RSR36_50S-only.pdb, chain E (#5) with 200502_cl7_50S-PP-
tRNA-YabO_RSR28_H69-full.pdb, chain E (#10), sequence alignment score = 1318.9
RMSD between 272 pruned atom pairs is 0.277 angstroms; (across all 272 pairs:
0.277)
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #8 models
> hide #!9 models
> hide #!1 models
Drag select of 26152 atoms, 2 pseudobonds
> select up
28062 atoms, 30299 bonds, 2 pseudobonds, 2 models selected
> select up
71949 atoms, 79431 bonds, 2 pseudobonds, 2 models selected
> delete sel
Drag select of 3608 atoms
Drag select of 6817 atoms, 4 pseudobonds
Drag select of 863 atoms
Drag select of 97 atoms
> select up
8881 atoms, 8926 bonds, 4 pseudobonds, 2 models selected
> select up
10597 atoms, 10701 bonds, 4 pseudobonds, 2 models selected
> select up
12911 atoms, 13056 bonds, 4 pseudobonds, 2 models selected
> delete sel
> hide #!10 atoms
> show #!10 cartoons
> show #!9 models
> show #8 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1.1 level 0.003503
> volume #1.1 level 0.00303
> volume #1.1 level 0.001612
> volume #1.1 level 0.0017
> volume #1.1 level 0.0018
> volume #1.1 level 0.0019
> volume #1.1 level 0.002
> volume #1.1 level 0.0021
> volume #1.1 level 0.0025
> volume #1.1 level 0.005
> volume #1.1 color #b2b2b2b9
> volume #1.1 color #b2b2b2bc
> volume #1.1 color #b2b2b2cb
> volume #1.1 color #b2b2b2d3
> volume #1.1 color #b2b2b2da
> volume #1.1 color #b2b2b2db
> volume #1.1 color #b2b2b2de
> volume #1.1 color #b2b2b2e0
> volume #1.1 color #b2b2b2e3
> volume #1.1 color #b2b2b2e4
> volume #1.1 color #b2b2b2e5
> volume #1.1 color #b2b2b2e9
> volume #1.1 color #b2b2b2eb
> volume #1.1 color #b2b2b2ed
> volume #1.1 color #b2b2b2ee
> volume #1.1 color #b2b2b2ef
> volume #1.1 color #b2b2b2f2
> volume #1.1 color #b2b2b2f3
> volume #1.1 color #b2b2b2f4
> volume #1.1 color #b2b2b2f1
> volume #1.1 color #b2b2b2e9
> volume #1.1 color #b2b2b2e7
> volume #1.1 color #b2b2b2d0
> volume #1.1 color #b2b2b2ae
> volume #1.1 color #b2b2b29a
> volume #1.1 color #b2b2b28e
> volume #1.1 color #b2b2b282
> volume #1.1 color #b2b2b264
> volume #1.1 color #b2b2b255
> volume #1.1 color #b2b2b253
> volume #1.1 color #b2b2b24f
> volume #1.1 color #b2b2b245
> volume #1.1 color #b2b2b240
> volume #1.1 color #b2b2b23c
> volume #1.1 color #b2b2b236
> volume #1.1 color #b2b2b231
> volume #1.1 color #b2b2b226
> volume #1.1 color #b2b2b225
> volume #1.1 color #b2b2b226
> volume #1.1 color #b2b2b227
> volume #1.1 color #b2b2b228
> volume #1.1 color #b2b2b22a
> volume #1.1 color #b2b2b22e
> volume #1.1 color #b2b2b234
> volume #1.1 color #b2b2b239
> volume #1.1 color #b2b2b23a
> volume #1.1 color #b2b2b23c
> volume #1.1 color #b2b2b240
> volume #1.1 color #b2b2b248
> volume #1.1 color #b2b2b24a
> volume #1.1 color #b2b2b249
> volume #1.1 color #b2b2b241
> volume #1.1 color #b2b2b240
> volume #1.1 color #b2b2b23c
> save /Users/crowe/Dropbox/rqcH-DR/200731_RqcH-DR-maps-comparison_02.cxs
> cartoon style radius 2
> cartoon style radius 2.5
> cartoon style thickness 2
> cartoon style thickness 1.5
> cartoon style thickness 1
> select clear
> hide #!1 models
> select #7/0:55
6 atoms, 5 bonds, 1 model selected
> select #7/0:54
7 atoms, 7 bonds, 1 model selected
> color sel red
> select clear
> show #!1 models
> open /Users/crowe/Dropbox/rqcH-project/modelling/EPA-
> cl1_modelling/1ehz_aligned.pdb
Chain information for 1ehz_aligned.pdb #11
---
Chain | Description
A | No description available
> mmaker #11 to #10
No chains in reference structure 200502_cl7_50S-PP-tRNA-
YabO_RSR28_H69-full.pdb #10 compatible with BLOSUM-62 similarity matrix
> mmaker #11 to #10 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 200502_cl7_50S-PP-tRNA-YabO_RSR28_H69-full.pdb, chain 2 (#10) with
1ehz_aligned.pdb, chain A (#11), sequence alignment score = 110
RMSD between 51 pruned atom pairs is 0.895 angstroms; (across all 62 pairs:
4.279)
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!10 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> color #11 skyblue
> color #11 byhetero
> select clear
> save /Users/crowe/Dropbox/rqcH-DR/200731_RqcH-DR-maps-comparison_03.cxs
opened ChimeraX session
> volume #1.1 level 0.007
> open /Users/crowe/Dropbox/rqcH-project/modelling/models-for-
> deposition/200724/200602_cl1-50S-P-tRNA-YabO-RqcH-RSR36_header-stripped.pdb
Chain information for 200602_cl1-50S-P-tRNA-YabO-RqcH-RSR36_header-
stripped.pdb #12
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
A | No description available
B | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
K | No description available
L | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
> mmaker #12 to #5
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 200616_cl1-RSR36_50S-only.pdb, chain E (#5) with 200602_cl1-50S-P-
tRNA-YabO-RqcH-RSR36_header-stripped.pdb, chain E (#12), sequence alignment
score = 1361.5
RMSD between 272 pruned atom pairs is 0.000 angstroms; (across all 272 pairs:
0.000)
> hide #!5 models
> hide #!7 models
> hide #8 models
> hide #!9 models
> hide #11 models
> show #!12 atoms
> hide #!12 atoms
> hide #!12 cartoons
> show #!12 cartoons
> color #12 grey
> color #12/A lightgrey
> color #12/0 darkviolet
> color #12/1 gold
> color #12/2 skyblue
> cartoon style modeHelix tube
> cartoon style thickness 1
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show "Side View"
> pwd
Current working directory is: /Users/crowe/Desktop
> cd /Users/crowe/Dropbox/rqcH-DR
Current working directory is: /Users/crowe/Dropbox/rqcH-DR
> cd figures
Current working directory is: /Users/crowe/Dropbox/rqcH-DR/figures
> save 200731_RqcH-cl1_01.png
> hide #!12 models
> show #11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #8 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!7 models
> show #!7 models
> save 200731_RqcH-cl5_01.png
> view name view1
> turn x 90
> turn x -180
> turn x 90
> turn x -90
> turn x 45
> save 200731_RqcH-cl5_02.png
> view name view2
> hide #!5 models
> hide #!7 models
> hide #8 models
> hide #!9 models
> hide #11 models
> show #!12 models
> save 200731_RqcH-cl1_02.png
> select #12/2:30
23 atoms, 25 bonds, 1 model selected
> select up
1563 atoms, 1744 bonds, 1 model selected
> select up
93796 atoms, 101893 bonds, 1 model selected
> select down
1563 atoms, 1744 bonds, 1 model selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 1563 atom styles
> show sel atoms
> select clear
> color sel red
> select clear
> color sel red
> view view2
> select clear
> save 200731_RqcH-cl1_02.png
> view view1
> save 200731_RqcH-cl1_01.png
> save 200731_RqcH-cl1_01a.png
> view name view1a
> hide #!12 models
> show #11 models
> show #!9 models
> show #8 models
> show #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> save 200731_RqcH-cl5_01a.png
> hide #!1 models
> show #!1 models
> show #!1.1 models
> view view1
> hide #!1 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> save /Users/crowe/Dropbox/rqcH-DR/200731_RqcH-DR-maps-comparison_04.cxs
opened ChimeraX session
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.7 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 32 GB
Boot ROM Version: 1037.140.50.0.0
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 9 days 2:00
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal: Supported, feature set macOS GPUFamily2 v1
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: No
Connection Type: Internal
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: YPPY075J05DS
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
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: 2.1.1
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
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: 1.0
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 , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during session save |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Hi Caillan,
--Eric