![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 21 months ago
#14574 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-11.7.10-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [3373]
Path: /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.7.1 (1.7.1.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [3373]
User ID: 502
Date/Time: 2024-02-11 15:44:47.378 -0800
OS Version: macOS 11.7.10 (20G1427)
Report Version: 12
Anonymous UUID: 9D5A82DA-5494-0043-33D6-18A4A6399DB6
Sleep/Wake UUID: 20B797C9-71E4-4BA0-9F7F-640D3A335D85
Time Awake Since Boot: 20000 seconds
Time Since Wake: 6100 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 100b7f000-100b83000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff2070b90e __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff2073a5bd pthread_kill + 263
2 libsystem_c.dylib 0x00007fff2061ebd5 raise + 26
3 org.python.python 0x0000000100e085d4 faulthandler_fatal_error + 388
4 libsystem_platform.dylib 0x00007fff2077fd7d _sigtramp + 29
5 ??? 000000000000000000 0 + 0
6 org.python.python 0x0000000100cb78f4 tupletraverse + 52
7 org.python.python 0x0000000100e04888 gc_collect_main + 2568
8 org.python.python 0x0000000100e06102 _PyObject_GC_Link + 306
9 org.python.python 0x0000000100e06197 _PyObject_GC_New + 119
10 org.python.python 0x0000000100c89d2b dictvalues_iter + 27
11 org.python.python 0x0000000100c66a65 list_extend + 405
12 org.python.python 0x0000000100c66745 list_vectorcall + 181
13 org.python.python 0x0000000100d66030 _PyEval_EvalFrameDefault + 67696
14 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
15 cymol.cpython-311-darwin.so 0x000000011ef54717 __Pyx_PyObject_CallOneArg(_object*, _object*) + 199
16 cymol.cpython-311-darwin.so 0x000000011ef8307e __pyx_pw_8chimerax_6atomic_5cymol_9CyResidue_47string(_object*, _object*, _object*) + 4366
17 org.python.python 0x0000000100c9b7c4 cfunction_call + 52
18 cymol.cpython-311-darwin.so 0x000000011ef5484c __Pyx_PyObject_CallNoArg(_object*) + 172
19 cymol.cpython-311-darwin.so 0x000000011ef77bd4 __pyx_pw_8chimerax_6atomic_5cymol_9CyResidue_9__str__(_object*) + 180
20 org.python.python 0x0000000100ca0aac PyObject_Str + 156
21 org.python.python 0x0000000100d65de9 _PyEval_EvalFrameDefault + 67113
22 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
23 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
24 org.python.python 0x0000000100cc4995 slot_tp_init + 181
25 org.python.python 0x0000000100cbab4a type_call + 122
26 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
27 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
28 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
29 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
30 org.python.python 0x0000000100cc4995 slot_tp_init + 181
31 org.python.python 0x0000000100cbab4a type_call + 122
32 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
33 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
34 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
35 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
36 org.python.python 0x0000000100cc4995 slot_tp_init + 181
37 org.python.python 0x0000000100cbab4a type_call + 122
38 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
39 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
40 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
41 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
42 org.python.python 0x0000000100cc4995 slot_tp_init + 181
43 org.python.python 0x0000000100cbab4a type_call + 122
44 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
45 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
46 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
47 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
48 org.python.python 0x0000000100cc4995 slot_tp_init + 181
49 org.python.python 0x0000000100cbab4a type_call + 122
50 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
51 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
52 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
53 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
54 org.python.python 0x0000000100cc4995 slot_tp_init + 181
55 org.python.python 0x0000000100cbab4a type_call + 122
56 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
57 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
58 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
59 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
60 org.python.python 0x0000000100cc4995 slot_tp_init + 181
61 org.python.python 0x0000000100cbab4a type_call + 122
62 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
63 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
64 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
65 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
66 org.python.python 0x0000000100cc4995 slot_tp_init + 181
67 org.python.python 0x0000000100cbab4a type_call + 122
68 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
69 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
70 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
71 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
72 org.python.python 0x0000000100cc4995 slot_tp_init + 181
73 org.python.python 0x0000000100cbab4a type_call + 122
74 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
75 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
76 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
77 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
78 org.python.python 0x0000000100cc4995 slot_tp_init + 181
79 org.python.python 0x0000000100cbab4a type_call + 122
80 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
81 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
82 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
83 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
84 org.python.python 0x0000000100cc4995 slot_tp_init + 181
85 org.python.python 0x0000000100cbab4a type_call + 122
86 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
87 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
88 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
89 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
90 org.python.python 0x0000000100cc4995 slot_tp_init + 181
91 org.python.python 0x0000000100cbab4a type_call + 122
92 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
93 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
94 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
95 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
96 org.python.python 0x0000000100cc4995 slot_tp_init + 181
97 org.python.python 0x0000000100cbab4a type_call + 122
98 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
99 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
100 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
101 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
102 org.python.python 0x0000000100cc4995 slot_tp_init + 181
103 org.python.python 0x0000000100cbab4a type_call + 122
104 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
105 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
106 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
107 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
108 org.python.python 0x0000000100cc4995 slot_tp_init + 181
109 org.python.python 0x0000000100cbab4a type_call + 122
110 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
111 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
112 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
113 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
114 org.python.python 0x0000000100cc4995 slot_tp_init + 181
115 org.python.python 0x0000000100cbab4a type_call + 122
116 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
117 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
118 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
119 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
120 org.python.python 0x0000000100cc4995 slot_tp_init + 181
121 org.python.python 0x0000000100cbab4a type_call + 122
122 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
123 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
124 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
125 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
126 org.python.python 0x0000000100cc4995 slot_tp_init + 181
127 org.python.python 0x0000000100cbab4a type_call + 122
128 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
129 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
130 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
131 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
132 org.python.python 0x0000000100cc4995 slot_tp_init + 181
133 org.python.python 0x0000000100cbab4a type_call + 122
134 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
135 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
136 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
137 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
138 org.python.python 0x0000000100cc4995 slot_tp_init + 181
139 org.python.python 0x0000000100cbab4a type_call + 122
140 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
141 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
142 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
143 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
144 org.python.python 0x0000000100cc4995 slot_tp_init + 181
145 org.python.python 0x0000000100cbab4a type_call + 122
146 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
147 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
148 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
149 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
150 org.python.python 0x0000000100cc4995 slot_tp_init + 181
151 org.python.python 0x0000000100cbab4a type_call + 122
152 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
153 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
154 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
155 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
156 org.python.python 0x0000000100cc4995 slot_tp_init + 181
157 org.python.python 0x0000000100cbab4a type_call + 122
158 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
159 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
160 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
161 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
162 org.python.python 0x0000000100cc4995 slot_tp_init + 181
163 org.python.python 0x0000000100cbab4a type_call + 122
164 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
165 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
166 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
167 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
168 org.python.python 0x0000000100cc4995 slot_tp_init + 181
169 org.python.python 0x0000000100cbab4a type_call + 122
170 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
171 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
172 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
173 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
174 org.python.python 0x0000000100cc4995 slot_tp_init + 181
175 org.python.python 0x0000000100cbab4a type_call + 122
176 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
177 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
178 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
179 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
180 org.python.python 0x0000000100cc4995 slot_tp_init + 181
181 org.python.python 0x0000000100cbab4a type_call + 122
182 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
183 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
184 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
185 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
186 org.python.python 0x0000000100cc4995 slot_tp_init + 181
187 org.python.python 0x0000000100cbab4a type_call + 122
188 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
189 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
190 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
191 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
192 org.python.python 0x0000000100cc4995 slot_tp_init + 181
193 org.python.python 0x0000000100cbab4a type_call + 122
194 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
195 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
196 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
197 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
198 org.python.python 0x0000000100cc4995 slot_tp_init + 181
199 org.python.python 0x0000000100cbab4a type_call + 122
200 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
201 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
202 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
203 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
204 org.python.python 0x0000000100cc4995 slot_tp_init + 181
205 org.python.python 0x0000000100cbab4a type_call + 122
206 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
207 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
208 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
209 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
210 org.python.python 0x0000000100cc4995 slot_tp_init + 181
211 org.python.python 0x0000000100cbab4a type_call + 122
212 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
213 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
214 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
215 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
216 org.python.python 0x0000000100cc4995 slot_tp_init + 181
217 org.python.python 0x0000000100cbab4a type_call + 122
218 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
219 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
220 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
221 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
222 org.python.python 0x0000000100cc4995 slot_tp_init + 181
223 org.python.python 0x0000000100cbab4a type_call + 122
224 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
225 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
226 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
227 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
228 org.python.python 0x0000000100cc4995 slot_tp_init + 181
229 org.python.python 0x0000000100cbab4a type_call + 122
230 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
231 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
232 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
233 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
234 org.python.python 0x0000000100cc4995 slot_tp_init + 181
235 org.python.python 0x0000000100cbab4a type_call + 122
236 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
237 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
238 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
239 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
240 org.python.python 0x0000000100cc4995 slot_tp_init + 181
241 org.python.python 0x0000000100cbab4a type_call + 122
242 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
243 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
244 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
245 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
246 org.python.python 0x0000000100cc4995 slot_tp_init + 181
247 org.python.python 0x0000000100cbab4a type_call + 122
248 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
249 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
250 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
251 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
252 org.python.python 0x0000000100cc4995 slot_tp_init + 181
253 org.python.python 0x0000000100cbab4a type_call + 122
254 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
255 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
256 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
257 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
258 org.python.python 0x0000000100cc4995 slot_tp_init + 181
259 org.python.python 0x0000000100cbab4a type_call + 122
260 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
261 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
262 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
263 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
264 org.python.python 0x0000000100cc4995 slot_tp_init + 181
265 org.python.python 0x0000000100cbab4a type_call + 122
266 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
267 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
268 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
269 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
270 org.python.python 0x0000000100cc4995 slot_tp_init + 181
271 org.python.python 0x0000000100cbab4a type_call + 122
272 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
273 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
274 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
275 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
276 org.python.python 0x0000000100cc4995 slot_tp_init + 181
277 org.python.python 0x0000000100cbab4a type_call + 122
278 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
279 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
280 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
281 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
282 org.python.python 0x0000000100cc4995 slot_tp_init + 181
283 org.python.python 0x0000000100cbab4a type_call + 122
284 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
285 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
286 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
287 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
288 org.python.python 0x0000000100cc4995 slot_tp_init + 181
289 org.python.python 0x0000000100cbab4a type_call + 122
290 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
291 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
292 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
293 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
294 org.python.python 0x0000000100cc4995 slot_tp_init + 181
295 org.python.python 0x0000000100cbab4a type_call + 122
296 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
297 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
298 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
299 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
300 org.python.python 0x0000000100cc4995 slot_tp_init + 181
301 org.python.python 0x0000000100cbab4a type_call + 122
302 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
303 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
304 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
305 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
306 org.python.python 0x0000000100cc4995 slot_tp_init + 181
307 org.python.python 0x0000000100cbab4a type_call + 122
308 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
309 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
310 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
311 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
312 org.python.python 0x0000000100cc4995 slot_tp_init + 181
313 org.python.python 0x0000000100cbab4a type_call + 122
314 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
315 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
316 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
317 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
318 org.python.python 0x0000000100cc4995 slot_tp_init + 181
319 org.python.python 0x0000000100cbab4a type_call + 122
320 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
321 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
322 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
323 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
324 org.python.python 0x0000000100cc4995 slot_tp_init + 181
325 org.python.python 0x0000000100cbab4a type_call + 122
326 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
327 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
328 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
329 org.python.python 0x0000000100c36670 _PyObject_FastCallDictTstate + 96
330 org.python.python 0x0000000100cc4995 slot_tp_init + 181
331 org.python.python 0x0000000100cbab4a type_call + 122
332 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
333 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
334 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
335 org.python.python 0x0000000100c36f78 _PyVectorcall_Call + 120
336 org.python.python 0x0000000100d6754a _PyEval_EvalFrameDefault + 73098
337 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
338 org.python.python 0x0000000100c3a79e method_vectorcall + 334
339 org.python.python 0x0000000100c36f78 _PyVectorcall_Call + 120
340 org.python.python 0x0000000100d6754a _PyEval_EvalFrameDefault + 73098
341 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
342 org.python.python 0x0000000100c36f78 _PyVectorcall_Call + 120
343 org.python.python 0x0000000100d6754a _PyEval_EvalFrameDefault + 73098
344 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
345 org.python.python 0x0000000100c3a816 method_vectorcall + 454
346 QtCore.abi3.so 0x000000010bc51f98 PyQtSlot::call(_object*, _object*) const + 40
347 QtCore.abi3.so 0x000000010bc51e9a PyQtSlot::invoke(void**, _object*, void*, bool) const + 362
348 QtCore.abi3.so 0x000000010bc52de5 PyQtSlotProxy::unislot(void**) + 85
349 QtCore.abi3.so 0x000000010bc52d5a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
350 QtCore 0x000000010bf68d67 0x10beab000 + 777575
351 QtWidgets 0x000000010eb9fbe1 0x10e9b1000 + 2026465
352 QtCore 0x000000010bf69022 0x10beab000 + 778274
353 QtWidgets 0x000000010eae353f 0x10e9b1000 + 1254719
354 QtWidgets 0x000000010eae33dc 0x10e9b1000 + 1254364
355 QtWidgets 0x000000010eae4499 QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 185
356 QtWidgets 0x000000010ea0ffd5 QWidget::event(QEvent*) + 389
357 QtWidgets 0x000000010e9bda87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
358 QtWidgets 0x000000010e9bffc2 QApplication::notify(QObject*, QEvent*) + 6002
359 QtWidgets.abi3.so 0x000000010e4da1e6 sipQApplication::notify(QObject*, QEvent*) + 230
360 QtCore 0x000000010bf18c3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
361 QtWidgets 0x000000010e9be197 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 935
362 QtWidgets 0x000000010ea2680e 0x10e9b1000 + 481294
363 QtWidgets 0x000000010ea25689 0x10e9b1000 + 476809
364 QtWidgets 0x000000010e9bda87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247
365 QtWidgets 0x000000010e9bea43 QApplication::notify(QObject*, QEvent*) + 499
366 QtWidgets.abi3.so 0x000000010e4da1e6 sipQApplication::notify(QObject*, QEvent*) + 230
367 QtCore 0x000000010bf18c3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170
368 QtGui 0x000000010f1e76dc QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 2332
369 QtGui 0x000000010f1e7478 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 1720
370 QtGui 0x000000010f23f29c QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 444
371 libqcocoa.dylib 0x000000011bafd29b 0x11bae3000 + 107163
372 com.apple.CoreFoundation 0x00007fff20832cdc __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
373 com.apple.CoreFoundation 0x00007fff20832c44 __CFRunLoopDoSource0 + 180
374 com.apple.CoreFoundation 0x00007fff208329c4 __CFRunLoopDoSources0 + 242
375 com.apple.CoreFoundation 0x00007fff208313ec __CFRunLoopRun + 893
376 com.apple.CoreFoundation 0x00007fff208309ac CFRunLoopRunSpecific + 563
377 com.apple.HIToolbox 0x00007fff28a7b1f3 RunCurrentEventLoopInMode + 292
378 com.apple.HIToolbox 0x00007fff28a7ae26 ReceiveNextEventCommon + 284
379 com.apple.HIToolbox 0x00007fff28a7acf3 _BlockUntilNextEventMatchingListInModeWithFilter + 70
380 com.apple.AppKit 0x00007fff2303aad2 _DPSNextEvent + 864
381 com.apple.AppKit 0x00007fff230392a5 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1364
382 com.apple.AppKit 0x00007fff2302b5c9 -[NSApplication run] + 586
383 libqcocoa.dylib 0x000000011bafc0ac 0x11bae3000 + 102572
384 QtCore 0x000000010bf22326 QEventLoop::exec(QFlags) + 486
385 QtCore 0x000000010bf19235 QCoreApplication::exec() + 133
386 QtWidgets.abi3.so 0x000000010e5c6d9a meth_QApplication_exec(_object*, _object*) + 90
387 org.python.python 0x0000000100c9b7ea cfunction_call + 90
388 org.python.python 0x0000000100c363b1 _PyObject_MakeTpCall + 129
389 org.python.python 0x0000000100d643e7 _PyEval_EvalFrameDefault + 60455
390 org.python.python 0x0000000100d5447a PyEval_EvalCode + 282
391 org.python.python 0x0000000100d4ece3 builtin_exec + 483
392 org.python.python 0x0000000100c9c144 cfunction_vectorcall_FASTCALL_KEYWORDS + 68
393 org.python.python 0x0000000100d642ef _PyEval_EvalFrameDefault + 60207
394 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
395 org.python.python 0x0000000100e016fd pymain_run_module + 253
396 org.python.python 0x0000000100e011c1 Py_RunMain + 2225
397 org.python.python 0x0000000100e0217b pymain_main + 43
398 org.python.python 0x0000000100e0214a Py_Main + 42
399 edu.ucsf.cgl.ChimeraX 0x0000000100b82d9a main + 122
400 libdyld.dylib 0x00007fff20755f3d start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff20707cbe __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2073ae49 _pthread_cond_wait + 1298
2 libopenblas64_.0.dylib 0x00000001024fb67f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
4 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 2:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff2070e1b2 kevent64 + 10
1 QtWebEngineCore 0x0000000114003a2a 0x1100a3000 + 66456106
2 QtWebEngineCore 0x0000000114003927 0x1100a3000 + 66455847
3 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
4 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
5 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
6 QtWebEngineCore 0x0000000113f8a2ad 0x1100a3000 + 65958573
7 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
8 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
9 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 3:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff2070e1b2 kevent64 + 10
1 QtWebEngineCore 0x0000000114003a2a 0x1100a3000 + 66456106
2 QtWebEngineCore 0x0000000114003927 0x1100a3000 + 66455847
3 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
4 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
5 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
6 QtWebEngineCore 0x0000000112ec83a2 0x1100a3000 + 48386978
7 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
8 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
9 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
10 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 4:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 5:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff20707cbe __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2073ae49 _pthread_cond_wait + 1298
2 QtWebEngineCore 0x0000000113fc9d1b 0x1100a3000 + 66219291
3 QtWebEngineCore 0x000000011609792d 0x1100a3000 + 100616493
4 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
5 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
6 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 6:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 7:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff2070e1b2 kevent64 + 10
1 QtWebEngineCore 0x0000000114003a2a 0x1100a3000 + 66456106
2 QtWebEngineCore 0x0000000114003927 0x1100a3000 + 66455847
3 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
4 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
5 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
6 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
7 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
8 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 9:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 10:: NetworkService
0 libsystem_kernel.dylib 0x00007fff2070e1b2 kevent64 + 10
1 QtWebEngineCore 0x0000000114003a2a 0x1100a3000 + 66456106
2 QtWebEngineCore 0x0000000114003927 0x1100a3000 + 66455847
3 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
4 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
5 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
6 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
7 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
8 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
9 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 12:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113f967bf 0x1100a3000 + 66009023
4 QtWebEngineCore 0x0000000113f9726c 0x1100a3000 + 66011756
5 QtWebEngineCore 0x0000000113f96ecd 0x1100a3000 + 66010829
6 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
7 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 14:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113f967bf 0x1100a3000 + 66009023
4 QtWebEngineCore 0x0000000113f9726c 0x1100a3000 + 66011756
5 QtWebEngineCore 0x0000000113f96ddd 0x1100a3000 + 66010589
6 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
7 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 15:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff20832ebf __CFRunLoopServiceMachPort + 316
3 com.apple.CoreFoundation 0x00007fff2083159f __CFRunLoopRun + 1328
4 com.apple.CoreFoundation 0x00007fff208309ac CFRunLoopRunSpecific + 563
5 com.apple.AppKit 0x00007fff231c0b7a _NSEventThread + 124
6 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
7 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 16:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113fd1bef 0x1100a3000 + 66251759
4 QtWebEngineCore 0x0000000113f071c9 0x1100a3000 + 65421769
5 QtWebEngineCore 0x0000000113f80a5c 0x1100a3000 + 65919580
6 QtWebEngineCore 0x0000000113f38998 0x1100a3000 + 65624472
7 QtWebEngineCore 0x0000000113fa2eb8 0x1100a3000 + 66059960
8 QtWebEngineCore 0x0000000113fa304a 0x1100a3000 + 66060362
9 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
10 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
11 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 17:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113f967bf 0x1100a3000 + 66009023
4 QtWebEngineCore 0x0000000113f96f9a 0x1100a3000 + 66011034
5 QtWebEngineCore 0x0000000113f96e0d 0x1100a3000 + 66010637
6 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
7 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 18:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113f967bf 0x1100a3000 + 66009023
4 QtWebEngineCore 0x0000000113f9726c 0x1100a3000 + 66011756
5 QtWebEngineCore 0x0000000113f96e6d 0x1100a3000 + 66010733
6 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
7 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 19:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff2070529a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff2070560c mach_msg + 60
2 QtWebEngineCore 0x0000000113fd1e26 0x1100a3000 + 66252326
3 QtWebEngineCore 0x0000000113f967bf 0x1100a3000 + 66009023
4 QtWebEngineCore 0x0000000113f9726c 0x1100a3000 + 66011756
5 QtWebEngineCore 0x0000000113f96e6d 0x1100a3000 + 66010733
6 QtWebEngineCore 0x0000000113fca908 0x1100a3000 + 66222344
7 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
8 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 20:
0 libsystem_pthread.dylib 0x00007fff20736420 start_wqthread + 0
Thread 21:
0 libsystem_pthread.dylib 0x00007fff20736420 start_wqthread + 0
Thread 22:
0 libsystem_pthread.dylib 0x00007fff20736420 start_wqthread + 0
Thread 23:
0 libsystem_kernel.dylib 0x00007fff20707cbe __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff2073ae49 _pthread_cond_wait + 1298
2 org.python.python 0x0000000100dee214 PyThread_acquire_lock_timed + 340
3 org.python.python 0x0000000100e71d9e acquire_timed + 318
4 org.python.python 0x0000000100e71fdc lock_PyThread_acquire_lock + 44
5 org.python.python 0x0000000100c47b07 method_vectorcall_VARARGS_KEYWORDS + 167
6 org.python.python 0x0000000100d642ef _PyEval_EvalFrameDefault + 60207
7 org.python.python 0x0000000100d6a4d0 _PyEval_Vector + 128
8 org.python.python 0x0000000100c3a816 method_vectorcall + 454
9 org.python.python 0x0000000100e72b26 thread_run + 230
10 org.python.python 0x0000000100dedea4 pythread_wrapper + 36
11 libsystem_pthread.dylib 0x00007fff2073a8fc _pthread_start + 224
12 libsystem_pthread.dylib 0x00007fff20736443 thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010f122e00 rcx: 0x00007fd2ed5dd9e8 rdx: 0x0000000000000000
rdi: 0x0000000000000103 rsi: 0x000000000000000b rbp: 0x00007fd2ed5dda10 rsp: 0x00007fd2ed5dd9e8
r8: 0x0000000000000002 r9: 0xcccccccccccccccd r10: 0x000000010f122e00 r11: 0x0000000000000246
r12: 0x0000000000000103 r13: 0x000000013a489c01 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff2070b90e rfl: 0x0000000000000246 cr2: 0x0000000100dd1630
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream:
ff ff ff ff 48 89 d8 48-8b 00 48 ff c2 48 39 c3 ....H..H..H..H9.
75 f5 48 8d 3d c5 12 16-00 48 8d b5 70 ff ff ff u.H.=....H..p...
31 c0 e8 bf 83 fe ff 48-8b 05 68 e7 16 00 48 8b 1......H..h...H.
00 48 3b 45 d8 75 0d 48-83 c4 70 5b 41 5c 41 5e .H;E.u.H..p[A\A^
41 5f 5d c3 e8 cd ae 0e-00 66 2e 0f 1f 84 00 00 A_]......f......
00 00 00 0f 1f 00 55 48-89 e5 53 50 48 8b 47 08 ......UH..SPH.G.
[f6]80 a9 00 00 00 40 75-09 31 c0 48 83 c4 08 5b ......@u.1.H...[ /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX
0x100b90000 - 0x100f73fff +org.python.python (3.11.2, [c] 2001-2023 Python Software Foundation. - 3.11.2) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/Python
0x1014cd000 - 0x1014d8fff +math.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/math.cpython-311-darwin.so
0x1015e9000 - 0x1015f8fff +_datetime.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_datetime.cpython-311-darwin.so
0x10160d000 - 0x101610fff +_typing.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_typing.cpython-311-darwin.so
0x10171d000 - 0x101724fff +zlib.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/zlib.cpython-311-darwin.so
0x101735000 - 0x101738fff +_bz2.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_bz2.cpython-311-darwin.so
0x101745000 - 0x101774fff +_lzma.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_lzma.cpython-311-darwin.so
0x101789000 - 0x10178cfff +_bisect.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_bisect.cpython-311-darwin.so
0x101799000 - 0x10179cfff +_random.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_random.cpython-311-darwin.so
0x1017a9000 - 0x1017b0fff +_sha512.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_sha512.cpython-311-darwin.so
0x1018bd000 - 0x1018c4fff +binascii.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/binascii.cpython-311-darwin.so
0x1018d1000 - 0x1018d8fff +_struct.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_struct.cpython-311-darwin.so
0x1018e9000 - 0x1018ecfff +fcntl.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/fcntl.cpython-311-darwin.so
0x1018f9000 - 0x1018fcfff +_posixsubprocess.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_posixsubprocess.cpython-311-darwin.so
0x101909000 - 0x101910fff +select.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/select.cpython-311-darwin.so
0x101a1d000 - 0x101a20fff +_arrays.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/arrays/_arrays.cpython-311-darwin.so
0x101a2d000 - 0x101b40fff +libarrays.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/arrays/lib/libarrays.dylib
0x101b6d000 - 0x101b74fff +_json.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_json.cpython-311-darwin.so
0x101b81000 - 0x102034fff +_multiarray_umath.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-darwin.so
0x1021ad000 - 0x105eccfff +libopenblas64_.0.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libopenblas64_.0.dylib
0x10618d000 - 0x1067cffff +libgfortran.5.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libgfortran.5.dylib
0x10680a000 - 0x106857fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x106861000 - 0x106871fff +libgcc_s.1.1.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/.dylibs/libgcc_s.1.1.dylib
0x108a83000 - 0x108a9efff +_pickle.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_pickle.cpython-311-darwin.so
0x108ab3000 - 0x108ab6fff +_contextvars.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_contextvars.cpython-311-darwin.so
0x108ac3000 - 0x108ad6fff +_multiarray_tests.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_multiarray_tests.cpython-311-darwin.so
0x108bef000 - 0x108c02fff +_ctypes.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so
0x108c1b000 - 0x108c3afff +_umath_linalg.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/linalg/_umath_linalg.cpython-311-darwin.so
0x108d53000 - 0x108d66fff +_pocketfft_internal.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/fft/_pocketfft_internal.cpython-311-darwin.so
0x108d73000 - 0x108de6fff +mtrand.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/mtrand.cpython-311-darwin.so
0x108e4b000 - 0x108e6afff +bit_generator.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/bit_generator.cpython-311-darwin.so
0x108e8f000 - 0x108ebefff +_common.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_common.cpython-311-darwin.so
0x108edf000 - 0x108ee6fff +_hashlib.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_hashlib.cpython-311-darwin.so
0x108ef7000 - 0x10911efff +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/libcrypto.1.1.dylib
0x1091bf000 - 0x1091c6fff +_blake2.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_blake2.cpython-311-darwin.so
0x1091d3000 - 0x109226fff +_bounded_integers.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_bounded_integers.cpython-311-darwin.so
0x109257000 - 0x109266fff +_mt19937.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_mt19937.cpython-311-darwin.so
0x10927b000 - 0x109286fff +_philox.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_philox.cpython-311-darwin.so
0x10929b000 - 0x1092aafff +_pcg64.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_pcg64.cpython-311-darwin.so
0x1092bf000 - 0x1092c6fff +_sfc64.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_sfc64.cpython-311-darwin.so
0x1092d7000 - 0x109366fff +_generator.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/random/_generator.cpython-311-darwin.so
0x1094d3000 - 0x1094d6fff +_opcode.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_opcode.cpython-311-darwin.so
0x10b5e3000 - 0x10b606fff +_geometry.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/_geometry.cpython-311-darwin.so
0x10bb1f000 - 0x10bca2fff +QtCore.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtCore.abi3.so
0x10beab000 - 0x10c3aefff +QtCore (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtCore.framework/Versions/A/QtCore
0x10e371000 - 0x10e388fff +sip.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/sip.cpython-311-darwin.so
0x10e3a1000 - 0x10e64cfff +QtWidgets.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWidgets.abi3.so
0x10e9b1000 - 0x10ee6cfff +QtWidgets (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWidgets.framework/Versions/A/QtWidgets
0x10efc9000 - 0x10efd8fff +QtWebEngineWidgets.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWebEngineWidgets.abi3.so
0x10efed000 - 0x10f000fff +QtWebEngineWidgets (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWebEngineWidgets.framework/Versions/A/QtWebEngineWidgets
0x10f019000 - 0x10f02cfff +QtQuickWidgets (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQuickWidgets.framework/Versions/A/QtQuickWidgets
0x10f04b000 - 0x10f0e6fff dyld (852.2) /usr/lib/dyld
0x10f163000 - 0x10f80afff +QtGui (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtGui.framework/Versions/A/QtGui
0x10f937000 - 0x10f9c2fff +QtDBus (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtDBus.framework/Versions/A/QtDBus
0x10f9e7000 - 0x10fb4efff +QtGui.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtGui.abi3.so
0x110027000 - 0x110072fff +QtPrintSupport (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtPrintSupport.framework/Versions/A/QtPrintSupport
0x1100a3000 - 0x119e0afff +QtWebEngineCore (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWebEngineCore.framework/Versions/A/QtWebEngineCore
0x11aa9f000 - 0x11ae82fff +QtQuick (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQuick.framework/Versions/A/QtQuick
0x11afe3000 - 0x11b04afff +QtOpenGL (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtOpenGL.framework/Versions/A/QtOpenGL
0x11b07b000 - 0x11b102fff +QtQmlModels (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQmlModels.framework/Versions/A/QtQmlModels
0x11b133000 - 0x11b166fff +QtWebChannel (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtWebChannel.framework/Versions/A/QtWebChannel
0x11b17f000 - 0x11b562fff +QtQml (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtQml.framework/Versions/A/QtQml
0x11b61f000 - 0x11b752fff +QtNetwork (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtNetwork.framework/Versions/A/QtNetwork
0x11b7a3000 - 0x11b81afff +QtPositioning (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/lib/QtPositioning.framework/Versions/A/QtPositioning
0x11b83f000 - 0x11b846fff +QtWebChannel.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWebChannel.abi3.so
0x11b857000 - 0x11b8c6fff +QtNetwork.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtNetwork.abi3.so
0x11b96f000 - 0x11b99efff +QtWebEngineCore.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtWebEngineCore.abi3.so
0x11ba03000 - 0x11ba26fff +QtPrintSupport.abi3.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/QtPrintSupport.abi3.so
0x11bae3000 - 0x11bb82fff +libqcocoa.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/plugins/platforms/libqcocoa.dylib
0x11cd43000 - 0x11cd52fff libobjc-trampolines.dylib (824.1) /usr/lib/libobjc-trampolines.dylib
0x11d7c8000 - 0x11d7effff +libqmacstyle.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/PyQt6/Qt6/plugins/styles/libqmacstyle.dylib
0x11d808000 - 0x11d817fff +_socket.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_socket.cpython-311-darwin.so
0x11e61c000 - 0x11e647fff +pyexpat.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/pyexpat.cpython-311-darwin.so
0x11e760000 - 0x11e76bfff +array.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/array.cpython-311-darwin.so
0x11e77c000 - 0x11e77ffff +_heapq.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_heapq.cpython-311-darwin.so
0x11e78c000 - 0x11e78ffff +_queue.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_queue.cpython-311-darwin.so
0x11e99c000 - 0x11e99ffff +grp.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/grp.cpython-311-darwin.so
0x11e9ac000 - 0x11e9b3fff +_csv.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/lib-dynload/_csv.cpython-311-darwin.so
0x11ecc0000 - 0x11ecc3fff +_load_libs.cpython-311-darwin.so (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic_lib/_load_libs.cpython-311-darwin.so
0x11ecd0000 - 0x11edf3fff +libatomstruct.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic_lib/lib/libatomstruct.dylib
0x11eea8000 - 0x11eeaffff +libelement.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic_lib/lib/libelement.dylib
0x11eec4000 - 0x11eec7fff +libpyinstance.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic_lib/lib/libpyinstance.dylib
0x11eed4000 - 0x11ef07fff +libmolc.dylib (0) /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/libmolc.dylib
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0x7fff6bc46000 - 0x7fff6bc4cfff libCoreFSCache.dylib (200.12) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x7fff6bc4d000 - 0x7fff6bc51fff libCoreVMClient.dylib (200.12) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x7fff6bc52000 - 0x7fff6bc61fff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff6bc62000 - 0x7fff6bc64fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x7fff6bc65000 - 0x7fff6bc6dfff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x7fff6bc6e000 - 0x7fff6bca1fff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x7fff6bca2000 - 0x7fff6bcdefff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff6bcdf000 - 0x7fff6be72fff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x7fff6be73000 - 0x7fff6be7dfff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x7fff6be7e000 - 0x7fff6bffbfff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x7fff6bffc000 - 0x7fff6c024fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x7fff6d2bd000 - 0x7fff6d315fff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff6e3bf000 - 0x7fff6e3c6fff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x7fff6e3c7000 - 0x7fff6e4aefff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x7fff6fa34000 - 0x7fff6fa46fff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging
0x7fff73d64000 - 0x7fff73d6ffff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x7fff73f85000 - 0x7fff73f9dfff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x7fff778ac000 - 0x7fff778b3fff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 640K 5
Activity Tracing 256K 1
CG backing stores 2880K 6
CG image 4192K 41
CG raster data 3896K 6
CoreAnimation 12.6M 42
CoreGraphics 12K 2
CoreUI image data 2876K 24
Foundation 32K 2
Kernel Alloc Once 8K 1
MALLOC 475.0M 445
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 384K 4
STACK GUARD 92K 23
Stack 162.7M 24
Stack Guard 56.0M 1
VM_ALLOCATE 160.8M 202
__DATA 37.9M 632
__DATA_CONST 25.8M 308
__DATA_DIRTY 1707K 211
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 532.1M 258
__OBJC_RO 70.3M 1
__OBJC_RW 2496K 2
__TEXT 653.9M 622
__UNICODE 588K 1
mapped file 609.5M 79
shared memory 3096K 28
=========== ======= =======
TOTAL 3.0G 2985
TOTAL, minus reserved VM space 2.8G 2985
System Profile:
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1
Boot Volume File System Type: apfs
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1867 MHz, 0x80AD, 0x483943434E4E4E424C54414C41522D4E5544
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1867 MHz, 0x80AD, 0x483943434E4E4E424C54414C41522D4E5544
USB Device: USB 3.0 Bus
USB Device: Bluetooth USB Host Controller
USB Device: USB Receiver
USB Device: USB Receiver
Serial ATA Device: APPLE SSD SM0128G, 121.33 GB
Model: MacBookPro12,1, BootROM 481.0.0.0.0, 2 processors, Dual-Core Intel Core i5, 2.7 GHz, 8 GB, SMC 2.28f7
Graphics: kHW_IntelIris6100Item, Intel Iris Graphics 6100, spdisplays_builtin
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x133), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1680.11)
Bluetooth: Version 8.0.5d7, 3 services, 18 devices, 1 incoming serial ports
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> fetch 4UN3
Unknown command: fetch 4UN3
> open 4UN3 format mmcif fromDatabase pdb
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #1
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #1
---
MG — magnesium ion
> delete solvent
> addh
Summary of feedback from adding hydrogens to 4un3 #1
---
warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond
partners
notes | Termini for 4un3 (#1) chain A determined from SEQRES records
Termini for 4un3 (#1) chain B determined from SEQRES records
Termini for 4un3 (#1) chain C determined from SEQRES records
Termini for 4un3 (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B
SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B
ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364
Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2
1358 hydrogen bonds
Adding 'H' to /B LYS 4
Adding 'H' to /B THR 386
Adding 'H' to /B SER 719
Adding 'H' to /B ASN 776
Adding 'H' to /B GLY 1030
2 messages similar to the above omitted
/B GLN 1364 is not terminus, removing H atom from 'C'
/D DA 2 is not terminus, removing H atom from O5'
12183 hydrogens added
> set bgColor white
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
Drag select of 151 atoms, 1426 residues, 19 pseudobonds, 132 bonds, 142 shapes
> color (#!1 & sel) gray
> select clear
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> color sel orange red
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> color sel blue
> select clear
Drag select of 119 atoms, 848 residues, 12 pseudobonds, 108 bonds, 57 shapes
> hide sel cartoons
> hide sel atoms
Drag select of 18 atoms, 179 residues, 1 pseudobonds, 16 bonds, 8 shapes
Drag select of 2 atoms, 247 residues, 2 pseudobonds, 36 shapes
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 70 residues
> hide sel atoms
> hide sel cartoons
Drag select of 16 atoms, 29 residues, 1 pseudobonds, 13 bonds, 8 shapes
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 59 residues, 8 shapes
> hide sel atoms
> hide sel cartoons
Drag select of 5 residues
> hide sel cartoons
> hide sel atoms
> select /D
353 atoms, 381 bonds, 11 residues, 1 model selected
> select subtract /D:7
320 atoms, 344 bonds, 10 residues, 1 model selected
> select subtract /D:6
287 atoms, 308 bonds, 9 residues, 1 model selected
> select subtract /D:5
255 atoms, 274 bonds, 8 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /C
889 atoms, 956 bonds, 28 residues, 1 model selected
> select subtract /C:6
859 atoms, 923 bonds, 27 residues, 1 model selected
> select subtract /C:8
797 atoms, 887 bonds, 25 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A
2605 atoms, 2811 bonds, 48 pseudobonds, 85 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select clear
Drag select of 21 atoms, 146 residues, 19 bonds, 6 shapes
> show sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> select clear
Drag select of 488 atoms, 489 bonds
> hide sel atoms
Drag select of 449 atoms, 458 bonds
> hide sel atoms
Drag select of 550 atoms, 545 bonds
> hide sel atoms
Drag select of 28 atoms, 22 bonds
> hide sel atoms
Drag select of 99 atoms, 95 bonds
> hide sel atoms
Drag select of 21 atoms, 17 bonds
> hide sel atoms
Drag select of 21 atoms, 19 bonds
> hide sel atoms
Drag select of 49 atoms, 45 bonds
> hide sel atoms
> select clear
Drag select of 4 atoms
> hide sel cartoons
Drag select of 90 atoms, 86 bonds
> hide sel atoms
Drag select of 11 atoms, 8 bonds
> hide sel atoms
Drag select of 7 atoms, 5 bonds
> hide sel atoms
Drag select of 16 atoms, 16 bonds
> hide sel atoms
> select /D:7@OP1
1 atom, 1 residue, 1 model selected
> select add /B:1216@HG
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /D:7@OP1 /B:1216@HG
Distance between /D DG 7 OP1 and /B SER 1216 HG: 1.371Å
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> select clear
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> select add /D:6
66 atoms, 70 bonds, 2 residues, 1 model selected
> select add /D:5
98 atoms, 103 bonds, 3 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 98 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 98 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 98 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 98 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 98 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 98 atom styles
> select add /C:7
62 atoms, 31 bonds, 2 residues, 1 model selected
> select add /C:6
92 atoms, 62 bonds, 3 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 92 atom styles
> select clear
> select /B:1128
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add /B:1127
26 atoms, 25 bonds, 2 residues, 1 model selected
> select add /B:1133
33 atoms, 31 bonds, 3 residues, 1 model selected
> select add /B:1132
40 atoms, 37 bonds, 4 residues, 1 model selected
> select add /B:1131
61 atoms, 58 bonds, 5 residues, 1 model selected
> select clear
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to 4un3 #1
---
warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond
partners
notes | Termini for 4un3 (#1) chain A determined from SEQRES records
Termini for 4un3 (#1) chain B determined from SEQRES records
Termini for 4un3 (#1) chain C determined from SEQRES records
Termini for 4un3 (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B
SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B
ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364
Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2
1287 hydrogen bonds
/B GLN 1364 is not terminus, removing H atom from 'C'
/D DA 2 is not terminus, removing H atom from O5'
0 hydrogens added
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /C:8
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:7
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select add /C:7
60 atoms, 62 bonds, 2 residues, 1 model selected
> select add /C:8
92 atoms, 96 bonds, 3 residues, 1 model selected
> select add /D:5
124 atoms, 129 bonds, 4 residues, 1 model selected
> select add /D:6
157 atoms, 164 bonds, 5 residues, 1 model selected
> select add /D:7
190 atoms, 199 bonds, 6 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 showDist true reveal true
17 hydrogen bonds found
> select ~sel & ##selected
25217 atoms, 25688 bonds, 27 pseudobonds, 1428 residues, 5 models selected
> hide sel atoms
> hide sel cartoons
> show sel atoms
> show sel cartoons
> hide sel atoms
> select clear
> select add /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select add /D:7
70 atoms, 68 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 showDist true reveal true
9 hydrogen bonds found
> select /B
21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select clear
> select
> /B:59-94,96-103,121-132,134-145,150-164,177-196,207-214,217-228,236-246,270-283,286-307,315-343,346-352,358-364,368-383,386-395,406-427,430-446,477-494,512-525,541-552,560-574,591-609,612-626,628-642,644-654,663-669,678-685,692-699,703-709,719-726,730-751,776-792,794-799,802-806,808-817,832-836,851-853,860-865,872-889,893-906,909-922,925-940,959-970,980-1001,1004-1009,1030-1047,1078-1088,1127-1132,1170-1185,1191-1195,1229-1280,1283-1297,1301-1316,1340-1344
12485 atoms, 12539 bonds, 1 pseudobond, 744 residues, 2 models selected
> select /B:280
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:280
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:354
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:354
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel lime
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> color sel lime
> select clear
Drag select of 660 residues, 5 pseudobonds
> hide sel atoms
> hide sel cartoons
Drag select of 67 residues
> select clear
Drag select of 349 residues, 1 pseudobonds
> hide sel atoms
> hide sel cartoons
Drag select of 4 atoms, 13 residues, 6 bonds, 3 shapes
> select clear
Drag select of 99 residues
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 4 atoms, 13 residues, 8 bonds, 3 shapes
> select clear
Drag select of 79 residues
> hide sel atoms
> hide sel cartoons
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /B:1320
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1321
14 atoms, 14 bonds, 1 residue, 1 model selected
> select add /B:1320
24 atoms, 23 bonds, 2 residues, 1 model selected
> select add /B:1319
31 atoms, 29 bonds, 3 residues, 1 model selected
> select add /B:1322
41 atoms, 38 bonds, 4 residues, 1 model selected
> select add /B:1323
51 atoms, 47 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel cartoons
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel lime
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select /A:26
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /A:25
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /A:24
30 atoms, 31 bonds, 1 residue, 1 model selected
> select add /A:25
60 atoms, 62 bonds, 2 residues, 1 model selected
> select add /A:26
93 atoms, 97 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 7 residues
> show sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select clear
Drag select of 34 residues
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select clear
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1322-1323
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /B:1298
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1298-1299
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel lime
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel lime
> show sel atoms
> hide sel cartoons
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select /B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
Drag select of 18 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 24 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 10 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 7 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 6 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 9 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 3 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select clear
Drag select of 3 residues
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 12 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel atoms
> hide sel cartoons
> select add /C:10
157 atoms, 33 bonds, 8 residues, 1 model selected
> select add /C:9
189 atoms, 66 bonds, 9 residues, 1 model selected
> select add /C:11
221 atoms, 99 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select /D
353 atoms, 381 bonds, 11 residues, 1 model selected
> select subtract /D:5
321 atoms, 346 bonds, 10 residues, 1 model selected
> select subtract /D:6
288 atoms, 310 bonds, 9 residues, 1 model selected
> select subtract /D:7
255 atoms, 274 bonds, 8 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /D
353 atoms, 381 bonds, 11 residues, 1 model selected
> select /C
889 atoms, 956 bonds, 28 residues, 1 model selected
> select subtract /C:6
859 atoms, 923 bonds, 27 residues, 1 model selected
> select subtract /C:7
829 atoms, 891 bonds, 26 residues, 1 model selected
> select subtract /C:8
797 atoms, 856 bonds, 25 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 3 residues
> hide sel atoms
> hide sel cartoons
> select clear
> select add /B:1323
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 15 residues
> hide sel atoms
> hide sel cartoons
> select /B:1163
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add /B:1164
38 atoms, 36 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide sel atoms
Drag select of 5 residues
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide sel atoms
Drag select of 4 residues
> hide sel atoms
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
Drag select of 10 residues
> hide sel cartoons
> show sel atoms
> select clear
Drag select of 62 atoms, 3 residues, 61 bonds
> hide sel atoms
> hide sel cartoons
> select /B:1110
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select /B:1334
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select /B:1336
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
> select /B:1316
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add /B:1315
33 atoms, 31 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
Drag select of 12 residues
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select clear
Drag select of 54 atoms, 54 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 56 atoms, 56 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 7 atoms, 1 residues, 10 bonds
> select clear
Drag select of 13 atoms, 14 bonds
> hide sel atoms
Drag select of 5 atoms, 3 bonds
> hide sel atoms
> select add /B:1320
15 atoms, 12 bonds, 4 residues, 1 model selected
> select add /B:1321
29 atoms, 26 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
Drag select of 398 atoms, 11 residues, 10 pseudobonds, 392 bonds, 15 shapes
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select clear
Drag select of 469 atoms, 10 pseudobonds, 467 bonds, 15 shapes
> style sel sphere
Changed 469 atom styles
> style sel ball
Changed 469 atom styles
> lighting soft
> lighting simple
> lighting full
> lighting soft
> ui tool show "Selection Inspector"
> select clear
Drag select of 469 atoms, 10 pseudobonds, 467 bonds, 15 shapes
> style sel sphere
Changed 469 atom styles
> style sel sphere
Changed 469 atom styles
> style sel stick
Changed 469 atom styles
> style sel ball
Changed 469 atom styles
> select clear
Drag select of 469 atoms, 10 pseudobonds, 467 bonds, 15 shapes
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /B:1320@HB1
1 atom, 1 residue, 1 model selected
> select add /D:5@H2'
2 atoms, 2 residues, 1 model selected
> select clear
> select add /B:1320@HB1
1 atom, 1 residue, 1 model selected
> select add /D:5@H2'
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:1320@HB1 /D:5@H2'
Distance between /B ALA 1320 HB1 and /D DT 5 H2': 3.139Å
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel magenta
> select add /C:8
51 atoms, 52 bonds, 2 residues, 1 model selected
> select add /C:7
81 atoms, 83 bonds, 3 residues, 1 model selected
> select add /C:6
111 atoms, 114 bonds, 4 residues, 1 model selected
> style sel stick
Changed 111 atom styles
> hide sel cartoons
> hide sel atoms
> show sel atoms
> style sel sphere
Changed 111 atom styles
> style sel ball
Changed 111 atom styles
> select clear
> select /C:8@H5''
1 atom, 1 residue, 1 model selected
> select add /B:1111@HD23
2 atoms, 2 residues, 1 model selected
> distance /C:8@H5'' /B:1111@HD23
Distance between /C DA 8 H5'' and /B LEU 1111 HD23: 5.782Å
> select /B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel magenta
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:5
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:5-7
92 atoms, 98 bonds, 3 residues, 1 model selected
> select /D
353 atoms, 381 bonds, 11 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /D
Alignment identifier is 1/D
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel magenta
> show sel atoms
> hide sel cartoons
> select add /D:6@H2''
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /D:6@H2''
1 atom, 1 residue, 1 model selected
> select /B:1218@O
1 atom, 1 residue, 1 model selected
> select add /D:6@H2''
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:1218@O /D:6@H2''
Distance between /B GLY 1218 O and /D DG 6 H2'': 6.737Å
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select clear
> select /D:6@H2'
1 atom, 1 residue, 1 model selected
> select add /B:1219@OE1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /D:6@H2' /B:1219@OE1
Distance between /D DG 6 H2' and /B GLU 1219 OE1: 2.508Å
> select clear
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> select /D:8
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:6-8
98 atoms, 105 bonds, 3 residues, 1 model selected
> select /D:5-6
65 atoms, 69 bonds, 2 residues, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> color sel blue
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select /C:5
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:5-7
92 atoms, 98 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select /C:8
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> select /C:5
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:5-8
124 atoms, 133 bonds, 4 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /C:8
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> show sel atoms
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel yellow
> select /B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
Drag select of 5 atoms, 3 residues, 2 bonds
> hide sel cartoons
> hide sel atoms
> select /B:1136@CA
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel atoms
> show sel cartoons
> hide sel cartoons
> select clear
> select /B:1135@OD1
1 atom, 1 residue, 1 model selected
> select /D:7@O3'
1 atom, 1 residue, 1 model selected
> select add /B:1135@OD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /D:7@O3' /B:1135@OD1
Distance between /D DG 7 O3' and /B ASP 1135 OD1: 4.846Å
Drag select of 5 atoms, 6 bonds, 1 pseudobonds
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel cartoons
> select clear
> select /B:1213
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:1221
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /B:1213
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /B:1222
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add /B:1220
41 atoms, 39 bonds, 2 residues, 1 model selected
> select add /B:1214
60 atoms, 57 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 8 atoms, 8 bonds
Drag select of 23 atoms, 4 residues, 22 bonds
> show sel atoms
> show sel cartoons
> hide sel cartoons
> hide sel atoms
Drag select of 6 atoms, 3 residues, 6 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 10 atoms, 13 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 2 atoms
> hide sel atoms
> hide sel cartoons
Drag select of 4 atoms, 1 bonds
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 4 atoms, 2 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 8 atoms, 8 bonds, 1 pseudobonds
> hide sel cartoons
> hide sel atoms
> select /B:1136@N
1 atom, 1 residue, 1 model selected
> select add /B:1136@HG
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> select /B:1136@H
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:1218-1219
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /B:1218-1219
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /B:1215-1216
21 atoms, 20 bonds, 2 residues, 1 model selected
> select /B:1215-1216
21 atoms, 20 bonds, 2 residues, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /B:1218@H
1 atom, 1 residue, 1 model selected
> select add /D:7@OP1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:1218@H /D:7@OP1
Distance between /B GLY 1218 H and /D DG 7 OP1: 4.422Å
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel yellow
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> select /B:1322@HB2
1 atom, 1 residue, 1 model selected
> select add /D:5@OP2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:1322@HB2 /D:5@OP2
Distance between /B ALA 1322 HB2 and /D DT 5 OP2: 3.722Å
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel magenta
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel cyan
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> hide sel atoms
Drag select of 100 atoms, 5 residues, 93 bonds
> color sel black
> select clear
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> ~distance /C:8@H5'' /B:1111@HD23
> ~distance /D:7@OP1 /B:1216@HG
> ~distance /B:1322@HB2 /D:5@OP2
> ~distance /B:1218@H /D:7@OP1
> ~distance /D:6@H2' /B:1219@OE1
> ~distance /B:1320@HB1 /D:5@H2'
> ~distance /B:1218@O /D:6@H2''
> ~distance /D:7@O3' /B:1135@OD1
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 3 residues, 1 model selected
> show sel target ab
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 3 residues, 1 model selected
> show sel target ab
> select clear
Drag select of 290 atoms, 5 residues, 8 pseudobonds, 296 bonds, 15 shapes
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel atoms
> select clear
Drag select of 315 atoms, 8 pseudobonds, 321 bonds, 15 shapes
> ui tool show Contacts
> contacts ignoreHiddenModels true color #3eff4b
17602 contacts
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 29 pseudobonds, 3 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 92 atom styles
> color sel bynucleotide
> select /D:5-6
65 atoms, 69 bonds, 13 pseudobonds, 2 residues, 2 models selected
> select /D:5-7
98 atoms, 105 bonds, 27 pseudobonds, 3 residues, 2 models selected
> color sel bynucleotide
> nucleotides sel atoms
> style nucleic & sel stick
Changed 98 atom styles
> color sel byhetero
> color sel bychain
> color sel bypolymer
> color sel byhetero
> color sel bynucleotide
> select clear
Drag select of 31 atoms, 29 bonds, 6 pseudobonds
> color sel byhetero
Drag select of 84 atoms, 81 bonds, 23 pseudobonds
> color sel byhetero
Drag select of 16 atoms, 10 bonds, 8 pseudobonds
> color sel byhetero
Drag select of 84 atoms, 78 bonds, 26 pseudobonds
> color sel byhetero
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 29 pseudobonds, 3 residues, 2 models selected
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6-8
92 atoms, 98 bonds, 29 pseudobonds, 3 residues, 2 models selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 92 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 92 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 92 atom styles
> nucleotides sel tube/slab shape muffler
> nucleotides sel ladder
> nucleotides sel stubs
> nucleotides sel fill
> style nucleic & sel stick
Changed 92 atom styles
> color sel bynucleotide
> select /D:5
32 atoms, 33 bonds, 1 residue, 1 model selected
> select /D:5-7
98 atoms, 105 bonds, 27 pseudobonds, 3 residues, 2 models selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 98 atom styles
Drag select of 315 atoms, 160 pseudobonds, 321 bonds, 15 shapes
> ui tool show Contacts
> ui tool show H-Bonds
> hbonds sel color #000000 showDist true
25 hydrogen bonds found
> ui tool show Contacts
> contacts ignoreHiddenModels true color #3eff4b
17602 contacts
> select clear
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:6
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:7
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:7
30 atoms, 31 bonds, 1 residue, 1 model selected
> select /C:8
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /C:8
32 atoms, 34 bonds, 1 residue, 1 model selected
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:7
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:5-6
65 atoms, 69 bonds, 13 pseudobonds, 2 residues, 2 models selected
> select /D:5-6
65 atoms, 69 bonds, 13 pseudobonds, 2 residues, 2 models selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:6
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /D:5@C6
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 1 atoms, 2 bonds
> select clear
Drag select of 4 atoms, 3 bonds
> select clear
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select /B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui tool show Distances
> select clear
> select /B:1111@CD1
1 atom, 1 residue, 1 model selected
> select /B:1135@CB
1 atom, 1 residue, 1 model selected
> select add /B:1111@CD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:1135@CB /B:1111@CD1
Distance between /B ASP 1135 CB and LEU 1111 CD1: 3.538Å
> select /B:1111@HD13
1 atom, 1 residue, 1 model selected
> select /B:1135@HB2
1 atom, 1 residue, 1 model selected
> select add /B:1111@HD13
2 atoms, 2 residues, 1 model selected
> distance /B:1135@HB2 /B:1111@HD13
Distance between /B ASP 1135 HB2 and LEU 1111 HD13: 2.243Å
> select /B:1111@CD1
1 atom, 1 residue, 1 model selected
> select /B:1135@CG
1 atom, 1 residue, 1 model selected
> select add /B:1111@CD1
2 atoms, 2 residues, 1 model selected
> distance /B:1135@CG /B:1111@CD1
Distance between /B ASP 1135 CG and LEU 1111 CD1: 3.827Å
> select /B:1111@HD11
1 atom, 1 residue, 1 model selected
> select add /B:1135@CB
2 atoms, 2 residues, 1 model selected
> distance /B:1111@HD11 /B:1135@CB
Distance between /B LEU 1111 HD11 and ASP 1135 CB: 3.066Å
> select /B:1111@CD1
1 atom, 1 residue, 1 model selected
> select add /B:1135@HB2
2 atoms, 2 residues, 1 model selected
> distance /B:1111@CD1 /B:1135@HB2
Distance between /B LEU 1111 CD1 and ASP 1135 HB2: 2.924Å
> select /B:1111@HD13
1 atom, 1 residue, 1 model selected
> select add /B:1135@CB
2 atoms, 2 residues, 1 model selected
> distance /B:1111@HD13 /B:1135@CB
Distance between /B LEU 1111 HD13 and ASP 1135 CB: 3.060Å
> ~distance /B:1111@HD11 /B:1135@CB
> ~distance /B:1135@CG /B:1111@CD1
> ~distance /B:1111@CD1 /B:1135@HB2
> ~distance /B:1135@HB2 /B:1111@HD13
> ~distance /B:1111@HD13 /B:1135@CB
> ~distance /B:1135@CB /B:1111@CD1
> select clear
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 10 atoms, 11 bonds, 2 pseudobonds, 1 shapes
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1337@C
1 atom, 1 residue, 1 model selected
> select add /B:1218@O
2 atoms, 2 residues, 1 model selected
> select add /B:1337@O
3 atoms, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select /B:1337@C
1 atom, 1 residue, 1 model selected
> select add /B:1218@O
2 atoms, 2 residues, 1 model selected
> select /B:1218@O
1 atom, 1 residue, 1 model selected
> select add /B:1337@O
2 atoms, 2 residues, 1 model selected
> distance /B:1218@O /B:1337@O
Distance between /B GLY 1218 O and THR 1337 O: 2.895Å
> select add /B:1337@C
3 atoms, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select /B:1337@C
1 atom, 1 residue, 1 model selected
> select add /B:1218@O
2 atoms, 2 residues, 1 model selected
> distance /B:1337@C /B:1218@O
Distance between /B THR 1337 C and GLY 1218 O: 3.108Å
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218@H
1 atom, 1 residue, 1 model selected
> select add /B:1219@H
2 atoms, 2 residues, 1 model selected
> distance /B:1218@H /B:1219@H
Distance between /B GLY 1218 H and GLU 1219 H: 2.164Å
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> save /Users/celestekanne/Desktop/4UN3.cxs
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1217
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1216-1217
21 atoms, 20 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1219-1220
34 atoms, 33 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select /B:1217
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:1216-1217
21 atoms, 20 bonds, 1 pseudobond, 2 residues, 2 models selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select /B:1335@HE
1 atom, 1 residue, 1 model selected
> select subtract /B:1335@HE
Nothing selected
> select add /B:1335@HE
1 atom, 1 residue, 1 model selected
> select add /B:1219@OE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /B:1335@HE /B:1219@OE2
Distance between /B ARG 1335 HE and GLU 1219 OE2: 1.914Å
> select /B:1335@HB3
1 atom, 1 residue, 1 model selected
> select add /B:1219@OE2
2 atoms, 2 residues, 1 model selected
> distance /B:1335@HB3 /B:1219@OE2
Distance between /B ARG 1335 HB3 and GLU 1219 OE2: 2.571Å
> select /B:1219@OE1
1 atom, 1 residue, 1 model selected
> select add /D:6@H2'
2 atoms, 2 residues, 1 model selected
> distance /B:1219@OE1 /D:6@H2'
Distance between /B GLU 1219 OE1 and /D DG 6 H2': 2.508Å
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /B:1337@HA
1 atom, 1 residue, 1 model selected
> select add /B:1219@HA
2 atoms, 2 residues, 1 model selected
> distance /B:1337@HA /B:1219@HA
Distance between /B THR 1337 HA and GLU 1219 HA: 3.037Å
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> ~distance /B:1218@O /B:1337@O
> ~distance /B:1218@H /B:1219@H
> ~distance /B:1337@C /B:1218@O
> ~distance /B:1337@HA /B:1219@HA
> ~distance /B:1335@HE /B:1219@OE2
> ~distance /B:1335@HB3 /B:1219@OE2
> ~distance /B:1219@OE1 /D:6@H2'
Drag select of 291 atoms, 143 pseudobonds, 298 bonds, 15 shapes
> clear
Unknown command: clear
> label delete 4un3
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> ui tool show H-Bonds
> toolshed show
> ui tool show H-Bonds
> open 4un3 fromDatabase pdb format mmcif
4un3 title:
Crystal structure of Cas9 bound to PAM-containing DNA target [more info...]
Chain information for 4un3 #2
---
Chain | Description | UniProt
A | SGRNA |
B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368
C | TARGET DNA STRAND |
D | NON-TARGET DNA STRAND |
Non-standard residues in 4un3 #2
---
MG — magnesium ion
> undo
> select add #2
13643 atoms, 13721 bonds, 140 pseudobonds, 1840 residues, 5 models selected
> select add #1
39036 atoms, 39599 bonds, 17786 pseudobonds, 3273 residues, 10 models selected
> select subtract #1
13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 4 models selected
> hide #!1 models
> select subtract #2
Nothing selected
> hide #!2 models
> select add #2
13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 4 models selected
> show #!2 models
> select subtract #2
Nothing selected
Drag select of 102 atoms, 1426 residues, 34 pseudobonds, 63 bonds, 142 shapes
> select solvent
405 atoms, 405 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!2 models
> show #!1 models
Drag select of 291 atoms, 143 pseudobonds, 298 bonds, 15 shapes
> hide #!1 models
> select add #1
25407 atoms, 25891 bonds, 17646 pseudobonds, 1434 residues, 6 models selected
> show #!2 models
> select subtract #1
Nothing selected
> select add #2
13224 atoms, 13708 bonds, 125 pseudobonds, 1434 residues, 4 models selected
> select subtract #2
Nothing selected
> select add #2
13224 atoms, 13708 bonds, 125 pseudobonds, 1434 residues, 4 models selected
> select subtract #2
Nothing selected
> show #!1 models
> hide #!2 models
> hide #!1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
No distances to delete!
> show #!1.1 target m
> show #1.4 models
> hide #!1.1 models
> color #1.4 #f4fae3ff models
> color #1.4 #454640ff models
> select add #1.4
17602 pseudobonds, 1 model selected
> select subtract #1.4
Nothing selected
> select #1/B:1119
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1119
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select #1/B:1111@HD13
1 atom, 1 residue, 1 model selected
> select add #1/B:1135@HB2
2 atoms, 2 residues, 1 model selected
> distance #1/B:1111@HD13 #1/B:1135@HB2
Distance between 4un3 #1/B LEU 1111 HD13 and ASP 1135 HB2: 2.243Å
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1218@H
1 atom, 1 residue, 1 model selected
> select add #1/B:1219@H
2 atoms, 2 residues, 1 model selected
> distance #1/B:1218@H #1/B:1219@H
Distance between 4un3 #1/B GLY 1218 H and GLU 1219 H: 2.164Å
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1337@O
1 atom, 1 residue, 1 model selected
> select add #1/B:1218@O
2 atoms, 2 residues, 1 model selected
> distance #1/B:1337@O #1/B:1218@O
Distance between 4un3 #1/B THR 1337 O and GLY 1218 O: 2.895Å
> select #1/B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:1219@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:1335@HB3
2 atoms, 2 residues, 1 model selected
> distance #1/B:1219@OE2 #1/B:1335@HB3
Distance between 4un3 #1/B GLU 1219 OE2 and ARG 1335 HB3: 2.571Å
> select #1/B:1219@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:1335@HE
2 atoms, 2 residues, 1 model selected
> distance #1/B:1219@OE2 #1/B:1335@HE
Distance between 4un3 #1/B GLU 1219 OE2 and ARG 1335 HE: 1.914Å
> select #1/B:1219@OE1
1 atom, 1 residue, 1 model selected
> select add #1/B:1335@HH21
2 atoms, 2 residues, 1 model selected
> distance #1/B:1219@OE1 #1/B:1335@HH21
Distance between 4un3 #1/B GLU 1219 OE1 and ARG 1335 HH21: 2.002Å
> select #1/B:1219@OE1
1 atom, 1 residue, 1 model selected
> select add #1/D:6@H2'
2 atoms, 2 residues, 1 model selected
> distance #1/B:1219@OE1 #1/D:6@H2'
Distance between 4un3 #1/B GLU 1219 OE1 and /D DG 6 H2': 2.508Å
> select #1/B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/D:5@OP2
1 atom, 1 residue, 1 model selected
> select add #1/B:1322@HB2
2 atoms, 2 residues, 1 model selected
> distance #1/D:5@OP2 #1/B:1322@HB2
Distance between 4un3 #1/D DT 5 OP2 and /B ALA 1322 HB2: 3.722Å
> ~distance #1/D:5@OP2 #1/B:1322@HB2
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1335@HH22
1 atom, 1 residue, 1 model selected
> select add #1/D:7@N7
2 atoms, 2 residues, 1 model selected
> distance #1/B:1335@HH22 #1/D:7@N7
Distance between 4un3 #1/B ARG 1335 HH22 and /D DG 7 N7: 2.033Å
> select #1/B:1335@HH12
1 atom, 1 residue, 1 model selected
> select add #1/D:7@O6
2 atoms, 2 residues, 1 model selected
> distance #1/B:1335@HH12 #1/D:7@O6
Distance between 4un3 #1/B ARG 1335 HH12 and /D DG 7 O6: 1.613Å
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> ~distance #1/B:1219@OE1 #1/B:1335@HH21
> ~distance #1/B:1335@HH12 #1/D:7@O6
> ~distance #1/B:1218@H #1/B:1219@H
> ~distance #1/B:1335@HH22 #1/D:7@N7
> ~distance #1/B:1337@O #1/B:1218@O
> ~distance #1/B:1219@OE2 #1/B:1335@HE
> ~distance #1/B:1219@OE1 #1/D:6@H2'
> ~distance #1/B:1219@OE2 #1/B:1335@HB3
> ~distance #1/B:1111@HD13 #1/B:1135@HB2
> hide #1.4 models
Drag select of 291 atoms, 298 bonds, 15 shapes
> ui tool show H-Bonds
> ui tool show "Add Hydrogens"
> addh #!1
Summary of feedback from adding hydrogens to 4un3 #1
---
warnings | Not adding hydrogens to 4un3 #1/A A 1 P because it is missing
heavy-atom bond partners
Not adding hydrogens to 4un3 #1/B LYS 797 CB because it is missing heavy-atom
bond partners
notes | Termini for 4un3 (#1) chain A determined from SEQRES records
Termini for 4un3 (#1) chain B determined from SEQRES records
Termini for 4un3 (#1) chain C determined from SEQRES records
Termini for 4un3 (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 4un3 #1/B LYS 4, 4un3
#1/B THR 386, 4un3 #1/B SER 719, 4un3 #1/B ASN 776, 4un3 #1/B GLY 1030, 4un3
#1/B LYS 1059, 4un3 #1/B GLU 1253
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 4un3 #1/B ASP 384, 4un3
#1/B LYS 710, 4un3 #1/B ARG 765, 4un3 #1/B ASP 1012, 4un3 #1/B ILE 1050, 4un3
#1/B HIS 1241, 4un3 #1/B GLN 1364
Chain-initial residues that are not actual 5' termini: 4un3 #1/A A 1, 4un3
#1/D DA 2
1287 hydrogen bonds
4un3 #1/B GLN 1364 is not terminus, removing H atom from 'C'
4un3 #1/D DA 2 is not terminus, removing H atom from O5'
0 hydrogens added
> show #!1.1 models
> ui tool show H-Bonds
> hbonds sel color #000000 showDist true
67 hydrogen bonds found
> hide #!3 models
> show #!3 models
> show #1.4 models
> hide #3.1 models
> color #3 #878787ff models
> color #3 #7e2d87ff models
> hide #!3 models
> show #!3 models
> hide #1.4 models
> show #1.3 models
> hide #1.3 models
> show #3.1 models
> color #1.4 #580c35ff models
> color #1.4 #b91970ff models
> color #1.4 #eb208eff models
> show #1.4 models
> show sel cartoons
> hide sel atoms
> show sel atoms
> style sel sphere
Changed 291 atom styles
> style sel ball
Changed 291 atom styles
> hide sel cartoons
> show sel atoms
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111-1345
3715 atoms, 3748 bonds, 2161 pseudobonds, 224 residues, 4 models selected
> select #1/B:1281-1337
937 atoms, 946 bonds, 481 pseudobonds, 57 residues, 2 models selected
> select #1/B:1111-1337
3596 atoms, 3629 bonds, 2034 pseudobonds, 216 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select clear
Drag select of 190 atoms, 5 residues, 203 bonds, 111 pseudobonds, 15 shapes
> select clear
Drag select of 190 atoms, 3 residues, 203 bonds, 109 pseudobonds, 15 shapes
> select clear
Drag select of 181 atoms, 197 bonds, 109 pseudobonds, 15 shapes
> select clear
Drag select of 187 atoms, 2 residues, 203 bonds, 109 pseudobonds, 15 shapes
> select #1/B:1321
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
Drag select of 188 atoms, 3 residues, 203 bonds, 109 pseudobonds, 15 shapes
> select clear
Drag select of 190 atoms, 3 residues, 203 bonds, 109 pseudobonds, 15 shapes
> select subtract #1/B:1320
228 atoms, 203 bonds, 109 pseudobonds, 8 residues, 3 models selected
> select subtract #1/B:1335
204 atoms, 203 bonds, 109 pseudobonds, 7 residues, 3 models selected
> select subtract #1/B:1321
190 atoms, 203 bonds, 109 pseudobonds, 6 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 190 atom styles
> show sel cartoons
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 190 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 190 atom styles
> style sel ball
Changed 190 atom styles
> style sel stick
Changed 190 atom styles
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 190 atom styles
> style sel ball
Changed 190 atom styles
> color sel byhetero
> select clear
Drag select of 14 atoms, 180 residues, 15 bonds, 405 pseudobonds
> select clear
Drag select of 190 atoms, 216 residues, 203 bonds, 600 pseudobonds
> hide #1.4 models
> ui tool show Contacts
> contacts ignoreHiddenModels true color #3eff4b name "polar and nonpolar
> interactions" reveal true
17602 contacts
> hide #4 models
> select ~sel & ##selected
21621 atoms, 22059 bonds, 30890 pseudobonds, 1212 residues, 6 models selected
> hide (#!1 & sel) target a
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111-1337
3596 atoms, 3629 bonds, 4059 pseudobonds, 216 residues, 5 models selected
> hide (#!1 & sel) target a
> select clear
> select #1/B:1111-1337
3596 atoms, 3629 bonds, 4059 pseudobonds, 216 residues, 5 models selected
> select clear
> select #1/B:1110-1111
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/B:1110-1111
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:1121
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/B:1121
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> select #1/B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B
21560 atoms, 21743 bonds, 26988 pseudobonds, 1310 residues, 6 models selected
> show sel cartoons
> show #4 models
> select #1/B
21560 atoms, 21743 bonds, 26988 pseudobonds, 1310 residues, 6 models selected
> color (#!1 & sel) light gray
> hide #4 models
> hide #3.1 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> hide #!3 models
> show #!3 models
> select #1/C
889 atoms, 956 bonds, 766 pseudobonds, 28 residues, 3 models selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 889 atom styles
> ui tool show "Color Actions"
> color sel wheat
> color sel khaki
> color sel orchid
> select #1/D
353 atoms, 381 bonds, 290 pseudobonds, 11 residues, 3 models selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 353 atom styles
> color (#!1 & sel) #ff93efff
> color (#!1 & sel) #ffacf7ff
> color (#!1 & sel) #ffbdf7ff
> ui tool show "Color Actions"
> color sel plum
> color sel lavender
> color sel plum
> color sel thistle
> color sel plum
> select #1/C
889 atoms, 956 bonds, 766 pseudobonds, 28 residues, 3 models selected
> color sel plum
> color sel slate blue
> color sel medium violet red
> color sel pale violet red
> color sel medium violet red
> color sel pale violet red
> color sel light cyan
> color sel light pink
> color sel gold
> color sel burly wood
> color sel khaki
> color sel sandy brown
> color sel goldenrod
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
No Surface models open
> lighting soft
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> lighting full
> lighting simple
> lighting soft
> color (#!1 & sel) yellow
> color (#!1 & sel) orange
> select #1/D
353 atoms, 381 bonds, 290 pseudobonds, 11 residues, 3 models selected
> color (#!1 & sel) dim gray
> select #1/B
21560 atoms, 21743 bonds, 26988 pseudobonds, 1310 residues, 6 models selected
> ui tool show "Color Actions"
> color sel bisque
> color sel moccasin
> color sel cornsilk
> color sel ivory
> color sel lemon chiffon
> color sel cornsilk
> color sel papaya whip
> color sel blanched almond
> select clear
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> label sel attribute label_specifier
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> style sel ball
Changed 12 atom styles
> style sel sphere
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> select #1/B
21560 atoms, 21743 bonds, 26988 pseudobonds, 1310 residues, 6 models selected
> lighting flat
> lighting full
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting soft
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume style image
No volumes specified
> volume hide
No volumes specified
> volume hide
No volumes specified
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> lighting full
> lighting soft
> hide sel atoms
> show sel atoms
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> surface style mesh
> surface style solid
> ui tool show "Color Actions"
> color (#!1 & sel) medium blue
> color (#!1 & sel) light sea green
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) light sea green
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1218
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) light sea green
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 7 atom styles
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> select #1/B:1223-1224
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:1223-1224
21 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:1223
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1223
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/B:1219
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 15 atom styles
> color (#!1 & sel) light sea green
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/B:1322
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 10 atom styles
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> color (#!1 & sel) light sea green
> style sel stick
Changed 10 atom styles
> select #1/B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1333
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/B:1335
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 24 atom styles
> color (#!1 & sel) light sea green
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B:1337
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 14 atom styles
> color (#!1 & sel) light sea green
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #1/C
889 atoms, 956 bonds, 766 pseudobonds, 28 residues, 3 models selected
> label (#!1 & sel) attribute name
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #1/D
353 atoms, 381 bonds, 290 pseudobonds, 11 residues, 3 models selected
> label (#!1 & sel) atoms attribute name
> ~label (#!1 & sel) atoms
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #1/B:836
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/B:835
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:834
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:833
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/B:835
31 atoms, 29 bonds, 2 residues, 2 models selected
> select add #1/B:834
42 atoms, 39 bonds, 3 residues, 2 models selected
> select add #1/B:832
66 atoms, 62 bonds, 4 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> select #1/B:831
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/B:830
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #1/B:831
33 atoms, 31 bonds, 2 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #1/D
353 atoms, 381 bonds, 290 pseudobonds, 11 residues, 3 models selected
> color sel bynucleotide
> undo
> color sel byhetero
> select #1/C
889 atoms, 956 bonds, 766 pseudobonds, 28 residues, 3 models selected
> color sel bychain
> undo
> color sel byhetero
> select clear
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1111
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:1135
12 atoms, 11 bonds, 1 residue, 1 model selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
4un3 #1/B LYS 797 CG
4un3 #1/B LYS 797 CE
4un3 #1/B LYS 797 CD
4un3 #1/B LYS 797 NZ
Using Amber 20 recommended default charges and atom types for standard
residues
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-16.5.14
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 481.0.0.0.0
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 11.7.10 (20G1427)
Kernel Version: Darwin 20.6.0
Time since boot: 3 days 8:10
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| 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 , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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