![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Last modified 4 years ago
#6121 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [51598]
Path: /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.1.1 (1.1.1.0)
Code Type: X86-64 (Native)
Parent Process: bash [46123]
Responsible: Terminal [31244]
User ID: 503
Date/Time: 2022-02-08 14:38:19.030 +0100
OS Version: Mac OS X 10.15.7 (19H15)
Report Version: 12
Bridge OS Version: 4.6 (17P6610)
Anonymous UUID: 9CD0F012-424A-FE63-2807-DF64AFF584DB
Sleep/Wake UUID: E9BD63A2-CCC1-465F-9857-E2432FD2FDD3
Time Awake Since Boot: 6100000 seconds
Time Since Wake: 22000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics hardware encountered an error and was reset: 0x00000002
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff68a9533a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff68b51e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff689ac93e raise + 26
3 libsystem_platform.dylib 0x00007fff68b465fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff68a1c808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff4fd470a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff4fd3e18f gpusGenerateCrashLog + 89
8 com.apple.AMDRadeonX6000GLDriver 0x0000000124ecf7ed gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff4fd3f6a1 gpusSubmitDataBuffers + 490
10 com.apple.AMDRadeonX6000GLDriver 0x0000000124ef83cb glrATI_Hwl_SubmitPacketsWithToken + 101
11 com.apple.AMDRadeonX6000GLDriver 0x0000000124ebe93e glrAMD_GFX10_ResourceMgrValidateConstantState + 1975
12 com.apple.AMDRadeonX6000GLDriver 0x0000000124ee8f4e glrdAMD_GFX10_RenderIndexed + 86
13 com.apple.AMDRadeonX6000GLDriver 0x0000000124eec58a glrdAMD_RenderVertexArray + 2865
14 GLEngine 0x00007fff39640044 glDrawElementsInstanced_ACC_GL3Exec + 432
15 _ctypes.cpython-37m-darwin.so 0x000000010e414e17 ffi_call_unix64 + 79
16 _ctypes.cpython-37m-darwin.so 0x000000010e4156a5 ffi_call + 901
17 _ctypes.cpython-37m-darwin.so 0x000000010e40ff62 _ctypes_callproc + 882
18 _ctypes.cpython-37m-darwin.so 0x000000010e4096dc PyCFuncPtr_call + 1196
19 org.python.python 0x0000000100cec9d8 PyObject_Call + 136
20 org.python.python 0x0000000100d3f916 slot_tp_call + 198
21 wrapper.cpython-37m-darwin.so 0x000000010efb4181 __Pyx_PyObject_Call + 97
22 wrapper.cpython-37m-darwin.so 0x000000010efc128d __pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3__call__ + 765
23 latebind.cpython-37m-darwin.so 0x000000010f01dfa1 __Pyx_PyObject_Call + 97
24 latebind.cpython-37m-darwin.so 0x000000010f01d522 __pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_11__call__ + 306
25 org.python.python 0x0000000100cec6df _PyObject_FastCallKeywords + 575
26 org.python.python 0x0000000100dc1bcd call_function + 765
27 org.python.python 0x0000000100dbe817 _PyEval_EvalFrameDefault + 26567
28 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
29 org.python.python 0x0000000100cec879 _PyFunction_FastCallKeywords + 217
30 org.python.python 0x0000000100dc1bd4 call_function + 772
31 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
32 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
33 org.python.python 0x0000000100dc1bd4 call_function + 772
34 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
35 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
36 org.python.python 0x0000000100cec879 _PyFunction_FastCallKeywords + 217
37 org.python.python 0x0000000100dc1bd4 call_function + 772
38 org.python.python 0x0000000100db85c4 _PyEval_EvalFrameDefault + 1396
39 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
40 org.python.python 0x0000000100dc1bd4 call_function + 772
41 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
42 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
43 org.python.python 0x0000000100dc1bd4 call_function + 772
44 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
45 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
46 org.python.python 0x0000000100dc1bd4 call_function + 772
47 org.python.python 0x0000000100dbe8ae _PyEval_EvalFrameDefault + 26718
48 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
49 org.python.python 0x0000000100dc1bd4 call_function + 772
50 org.python.python 0x0000000100dbe8ae _PyEval_EvalFrameDefault + 26718
51 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
52 org.python.python 0x0000000100cec879 _PyFunction_FastCallKeywords + 217
53 org.python.python 0x0000000100dc1bd4 call_function + 772
54 org.python.python 0x0000000100db85c4 _PyEval_EvalFrameDefault + 1396
55 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
56 org.python.python 0x0000000100dc1bd4 call_function + 772
57 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
58 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
59 org.python.python 0x0000000100dc1bd4 call_function + 772
60 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
61 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
62 org.python.python 0x0000000100dc1bd4 call_function + 772
63 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
64 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
65 org.python.python 0x0000000100cec879 _PyFunction_FastCallKeywords + 217
66 org.python.python 0x0000000100dc1bd4 call_function + 772
67 org.python.python 0x0000000100db85c4 _PyEval_EvalFrameDefault + 1396
68 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
69 org.python.python 0x0000000100dc1bd4 call_function + 772
70 org.python.python 0x0000000100dbe7fa _PyEval_EvalFrameDefault + 26538
71 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
72 org.python.python 0x0000000100ced873 _PyObject_Call_Prepend + 131
73 org.python.python 0x0000000100cec9d8 PyObject_Call + 136
74 QtCore.so 0x000000011ac70f17 PyQtSlot::call(_object*, _object*) const + 39
75 QtCore.so 0x000000011ac70e26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
76 QtCore.so 0x000000011ac71925 PyQtSlotProxy::unislot(void**) + 85
77 QtCore.so 0x000000011ac7189a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
78 QtCore 0x0000000116ac913d QMetaObject::activate(QObject*, int, int, void**) + 1773
79 QtCore 0x0000000116ad11f2 QTimer::timerEvent(QTimerEvent*) + 98
80 QtCore.so 0x000000011ab67028 sipQTimer::timerEvent(QTimerEvent*) + 120
81 QtCore 0x0000000116ac1ab6 QObject::event(QEvent*) + 102
82 QtCore.so 0x000000011ab66e9b sipQTimer::event(QEvent*) + 187
83 QtWidgets 0x0000000115dac67d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
84 QtWidgets 0x0000000115dada82 QApplication::notify(QObject*, QEvent*) + 594
85 QtWidgets.so 0x000000011596c3ca sipQApplication::notify(QObject*, QEvent*) + 234
86 QtCore 0x0000000116a98324 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
87 QtCore 0x0000000116af193f QTimerInfoList::activateTimers() + 991
88 libqcocoa.dylib 0x000000012283a032 0x122805000 + 217138
89 com.apple.CoreFoundation 0x00007fff2ea76d52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
90 com.apple.CoreFoundation 0x00007fff2ea76cf1 __CFRunLoopDoSource0 + 103
91 com.apple.CoreFoundation 0x00007fff2ea76b67 __CFRunLoopDoSources0 + 301
92 com.apple.CoreFoundation 0x00007fff2ea7583a __CFRunLoopRun + 927
93 com.apple.CoreFoundation 0x00007fff2ea74e3e CFRunLoopRunSpecific + 462
94 com.apple.HIToolbox 0x00007fff2d6a1abd RunCurrentEventLoopInMode + 292
95 com.apple.HIToolbox 0x00007fff2d6a16f4 ReceiveNextEventCommon + 359
96 com.apple.HIToolbox 0x00007fff2d6a1579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
97 com.apple.AppKit 0x00007fff2bce7039 _DPSNextEvent + 883
98 com.apple.AppKit 0x00007fff2bce5880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
99 com.apple.AppKit 0x00007fff2bcd758e -[NSApplication run] + 658
100 libqcocoa.dylib 0x000000012283ade3 0x122805000 + 220643
101 QtCore 0x0000000116a9393f QEventLoop::exec(QFlags) + 431
102 QtCore 0x0000000116a98932 QCoreApplication::exec() + 130
103 QtWidgets.so 0x0000000115a5b7d2 meth_QApplication_exec_(_object*, _object*) + 82
104 org.python.python 0x0000000100ced382 _PyMethodDef_RawFastCallKeywords + 226
105 org.python.python 0x0000000100cec8b9 _PyCFunction_FastCallKeywords + 41
106 org.python.python 0x0000000100dc1b60 call_function + 656
107 org.python.python 0x0000000100dbe817 _PyEval_EvalFrameDefault + 26567
108 org.python.python 0x0000000100cecd61 function_code_fastcall + 177
109 org.python.python 0x0000000100dc1bd4 call_function + 772
110 org.python.python 0x0000000100dbe817 _PyEval_EvalFrameDefault + 26567
111 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
112 org.python.python 0x0000000100cec879 _PyFunction_FastCallKeywords + 217
113 org.python.python 0x0000000100dc1bd4 call_function + 772
114 org.python.python 0x0000000100dbe8ae _PyEval_EvalFrameDefault + 26718
115 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
116 org.python.python 0x0000000100db7fb0 PyEval_EvalCode + 48
117 org.python.python 0x0000000100db5547 builtin_exec + 583
118 org.python.python 0x0000000100ced52d _PyMethodDef_RawFastCallKeywords + 653
119 org.python.python 0x0000000100cec8b9 _PyCFunction_FastCallKeywords + 41
120 org.python.python 0x0000000100dc1b60 call_function + 656
121 org.python.python 0x0000000100dbe8ae _PyEval_EvalFrameDefault + 26718
122 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
123 org.python.python 0x0000000100cec879 _PyFunction_FastCallKeywords + 217
124 org.python.python 0x0000000100dc1bd4 call_function + 772
125 org.python.python 0x0000000100dbe8ae _PyEval_EvalFrameDefault + 26718
126 org.python.python 0x0000000100dc2a2c _PyEval_EvalCodeWithName + 3276
127 org.python.python 0x0000000100cec377 _PyFunction_FastCallDict + 455
128 org.python.python 0x0000000100e1caf3 pymain_run_module + 147
129 org.python.python 0x0000000100e1bbdc pymain_main + 5900
130 org.python.python 0x0000000100e1a4c3 Py_Main + 51
131 edu.ucsf.cgl.ChimeraX 0x0000000100cbddc8 main + 120
132 libdyld.dylib 0x00007fff6894dcc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 6:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 7:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000102630c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 8:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2ea76ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2ea759c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2ea74e3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2be88954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 9:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe22f 0x11b25c000 + 35267119
4 QtWebEngineCore 0x000000011d3b205d 0x11b25c000 + 34955357
5 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
6 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 10:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff68a93766 kevent + 10
1 QtWebEngineCore 0x000000011d6bf9a9 0x11b25c000 + 38156713
2 QtWebEngineCore 0x000000011d6bccbd 0x11b25c000 + 38145213
3 QtWebEngineCore 0x000000011d473cdc 0x11b25c000 + 35749084
4 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
5 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
6 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
7 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 11:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff68a93766 kevent + 10
1 QtWebEngineCore 0x000000011d6bf9a9 0x11b25c000 + 38156713
2 QtWebEngineCore 0x000000011d6bccbd 0x11b25c000 + 38145213
3 QtWebEngineCore 0x000000011d473cc4 0x11b25c000 + 35749060
4 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
5 QtWebEngineCore 0x000000011d41ca74 0x11b25c000 + 35392116
6 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 12:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe421 0x11b25c000 + 35267617
4 QtWebEngineCore 0x000000011d415d28 0x11b25c000 + 35364136
5 QtWebEngineCore 0x000000011d41665b 0x11b25c000 + 35366491
6 QtWebEngineCore 0x000000011d4162c4 0x11b25c000 + 35365572
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 13:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe421 0x11b25c000 + 35267617
4 QtWebEngineCore 0x000000011d415d28 0x11b25c000 + 35364136
5 QtWebEngineCore 0x000000011d41665b 0x11b25c000 + 35366491
6 QtWebEngineCore 0x000000011d4162c4 0x11b25c000 + 35365572
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 14:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe421 0x11b25c000 + 35267617
4 QtWebEngineCore 0x000000011d415d28 0x11b25c000 + 35364136
5 QtWebEngineCore 0x000000011d41665b 0x11b25c000 + 35366491
6 QtWebEngineCore 0x000000011d416234 0x11b25c000 + 35365428
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 15:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff68a93766 kevent + 10
1 QtWebEngineCore 0x000000011d6bf9a9 0x11b25c000 + 38156713
2 QtWebEngineCore 0x000000011d6bccbd 0x11b25c000 + 38145213
3 QtWebEngineCore 0x000000011d473cc4 0x11b25c000 + 35749060
4 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
5 QtWebEngineCore 0x000000011cd49fe4 0x11b25c000 + 28237796
6 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 16:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe22f 0x11b25c000 + 35267119
4 QtWebEngineCore 0x000000011d415d1a 0x11b25c000 + 35364122
5 QtWebEngineCore 0x000000011d4163bf 0x11b25c000 + 35365823
6 QtWebEngineCore 0x000000011d416264 0x11b25c000 + 35365476
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 17:: CompositorTileWorker1/69891
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011d46bfa8 0x11b25c000 + 35717032
3 QtWebEngineCore 0x000000011e3f24c8 0x11b25c000 + 51995848
4 QtWebEngineCore 0x000000011d42c694 0x11b25c000 + 35456660
5 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
6 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 18:: AudioThread
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe22f 0x11b25c000 + 35267119
4 QtWebEngineCore 0x000000011d3b205d 0x11b25c000 + 34955357
5 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
6 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 19:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe22f 0x11b25c000 + 35267119
4 QtWebEngineCore 0x000000011d3b205d 0x11b25c000 + 34955357
5 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
6 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 20:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3b2052 0x11b25c000 + 34955346
4 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
5 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
6 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
7 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 21:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff68a93766 kevent + 10
1 QtWebEngineCore 0x000000011d6bf9a9 0x11b25c000 + 38156713
2 QtWebEngineCore 0x000000011d6bccbd 0x11b25c000 + 38145213
3 QtWebEngineCore 0x000000011d473cdc 0x11b25c000 + 35749084
4 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
5 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
6 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
7 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 22:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe22f 0x11b25c000 + 35267119
4 QtWebEngineCore 0x000000011d415d1a 0x11b25c000 + 35364122
5 QtWebEngineCore 0x000000011d41665b 0x11b25c000 + 35366491
6 QtWebEngineCore 0x000000011d416324 0x11b25c000 + 35365668
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 23:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe22f 0x11b25c000 + 35267119
4 QtWebEngineCore 0x000000011d3b205d 0x11b25c000 + 34955357
5 QtWebEngineCore 0x000000011d3db085 0x11b25c000 + 35123333
6 QtWebEngineCore 0x000000011d42d9bc 0x11b25c000 + 35461564
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 24:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff68a8edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff68a8f170 mach_msg + 60
2 QtWebEngineCore 0x000000011d3fe32d 0x11b25c000 + 35267373
3 QtWebEngineCore 0x000000011d3fe421 0x11b25c000 + 35267617
4 QtWebEngineCore 0x000000011d415d28 0x11b25c000 + 35364136
5 QtWebEngineCore 0x000000011d41665b 0x11b25c000 + 35366491
6 QtWebEngineCore 0x000000011d416234 0x11b25c000 + 35365428
7 QtWebEngineCore 0x000000011d46d717 0x11b25c000 + 35723031
8 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 31:
0 libsystem_kernel.dylib 0x00007fff68a91882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68b52425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000159274c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68b52109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff68b4db8b thread_start + 15
Thread 32:
0 libsystem_pthread.dylib 0x00007fff68b4db68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010f7aedc0 rcx: 0x00007f8ec808fa58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007f8ec808fa80 rsp: 0x00007f8ec808fa58
r8: 0x00007f8ec808ff48 r9: 0x634fcb3ec14512be r10: 0x000000010f7aedc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000000000000 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff68a9533a rfl: 0x0000000000000246 cr2: 0x00000001029a6000
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x10175d000 - 0x10175effb +_random.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_random.cpython-37m-darwin.so
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0x101875000 - 0x101882ff7 +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so
0x101898000 - 0x1018a1ffb +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so
0x1018f3000 - 0x1018f6fff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so
0x101901000 - 0x101905ffb +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so
0x101913000 - 0x101917ff7 +binascii.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/binascii.cpython-37m-darwin.so
0x101a20000 - 0x101a2eff3 +_datetime.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_datetime.cpython-37m-darwin.so
0x101a7e000 - 0x101a7eff3 +_scproxy.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_scproxy.cpython-37m-darwin.so
0x101a86000 - 0x101ac4ff7 +_decimal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_decimal.cpython-37m-darwin.so
0x101b28000 - 0x101b55ff3 +pyexpat.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/pyexpat.cpython-37m-darwin.so
0x101b6d000 - 0x101b6eff3 +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so
0x101c37000 - 0x101c38fff +_posixsubprocess.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_posixsubprocess.cpython-37m-darwin.so
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0x101ce3000 - 0x101ce6ffb +_csv.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_csv.cpython-37m-darwin.so
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0x1022fa000 - 0x105d65ae7 +libopenblasp-r0.3.7.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libopenblasp-r0.3.7.dylib
0x10606f000 - 0x106186ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib
0x1061f4000 - 0x10622afff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libquadmath.0.dylib
0x10623e000 - 0x106253ff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgcc_s.1.dylib
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0x10e78d000 - 0x10e7e1fff +_bounded_integers.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bounded_integers.cpython-37m-darwin.so
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0x10e878000 - 0x10e8fafff +_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_generator.cpython-37m-darwin.so
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0x10ea63000 - 0x10ea64ffb +libappdirs.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libappdirs.dylib
0x10ea6c000 - 0x10ea8dffb +_serialize.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/_serialize.cpython-37m-darwin.so
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0x7fff677c6000 - 0x7fff677c7ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff677d8000 - 0x7fff677dcfff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff677df000 - 0x7fff67815ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff67855000 - 0x7fff67863ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff67899000 - 0x7fff678b1fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff678b3000 - 0x7fff678f7ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff678f8000 - 0x7fff6790aff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6790b000 - 0x7fff6790cff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6790d000 - 0x7fff67af7ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff67beb000 - 0x7fff67c18ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff67ced000 - 0x7fff67d47ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff67d48000 - 0x7fff67d4bffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff67d4c000 - 0x7fff67d59ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff67d5f000 - 0x7fff67e41fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff67e45000 - 0x7fff67e6dfff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff67e6e000 - 0x7fff67e80ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6872f000 - 0x7fff68734ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff68735000 - 0x7fff68740fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff68741000 - 0x7fff68748fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff68749000 - 0x7fff68752ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff68753000 - 0x7fff687e5fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff688f2000 - 0x7fff68932ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff68933000 - 0x7fff68969fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff6896a000 - 0x7fff6896affb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6896b000 - 0x7fff68977ff3 libkxld.dylib (6153.141.2.2) /usr/lib/system/libkxld.dylib
0x7fff68978000 - 0x7fff68978ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff68979000 - 0x7fff6897eff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6897f000 - 0x7fff68981ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff68982000 - 0x7fff68983ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff68984000 - 0x7fff6899bff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff6899c000 - 0x7fff6899cff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6899d000 - 0x7fff68a24fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff68a25000 - 0x7fff68a28ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff68a29000 - 0x7fff68a2cfff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff68a2d000 - 0x7fff68a35fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff68a36000 - 0x7fff68a3dfff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff68a3e000 - 0x7fff68a3fffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff68a40000 - 0x7fff68a8dff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff68a8e000 - 0x7fff68abaff7 libsystem_kernel.dylib (6153.141.2.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff68abb000 - 0x7fff68b02fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff68b03000 - 0x7fff68b2afff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff68b2b000 - 0x7fff68b38ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff68b39000 - 0x7fff68b42ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff68b43000 - 0x7fff68b4bfef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff68b4c000 - 0x7fff68b56fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff68b57000 - 0x7fff68b5bff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff68b5c000 - 0x7fff68b5efff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff68b5f000 - 0x7fff68b66ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff68b67000 - 0x7fff68b7dff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff68b7f000 - 0x7fff68b84ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff68b85000 - 0x7fff68bbaffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 251
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: 546039492
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)
Writable regions: Total=8.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.8G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 4
Activity Tracing 256K 1
CG backing stores 1232K 2
CG image 172K 13
CoreAnimation 108K 13
CoreGraphics 8K 1
CoreImage 24K 2
CoreUI image data 3200K 27
Dispatch continuations 32.0M 1
Foundation 24K 2
Kernel Alloc Once 8K 1
MALLOC 6.0G 691
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 1.1G 13 reserved VM address space (unallocated)
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 128K 32
Stack 144.2M 33
Stack Guard 56.0M 1
VM_ALLOCATE 1.2G 765
VM_ALLOCATE (reserved) 384.0M 4 reserved VM address space (unallocated)
__DATA 66.8M 637
__DATA_CONST 132K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 438.7M 208
__OBJC_RO 32.3M 1
__OBJC_RW 1904K 1
__TEXT 665.0M 581
__UNICODE 564K 1
mapped file 89.6M 65
shared memory 664K 21
=========== ======= =======
TOTAL 10.2G 3145
TOTAL, minus reserved VM space 8.7G 3145
System Profile:
Network Service: Wi-Fi, AirPort, en0
bridge_os_version: Bridge OS 4.6 (17P6610)
Boot Volume File System Type: apfs
bridge_model: iBridge2,14
Memory Module: BANK 0/ChannelA-DIMM0, 32 GB, DDR4, 2667 MHz, Micron, -
Memory Module: BANK 2/ChannelB-DIMM0, 32 GB, DDR4, 2667 MHz, Micron, -
USB Device: USB 3.1 Bus
USB Device: Apple T2 Bus
USB Device: Composite Device
USB Device: Touch Bar Backlight
USB Device: Touch Bar Display
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 55.3
Thunderbolt Bus: MacBook Pro, Apple Inc., 55.3
Model: MacBookPro16,1, BootROM 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0), 8 processors, 8-Core Intel Core i9, 2,3 GHz, 64 GB, SMC
Graphics: kHW_IntelUHDGraphics630Item, Intel UHD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro5500MItem, AMD Radeon Pro 5500M, spdisplays_pcie_device, 8 GB
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Apr 7 2020 13:09:12 version 9.30.357.41.32.5.49 FWID 01-617711e7
Bluetooth: Version 7.0.6f7, 3 services, 27 devices, 1 incoming serial ports
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open NPC_overview_9_flowchart.cxs
Log from Tue Feb 8 14:28:21 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open NPC_overview_9.cxs
Log from Tue Oct 12 21:47:38 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open NPC_overview_8.cxs
Log from Tue Oct 12 21:38:33 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open maps_and_models_overview5.cxs
Log from Fri Oct 1 08:33:08 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open maps_and_models_overview4.cxs
Log from Sun Sep 26 23:20:46 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open maps_and_models_overview3.cxs
Log from Sun Sep 26 16:24:21 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open maps_and_models_overview1.cxs
Log from Fri Sep 24 17:21:17 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open maps_and_models_overview.cxc.cxs
Log from Thu Sep 23 23:28:22 2021UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/pore_whole_resample.mrc
Opened pore_whole_resample.mrc, grid size 576,576,576, pixel 3.37, shown at
level 4.08, step 4, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/cr_whole_resample.mrc
Opened cr_whole_resample.mrc, grid size 576,576,576, pixel 3.37, shown at
level 0.238, step 4, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/sr_whole_resample.mrc
Opened sr_whole_resample.mrc, grid size 576,576,576, pixel 3.37, shown at
level 0.453, step 4, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/nr_whole_resample.mrc
Opened nr_whole_resample.mrc, grid size 576,576,576, pixel 3.37, shown at
level 1.79, step 4, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/membrane_masked_r180_resample.mrc
Opened membrane_masked_r180_resample.mrc, grid size 576,576,576, pixel 3.37,
shown at level 0.00753, step 4, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/membrane_masked_r200_resample.mrc
Opened membrane_masked_r200_resample.mrc, grid size 576,576,576, pixel 3.37,
shown at level 0.0118, step 4, values float32
> open /Users/agnieszka/NPC/human/NPC2.0/maps04/shyamal$ HKenv_full_fromBT.mrc
'/Users/agnieszka/NPC/human/NPC2.0/maps04/shyamal$' has no suffix
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/christian/Human/Hek_wt_fullm_cut_resample_onConstricted.mrc
Opened Hek_wt_fullm_cut_resample_onConstricted.mrc, grid size 37,50,60, pixel
13.5,13.5,13.5, shown at level 0.459, step 1, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/christian/Human/Hek_wt_fullm_resample_onConstricted.mrc
Opened Hek_wt_fullm_resample_onConstricted.mrc, grid size 576,576,576, pixel
3.37, shown at level 0.277, step 4, values float32
> volume #1-10 step 1 color #e6e6e633
> volume #1 level 2.38
> volume #2 level 0.238
> volume #3 level 0.453
> volume #4 level 1.79
> volume #5 level 0.01
> volume #6 level 0.01
> surface dust #1 size 100
> surface dust #2 size 100
> surface dust #3 size 100
> surface dust #4 size 100
> surface dust #5 size 100
> volume transparency 0.6
> lighting simple
> graphics bgColor white
> graphics silhouettes true width 3
> windowsize 1440 810
> hide #!1-4 target m
> hide #!5-6 target m
> volume #8 level 0.2089
> volume #8 level 0.1703
> volume #8 level 0.1794
> select #8
2 models selected
> select clear
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> volume #8 level 0.1179
> volume #7 level 0.118
> volume #8 level 0.01118
> volume #9 level 0.0118
No volumes specified
> surface dust #1 size 100
> surface dust #2 size 100
> surface dust #3 size 100
> surface dust #4 size 100
> surface dust #5 size 100
> surface dust #6 size 100
> surface dust #7 size 100
> surface dust #8 size 100
> surface dust #9 size 100
No surfaces specified
> volume #1-10 step 1 color #e6e6e633
> volume #1 level 2.38
> volume #2 level 0.238
> volume #3 level 0.453
> volume #4 level 1.79
> volume #5 level 0.01
> volume #6 level 0.01
> volume #7 level 0.0118
> volume #8 level 0.0118
> volume #8 level 0.02
> volume #8 level 0.1
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.CRouter.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.CRinner.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.NRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.NRinner.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.NRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/Y.NRouter.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_1_CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_1_CRouter.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_2_CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_2_CRouter.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_1_CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_1_CRinner.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_2_CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_2_CRinner.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_CRmiddle.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/hNup358_CRmiddle.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/IRcyt_outer.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/IRcyt_outer.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/IRcyt_inner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/IRcyt_inner.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/IRnuc_inner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/IRnuc_inner.pdb
> open /g/kosinski/agnieszka/NPC_human/const_AF_complex/IRnuc_outer.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/IRnuc_outer.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #9
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #10
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #11
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #12
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #13
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #14
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #15
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #16
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 272408
Duplicate atom serial number found: 272409
Duplicate atom serial number found: 272410
Duplicate atom serial number found: 272411
Duplicate atom serial number found: 272412
70 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #18
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #19
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #20
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #21
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> hide #!8 models
> select #19/C:832@CG2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel atoms
> hide sel atoms
> hide atoms #13-21
Expected ',' or a keyword
> hide #13-21
> hide #9-21
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!14 models
> show #!14 models
> hide #9-21
> ribbon #9-21
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb
> select #22/D:325
6 atoms, 5 bonds, 1 residue, 1 model selected
> color /F/F?/F?? #b4e400
> color /Y/Y?/Y?? #FF004A
> color /0/0?/0?? cyan
> color /E/E/E?? cyan
> color /4/4?/4?? #005887
> color /A #FF004A
> color /C #005887
> color /F #b4e400
> color /B #0075BE
> color /D #FA8072
> color /J #CAEF00
> color /K #0098EB
> color /Q #0098EB
> color /M #436495
> color /S #981E05
> color /T #00C9CA
> color /U #20639B
> color /V #ed553B
> color /W #00A567
> color /Z #FFA04D
> color /2 #23c6c8
> color /3 #FFC200
> color /4 #dc4c77
> color /8 #9D003D
> color /9 #5A3389
> color /L #FF5851
> color /N #4CC7ED
> color /R #FFC459
> color /P #FF8853
> color /O #007F7E
> color /H #00C9CA
> color /I #006686
> color /G #FF937A
> color /A? #FF004A
> color /C? #005887
> color /F? #b4e400
> color /B? #0075BE
> color /D? #FA8072
> color /J? #CAEF00
> color /K? #0098EB
> color /Q? #0098EB
> color /M? #436495
> color /S? #981E05
> color /T? #00C9CA
> color /U? #20639B
> color /V? #ed553B
> color /W? #00A567
> color /Z? #FFA04D
> color /2? #23c6c8
> color /3? #FFC200
> color /4? #dc4c77
> color /8? #9D003D
> color /9? #5A3389
> color /L? #FF5851
> color /N? #4CC7ED
> color /R? #FFC459
> color /P? #FF8853
> color /O? #007F7E
> color /H? #00C9CA
> color /I? #006686
> color /G? #FF937A
> color /A?? #FF004A
> color /C?? #005887
> color /F?? #b4e400
> color /B?? #0075BE
> color /D?? #FA8072
> color /J?? #CAEF00
> color /K?? #0098EB
> color /Q?? #0098EB
> color /M?? #436495
> color /S?? #981E05
> color /T?? #00C9CA
> color /U?? #20639B
> color /V?? #ed553B
> color /W?? #00A567
> color /Z?? #FFA04D
> color /2?? #23c6c8
> color /3?? #FFC200
> color /4?? #dc4c77
> color /8?? #9D003D
> color /9?? #5A3389
> color /L?? #FF5851
> color /N?? #4CC7ED
> color /R?? #FFC459
> color /P?? #FF8853
> color /O?? #007F7E
> color /H?? #00C9CA
> color /I?? #006686
> color /G?? #FF937A
> close #9-22
> color /G?? #FF937Aopen
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #9
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #11
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #12
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #13
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #14
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #15
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #16
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #21
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/YhNup155_NRconnector.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> hide #9-22
> hide #9-22
> ribbon #9-22
> color /F/F?/F?? #b4e400
> color /Y/Y?/Y?? #FF004A
> color /0/0?/0?? cyan
> color /E/E/E?? cyan
> color /4/4?/4?? #005887
> color /A #FF004A
> color /C #005887
> color /F #b4e400
> color /B #0075BE
> color /D #FA8072
> color /J #CAEF00
> color /K #0098EB
> color /Q #0098EB
> color /M #436495
> color /S #981E05
> color /T #00C9CA
> color /U #20639B
> color /V #ed553B
> color /W #00A567
> color /Z #FFA04D
> color /2 #23c6c8
> color /3 #FFC200
> color /4 #dc4c77
> color /8 #9D003D
> color /9 #5A3389
> color /L #FF5851
> color /N #4CC7ED
> color /R #FFC459
> color /P #FF8853
> color /O #007F7E
> color /H #00C9CA
> color /I #006686
> color /G #FF937A
> color /A? #FF004A
> color /C? #005887
> color /F? #b4e400
> color /B? #0075BE
> color /D? #FA8072
> color /J? #CAEF00
> color /K? #0098EB
> color /Q? #0098EB
> color /M? #436495
> color /S? #981E05
> color /T? #00C9CA
> color /U? #20639B
> color /V? #ed553B
> color /W? #00A567
> color /Z? #FFA04D
> color /2? #23c6c8
> color /3? #FFC200
> color /4? #dc4c77
> color /8? #9D003D
> color /9? #5A3389
> color /L? #FF5851
> color /N? #4CC7ED
> color /R? #FFC459
> color /P? #FF8853
> color /O? #007F7E
> color /H? #00C9CA
> color /I? #006686
> color /G? #FF937A
> color /A?? #FF004A
> color /C?? #005887
> color /F?? #b4e400
> color /B?? #0075BE
> color /D?? #FA8072
> color /J?? #CAEF00
> color /K?? #0098EB
> color /Q?? #0098EB
> color /M?? #436495
> color /S?? #981E05
> color /T?? #00C9CA
> color /U?? #20639B
> color /V?? #ed553B
> color /W?? #00A567
> color /Z?? #FFA04D
> color /2?? #23c6c8
> color /3?? #FFC200
> color /4?? #dc4c77
> color /8?? #9D003D
> color /9?? #5A3389
> color /L?? #FF5851
> color /N?? #4CC7ED
> color /R?? #FFC459
> color /P?? #FF8853
> color /O?? #007F7E
> color /H?? #00C9CA
> color /I?? #006686
> color /G?? #FF937A
> select #17/0:620
8 atoms, 7 bonds, 1 residue, 1 model selected
> color /0* #b4e400
> color /0* magenta
> color /0* yellow
> color /0* blue
> color /0* purple
> color /M* green
> color /K* purple
> color /0* blue
> color /0* light blue
> color /0* sky blue
> color /L* orange
> select #9/D:1094
5 atoms, 4 bonds, 1 residue, 1 model selected
> color /P* #85ff7a
> color /P* orange
> color /M* #85ff7a
> color /M* #45f248
> color /A* #FF004A
> color /C* #005887
> color /F* #b4e400
> color /B* #0075BE
> color /D* #FA8072
> color /J* #CAEF00
> color /K* #0098EB
> color /Q* #0098EB
> color /M* #436495
> color /S* #981E05
> color /T* #00C9CA
> color /U* #20639B
> color /V* #ed553B
> color /W* #00A567
> color /Z* #FFA04D
> color /2* #23c6c8
> color /3* #FFC200
> color /4* #dc4c77
> color /8* #9D003D
> color /9* #5A3389
> color /L* #FF5851
> color /N* #4CC7ED
> color /R* #FFC459
> color /P* #FF8853
> color /O* #007F7E
> color /H* #00C9CA
> color /I* #006686
> color /G* #FF937A
> color /M* #d4ffb2
> color /M* #45f248
> color /O* #159493
> color /N* magenta
> select #13/O:236
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> close #9-22
> color /N* magentaopen
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #9
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #11
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #12
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #13
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #14
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #15
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #16
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #21
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> hide #9-22
> ribbon #9-22
> color /A* #FF004A
> color /C* #005887
> color /F* #b4e400
> color /B* #0075BE
> color /D* #FA8072
> color /J* #CAEF00
> color /K* #0098EB
> color /Q* #0098EB
> color /M* #436495
> color /S* #981E05
> color /T* #00C9CA
> color /U* #20639B
> color /V* #ed553B
> color /W* #00A567
> color /Z* #FFA04D
> color /2* #23c6c8
> color /3* #FFC200
> color /4* #dc4c77
> color /8* #9D003D
> color /9* #5A3389
> color /L* #FF5851
> color /N* #4CC7ED
> color /R* #FFC459
> color /P* #FF8853
> color /O* #159493
> color /H* #00C9CA
> color /I* #006686
> color /G* #FF937A
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 272408
Duplicate atom serial number found: 272409
Duplicate atom serial number found: 272410
Duplicate atom serial number found: 272411
Duplicate atom serial number found: 272412
44904 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #23
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> close #9-23
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 272408
Duplicate atom serial number found: 272409
Duplicate atom serial number found: 272410
Duplicate atom serial number found: 272411
Duplicate atom serial number found: 272412
44904 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #9
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #11
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #12
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #13
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #14
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #15
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #16
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #21
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #23
---
Chain | Description
D | No description available
F | No description available
U | No description available
> hide #9-22
> ribbon #9-22
> color /A* #FF004A
> color /C* #005887
> color /F* #b4e400
> color /B* #0075BE
> color /D* #FA8072
> color /J* #CAEF00
> color /K* #0098EB
> color /Q* #0098EB
> color /M* #436495
> color /S* #981E05
> color /T* #00C9CA
> color /U* #20639B
> color /V* #ed553B
> color /W* #00A567
> color /Z* #FFA04D
> color /2* #23c6c8
> color /3* #FFC200
> color /4* #dc4c77
> color /8* #9D003D
> color /9* #5A3389
> color /L* #FF5851
> color /N* #4CC7ED
> color /R* #FFC459
> color /P* #FF8853
> color /O* #159493
> color /H* #00C9CA
> color /I* #006686
> color /G* #FF937A
> color /0* #0098EB
> select clear
> color /K* #45f248
> select #22/D:881
8 atoms, 7 bonds, 1 residue, 1 model selected
> color /L* #FF8853
> select #14/A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> color /P* #FF5851
> color /0* #0098EB
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #8f00f1
> color /M* #D99DE48f00f1
> color /M* #D99DE4
> color /M* #D99DE48f00f1
> color /N* #D99DE48f00f1
> color /M* #D99DE4
> color /M* #917db6
> color /C* #167a9e
> color /C* #168c9e
> color /C* #16939e
> color /C* #067fbf
> color /C* #11a6f5
> color /B* #11a6f5
> color /C* #005887
> color /C* #055d9c
> color /C* #0259b0
> color /M* #917db6
> color /B* #11a6f5
> color /B* #11a6f5
> color /M* #8c05fa
> color /M* #917db68c05fa
> select #14/C:1263
8 atoms, 7 bonds, 1 residue, 1 model selected
> color /M* #917db6
> color /0* #0098EB
> color /P* #FF8853
> color /L* #FF5851
> color /R* #45f248
> color /M* #917db6
> color /B* #11a6f5
> color /C* #0259b0917db6
> color /R* #99ffb2
> view
> color /R* #159493
> color /C* #0259b0159493
> color /C* #0259b0
> color /T* magenta
> color /T* #ac79c9
> color /T* #bd79c9
> color /R* #159493
> color /T* #45f248
> select #15/T:47
6 atoms, 5 bonds, 1 residue, 1 model selected
> color /T* #79f245
> color /T* #8df245
> color /T* #8df245
> color /K* #0098EB
> color /0* #0098EB
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #917db6
> color /B* #11a6f5
> color /C* #0259b0
> color /R* #159493
> color /T* #8df245
> color /K* #0098EB
> color /Q* #8df245
> color /O* cyan
> color /M* #8df245
> color /Q* #917db6
> color /0* #0098EB
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #917db6
> color /B* #11a6f5
> color /C* #0259b0
> color /R* #159493
> color /T* #8df245
> color /K* #0098EB
> color /N* #8df245
> color /O* cyan8df245
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /Q* yellow
> color /O* yellow
> color /Q* cyan
> color /D* pink
> color /D* #FFC459
> color /F* green
> color /F* lime green
> color /4* magenta
> color /F* #b4e400
> color /I* #b4e400
> color /J* orange
> color /J* magenta
> color /J* violet
> color /H* purple
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
7941 atoms, 8121 bonds, 1001 residues, 1 model selected
> color /I* #b4e400
> color /H* violet
> color /J* purple
> color /I* #b4e400
> color /H* violet
> color /J* purple
> select clear
> color /D* #FFC459
> color /D* #d3ffd8
> color /D* #daffd3
> color /D* #c4e3a6
> color /D* #feffba
> color /D* #fce88b
> color /F* #8df245
> color /4* #45f248
> color /R* #159493
> color /E* #159493
> color /K* purple
> color /F cyan
> color /A* #FF004A
> color /C* #005887
> color /F* #b4e400
> color /B* #0075BE
> color /D* #FA8072
> color /J* #CAEF00
> color /Q* #0098EB
> color /M* #436495
> color /S* #981E05
> color /T* #00C9CA
> color /U* #20639B
> color /V* #ed553B
> color /W* #00A567
> color /Z* #FFA04D
> color /2* #23c6c8
> color /3* #FFC200
> color /4* #dc4c77
> color /8* #9D003D
> color /9* #5A3389
> color /L* #FF5851
> color /N* #4CC7ED
> color /R* #FFC459
> color /P* #FF8853
> color /O* #159493
> color /H* #00C9CA
> color /I* #006686
> color /G* #FF937A
> color /0* #0098EB
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #917db6
> color /B* #11a6f5
> color /C* #0259b0
> color /R* #159493
> color /T* #8df245
> color /K* #0098EB
> color /N* #8df245
> color /O* yellow
> color /Q* cyan
> color /D* #FFC459
> color /F* #b4e400
> color /I* #b4e400
> color /H* violet
> color /D* #fce88b
> color /F* #8df245
> color /4* #45f248
> color /K* purple
> color /E* #159493
> color /J* purple
> color /V* #8df245
> color /V* #adf245
> color /U* magenta
> color /W* #00b5a3
> show #!1 models
> volume transparency ).7
Invalid "transparency" argument: Expected a number
> volume transparency 0.7
> volume transparency 0.9
> volume transparency 0.8
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!6 models
> hide #!5 models
> lighting soft
> graphics silhouettes true width 2
> volume transparency 0.6
> volume transparency 0.8
> lighting simple
> lighting soft
> lighting simple
> measure symmetry #1
Symmetry pore_whole_resample.mrc: C8, center 288 288 298
> sym #9-23 symmetry #1
> hide #!20 models
> show #!20 models
> view
> view
> view name ouside
> view name side_ouside
> view name top
> view side_ouside
> ui tool show "Side View"
> view side_ouside_cut
Expected an objects specifier or a view name or a keyword
> view name side_cut
> view name side_outside
> view name side_cut
> show #!8 models
> view name top
> hide #!8 models
> show #!8 models
> view name top
> show #!7 models
> hide #!6 models
> hide #!7 models
> view side
Expected an objects specifier or a view name or a keyword
> view side_outside
> show #!7 models
> hide #!7 models
> hide #!1 models
> hide #!8 models
> show #!1 models
> show #!6 models
> volume transparency 0.8
> volume transparency 0.7
> volume transparency 0.75
> close #19#9-18,20-23
> save
> /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview.cxc.cxs
opened ChimeraX session
> view side_outside
> turn x, 45
Expected an axis vector or a keyword
> turn x -45
> turn x 45
> turn x 45
> show #!7 models
> hide #!7 models
> show #!8 models
> view name tilt
> save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview1.cxs
> hide #!8 models
> ui tool show "Side View"
> view name tilt
> save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview1.cxs
opened ChimeraX session
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 272408
Duplicate atom serial number found: 272409
Duplicate atom serial number found: 272410
Duplicate atom serial number found: 272411
Duplicate atom serial number found: 272412
44904 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #9
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #11
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #12
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #13
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #14
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #15
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #16
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #21
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #23
---
Chain | Description
D | No description available
F | No description available
U | No description available
> set bgColor black
> hide #9-22
> ribbon #9-22
> view #17-21
> color #13 #a5e6fa
> color #14 #a7c0d6
> color #15-16 gray
> color #19 #004c61
> color #20 #18b8db
> color #18 #004f7d
> color #17 #2d6291
> color #20 #188dd6
> color #13/A:170-2000 #FF004A
> ~ribbon
> ribbon #17-21
> ribbon #13/A:170-2000#17-21
> ribbon style #17-21#13/A width 2.5 thickness 0.6
> volume #1 color #808080
> volume #1 transparency 0.75
> material ambientReflectivity 1
> material specularReflectivity 0
> lighting intensity 1.6
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> graphics silhouettes true width 3
> view 358_side1
Expected an objects specifier or a view name or a keyword
> save 358_side1.png supersample 3 transparentBackground true
> save 358_side1.png supersample 3 transparentBackground true
> save 358_side12png supersample 3 transparentBackground true
Cannot determine format for '358_side12png'
> save 358_side12.png supersample 3 transparentBackground true
> lighting simple
> save 358_side12.png supersample 3 transparentBackground true
> save 358_side12.png supersample 3 transparentBackground true
> volume #1 color #808080
> volume #1 transparency 0.75
> material ambientReflectivity 1
> material specularReflectivity 0
> lighting intensity 1.6
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> graphics silhouettes true width 3
> view 358_side1
Expected an objects specifier or a view name or a keyword
> save 358_side1.png supersample 3 transparentBackground true
> lighting simple
> save 358_side1.png supersample 3 transparentBackground true
> volume #1 transparency 0.75
> volume #1 color #808080
> volume #1 transparency 0.75
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 5
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 2
> save 358_side1.png supersample 3 transparentBackground true
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 3
> save 358_side1.png supersample 3 transparentBackground true
> material specularReflectivity 0
> lighting intensity 1
> lighting intensity 2
> material ambientReflectivity 0.5
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 0.1
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 0
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 4
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 3
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 1
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2.5
> save 358_side1.png supersample 3 transparentBackground true
> material specularReflectivity 0.1
> save 358_side1.png supersample 3 transparentBackground true
> material specularReflectivity 0.1
> material specularReflectivity 0
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 0
> lighting direction 1,-1,-2
> lighting direction -1,-1,-1
> save 358_side1.png supersample 3 transparentBackground true
> lighting direction -1,-1,1
> lighting direction -1,-1,1
> lighting direction 1,-1,-1
> lighting direction 1,-1,-2
> lighting direction 1,-1,-1
> lighting direction 1,-1,-2
> lighting direction 1,-2,-2
> lighting direction 1,-1,-2
> save 358_side1.png supersample 3 transparentBackground true
> lighting fillDirection 0,0,0
> save 358_side1.png supersample 3 transparentBackground true
> lighting direction -1,-1,-2
> save 358_side1.png supersample 3 transparentBackground true
> lighting fillDirection 0,0,0
> lighting fillDirection 0,0,-1
> lighting fillDirection 0,-1,-1
> lighting fillDirection -1,-1,-1
> lighting simple
> save 358_side1.png supersample 3 transparentBackground true
> lighting fillDirection -1,-1,-1
> lighting direction 1,-1,-2
> lighting direction 1,-1,-1
> lighting fillDirection 1,-1,-1
> lighting fillDirection -1,-1,-1
> lighting fillDirection -1,-1,1
> lighting fillDirection -1,1,1
> lighting fillDirection -1,-1,-1
> lighting fillDirection -1,-11,-1
> lighting fillDirection -1,-1,-1
> lighting direction 1,-1,-1
> lighting direction 1,-1,1
> lighting direction 0.5,-1,-1
> lighting direction 0,-1,-1
> lighting direction 1,-1,-1
> lighting direction 1,-1,-1
> material specularReflectivity 0
> material ambientReflectivity 0
> lighting intensity 2.5
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2.2
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 0.5
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 0.2
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2.4
> save 358_side1.png supersample 3 transparentBackground true
> material ambientReflectivity 0
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2.5
> lighting direction 1,-1,-2
> 123angle
123angle is provided by the uninstalled bundle SEQCROW
> save 358_side1.png supersample 3 transparentBackground true
> lighting fillDirection -1,-1,-1
> save 358_side1.png supersample 3 transparentBackground true
> lighting fillDirection 1,-1,-1
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2.3
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 1
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2
> save 358_side1.png supersample 3 transparentBackground true
> lighting intensity 2.2
> save 358_side1.png supersample 3 transparentBackground true
> volume #1 color #808080
> volume #1 transparency 0.75
> material ambientReflectivity 0
> material specularReflectivity 0
> lighting intensity 2.2
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-22
> save 358_side1.png supersample 3 transparentBackground true
> volume #1 color #808080
> volume #1 transparency 0.75
> material ambientReflectivity 0
> material specularReflectivity 0
> lighting intensity 2.2
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> save 358_side1.png supersample 3 transparentBackground true
> view name side3
> view side1
Expected an objects specifier or a view name or a keyword
> view side2
Expected an objects specifier or a view name or a keyword
> view name side1
> view side1
> hide #!1 models
> hide #!6 models
> view side1
> show #!1 models
> hide #!1 models
> show #!1 models
> view name side1
> view 358_side1
Expected an objects specifier or a view name or a keyword
> view 358_side2
Expected an objects specifier or a view name or a keyword
> view 358_side3
Expected an objects specifier or a view name or a keyword
> view name 358_side1
> select #1
4 models selected
> select clear
> volume #1 level 2.38
> volume #1 level 2.6
> volume #1 level 2.7
> volume #1 level 3
> volume #1 level 3.3
> volume #1 level 3
> volume #1 level 2.8
> view name 358_side2
> view name 358_top
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> volume #1 color #808080
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> volume #1 color #808080
> volume #1 transparency 0.75
> material ambientReflectivity 0
> material specularReflectivity 0
> lighting intensity 2.2
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> lighting intensity 2
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side2
> save NPC_overview/358_side2.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> color #19 #004c61
> color #20 #18b8db
> color #18 #004f7d
> color #17 #2d6291
> color #20 #188dd6
> color #13/A:170-2000 #FF004A
> color #19 #004c61
> color #20 #18b8db
> color #18 #004f7d
> color #17 #2d6291
> color #21 #188dd6
> color #21 #054266
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side2
> save NPC_overview/358_side2.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> color #19 #004c61
> color #20 #18aadb
> color #18 #004f7d
> color #17 #2d6291
> color #21 #054266
> graphics silhouettes true width 3
> view 358_side1
> save NPC_overview/358_side1.png supersample 3 transparentBackground true
> view 358_side2
> save NPC_overview/358_side2.png supersample 3 transparentBackground true
> view 358_top
> save NPC_overview/358_top.png supersample 3 transparentBackground true
> close #9-23
> save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview2.cxs
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
No such file/path:
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 272408
Duplicate atom serial number found: 272409
Duplicate atom serial number found: 272410
Duplicate atom serial number found: 272411
Duplicate atom serial number found: 272412
44904 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #9
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #11
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #12
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #13
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #14
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #15
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #16
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #21
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #23
---
Chain | Description
D | No description available
F | No description available
U | No description available
> hide #9-22
> ribbon #9-22
> color /A* #FF004A
> color /0* #0098EB
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #917db6
> color /B* #11a6f5
> color /C* #0259b0
> color /R* #159493
> color /T* #8df245
> color /K* #0098EB
> color /N* #8df245
> color /O* yellow
> color /Q* cyan
> color /D* #FFC459
> color /F* #b4e400
> color /I* #b4e400
> color /H* violet
> color /D* #fce88b
> color /F* #8df245
> color /4* #45f248
> color /K* purple
> color /E* #159493
> color /J* purple
> color /V* #adf245
> color /U* magenta
> color /W* #00b5a3
> view 358_side1
> view #13/C
> set bgColor white
> ~ribbon
> ribbon #13/C
> ~ribbon #13/C
> ~ribbon #14/C
> ribbon #14/C
> ribbon #14/A:94-155
> view #14/A:94-155/C
> ui tool show "Side View"
> view name 205_CRinner_side1
> save 205_side1.png supersample 3 transparentBackground true
> view name 205_CRinner_side2
> save 205_side2.png supersample 3 transparentBackground true
> view #13/V/W/J
> ~ribbon
> ribbon #13/V/W/J/U
> color /V* #adf245
> color /V* purple
> color /V* #b4e400
> color /J* violet
> color /J* purple
> color /U*magenta
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
> view 214_side1
Expected an objects specifier or a view name or a keyword
> view name 214_side1
> save 214_side1.png supersample 3 transparentBackground true
> set bgColor black
> ~ribbon
> ribbon #14/A:94-155/C
> view 205_side1
Expected an objects specifier or a view name or a keyword
> save 205_side1.png supersample 3 transparentBackground true
> view 205_side2
Expected an objects specifier or a view name or a keyword
> save 205_side2.png supersample 3 transparentBackground true
> view 205_side1
Expected an objects specifier or a view name or a keyword
> set bgColor black
> ~ribbon
> ribbon #14/A:94-155/C
> view 205_CRinner_side1
> save 205_side1.png supersample 3 transparentBackground true
> view 205_CRinner_side2
> save 205_side2.png supersample 3 transparentBackground true
> view 214_side1
> ~ribbon
> ribbon #13/V/W/J/U
> set bgColor black
> view 214_side1
> volume #1 level 3.314
> set bgColor white
> volume #1 level 2.8
> volume #1 level 3.2
> volume #1 level 1.5
> volume #1 level 1
> volume #1 level 0.5
> volume #1 level 0.1
> volume #1 level 0.01
> volume #1 level 2.8
> select /V:1-700
3183 atoms, 3257 bonds, 2 pseudobonds, 409 residues, 2 models selected
> select /V:1-650
3175 atoms, 3250 bonds, 408 residues, 1 model selected
> select /V:1-680
3175 atoms, 3250 bonds, 408 residues, 1 model selected
> select /V:1-690
3175 atoms, 3250 bonds, 408 residues, 1 model selected
> select /V:1-700
3183 atoms, 3257 bonds, 2 pseudobonds, 409 residues, 2 models selected
> select /V:1-699
3175 atoms, 3250 bonds, 408 residues, 1 model selected
> ~ribbon /V:1-700
> view 214_side1
> view name 214_side2
> ui mousemode right zoom
> view name 214_top1
> view name 214_side2
> ~ribbon /V:1-700
> set bgColor black
> view 214_side2
> save 214_side1.png supersample 3 transparentBackground true
> view 214_top1
> save 214_side1.png supersample 3 transparentBackground true
> ~ribbon
> ~ribbon
> ribbon #13/R/P/M
> view #13/R/P/M
> set bgColor white
> ribbon #13/N/O
> view name hub_side1
> ribbon #13/R/M/P/N/O
> view hub_side1
> set bgColor black
> save hub_side1.png supersample 3 transparentBackground true
> ligthing intensity 2
Unknown command: ligthing intensity 2
> lighting intensity 2
> lighting intensity 1.8
> save hub_side1.png supersample 3 transparentBackground true
> lighting intensity 1.5
> save hub_side1.png supersample 3 transparentBackground true
> lighting intensity 2
> save hub_side1.png supersample 3 transparentBackground true
> color /M #6a00d4
> color /M #6900d4
> color /M #6300d4
> set bgColor white
> color /M #7F00FF
> color /N #b4e400
> color /N #81c73c
> color /N #71ad36
> color /N #6fa638
> save hub_side1.png supersample 3 transparentBackground false
> ribbon #13/Q
> color /R #159493
> color /R #136e6d
> color /R #126b6a
> color /M #532bba
> color /Q cyan
> color /P #d46246
> color /P #ad4e36
> set bgColor black
> save hub_side1.png supersample 3 transparentBackground true
> ribbon #13/S
> ribbon #13/S/L/K
> set bgColor white
> color /K blue
> color /K purple
> show #!7 models
> hide #!7 models
> show #!6 models
> color /L #FF8853
> color /L #b5613c
> color /L #b57f3c
> view name Y_side1
> save Y_side1.png supersample 3 transparentBackground true
> view name Y_side1
> save Y_side1.png supersample 3 transparentBackground true
> view hub_side1
Drag select of 1 pore_whole_resample.mrc , 2 residues
> select clear
Drag select of 1 pore_whole_resample.mrc , 3 residues
> view hub_side1
> select clear
Drag select of 1 pore_whole_resample.mrc , 2 residues
> select clear
> save hub_side1.png supersample 3 transparentBackground true
> color /M #4f3299
> color /M #8f67f5
> color /M #533c8c
> color /M #533c8c
> color /R #126b6a
> color /N #6fa638
> color /P #ad4e36
> ribbon #13/R/M/P/N/O
> view hub_side1
> set bgColor black
> save hub_side1.png supersample 3 transparentBackground true
> save hub_side1_dark.png supersample 3 transparentBackground true
> volume #1 color #808080
> measure symmetry #1
Symmetry pore_whole_resample.mrc: C8, center 288 288 300
> sym #9-21 symmetry #1
> color #9-21 white
> volume #1 color #808080
> volume #1 transparency 0.8
> graphics silhouettes color white
> graphics silhouettes true width 3
> view hub_side1
> save hub_side1_back.png supersample 3 transparentBackground false
> save hub_side1_back.png supersample 3 transparentBackground true
> ribbon
> color #9-21 white
> view hib_side1
Expected an objects specifier or a view name or a keyword
> view hub_side1
> color #9-23 white
> view hub_side1
> sym #9-23 symmetry #1 copies true
> view hub_side1
> save hub_side1_back.png supersample 3 transparentBackground true
> volume #1 color white
> save hub_side1_back.png supersample 3 transparentBackground true
> volume #1 color white
> volume #1 transparency 0.8
> save hub_side1_back.png supersample 3 transparentBackground true
> graphics silhouettes true width 0
> save hub_side1_back.png supersample 3 transparentBackground true
> lighting intensity 1
> lighting intensity 5
> lighting intensity 4
> save hub_side1_back.png supersample 3 transparentBackground true
> lighting intensity 10
> save hub_side1_back.png supersample 3 transparentBackground true
> material ambientReflectivity 0.8
> lighting direction -1,-1,-1
> lighting direction 1,-1,-1
> hide #!1 models
> show #!1 models
> save hub_side1_back.png supersample 3 transparentBackground true
> lighting direction -1,-1,-1
> lighting direction -1,-1,1
> lighting direction 1,1,1
> lighting direction -1,-1,-1
> lighting intensity 1
> save hub_side1_back.png supersample 3 transparentBackground true
> hide #!1 models
> save hub_side1_back.png supersample 3 transparentBackground true
> transparency #9-23 0.7
> ribbon #9-23 trans 0.7
> cartoon #9-23 trans 0.7
Expected a keyword
> ribbon #9-23 trans 0.7
> cartoon #9-23 trans 0.7
Expected a keyword
> transparency #9-23 0.7
> save hub_side1_back.png supersample 3 transparentBackground true
> transparency #9-24 0.7
> view hub_side1
> transparency #9-23,r 0.7
Missing or invalid "percent" argument: Expected a number
> transparency #9-23 0.7 target r
> view hub_side1
> transparency #9-23 70 target r
> transparency #9-24 70 target r
> view hub_side1
> save hub_side1_back.png supersample 3 transparentBackground true
> set bgColor white
> save hub_side1_back.png supersample 3 transparentBackground true
> transparency #9-24 0 target r
> save hub_side1_back.png supersample 3 transparentBackground true
> save hub_side1_back.png supersample 3 transparentBackground true
> transparency #9-24 50 target r
> save hub_side1_back.png supersample 3 transparentBackground true
> transparency #9-24 40 target r
> save hub_side1_back.png supersample 3 transparentBackground true
> sym #22-23 symmetry #1
> hide #1
> measure symmetry
Missing or invalid "volumes" argument: empty atom specifier
> sym #9-23 symmetry #1
> color #9-24 white
> graphics silhouettes false
> transparency #9-24 50 target r
> set bgColor white
> view hub_side1
> save hub_side1_back.png supersample 3 transparentBackground true
> view 205_side1
Expected an objects specifier or a view name or a keyword
> save 205_side1_back.png supersample 3 transparentBackground true
> view 205_side2
Expected an objects specifier or a view name or a keyword
> save 205_side2_back.png supersample 3 transparentBackground true
> view 214_side2
> save 214_side2_back.png supersample 3 transparentBackground true
> view 214_top
Expected an objects specifier or a view name or a keyword
> save 214_top_back.png supersample 3 transparentBackground true
> view 358_top
> save 358_top_back.png supersample 3 transparentBackground true
> view 358_side1
> save 358_side1_back.png supersample 3 transparentBackground true
> view 358_side2
> save 358_side2_back.png supersample 3 transparentBackground true
> windowsize 1920 1080
> windowsize 1040 920
> windowsize 1440 810
> close #17#9-16,18-24#24.1-8
> windowsize 1440 810view 214_side1
Expected an integer >= 1 or a keyword
> view 214_side1
> view 205_side2
Expected an objects specifier or a view name or a keyword
> view 205_side1
Expected an objects specifier or a view name or a keyword
> view 205_CRinner_side1
> save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview3.cxs
opened ChimeraX session
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 272408
Duplicate atom serial number found: 272409
Duplicate atom serial number found: 272410
Duplicate atom serial number found: 272411
Duplicate atom serial number found: 272412
44904 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #9
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 616953
Duplicate atom serial number found: 616954
Duplicate atom serial number found: 616955
Duplicate atom serial number found: 616956
Duplicate atom serial number found: 616957
130 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 652149
Duplicate atom serial number found: 652150
Duplicate atom serial number found: 652151
Duplicate atom serial number found: 652152
Duplicate atom serial number found: 652153
130 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #11
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/IRnuc_outer.pdb
---
warnings | Duplicate atom serial number found: 687345
Duplicate atom serial number found: 687346
Duplicate atom serial number found: 687347
Duplicate atom serial number found: 687348
Duplicate atom serial number found: 687349
130 messages similar to the above omitted
Chain information for IRnuc_outer.pdb #12
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 848673
Duplicate atom serial number found: 848674
Duplicate atom serial number found: 848675
Duplicate atom serial number found: 848676
Duplicate atom serial number found: 848677
6155 messages similar to the above omitted
Chain information for Y.CRouter.pdb #13
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.CRinner.pdb
---
warnings | Duplicate atom serial number found: 811728
Duplicate atom serial number found: 811729
Duplicate atom serial number found: 811730
Duplicate atom serial number found: 811731
Duplicate atom serial number found: 811732
6155 messages similar to the above omitted
Chain information for Y.CRinner.pdb #14
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRinner.pdb
---
warnings | Duplicate atom serial number found: 885606
Duplicate atom serial number found: 885607
Duplicate atom serial number found: 885608
Duplicate atom serial number found: 885609
Duplicate atom serial number found: 885610
6155 messages similar to the above omitted
Chain information for Y.NRinner.pdb #15
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 922551
Duplicate atom serial number found: 922552
Duplicate atom serial number found: 922553
Duplicate atom serial number found: 922554
Duplicate atom serial number found: 922555
6155 messages similar to the above omitted
Chain information for Y.NRouter.pdb #16
---
Chain | Description
A | No description available
C | No description available
F | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
10570 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #21
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #22
---
Chain | Description
D | No description available
F | No description available
U | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7
THR A 20 1 14
Start residue of secondary structure not found: HELIX 2 2 LEU A 33 THR A 49 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN A 53 ARG A 67 1
15
Start residue of secondary structure not found: HELIX 4 4 ILE A 71 ALA A 83 1
13
Start residue of secondary structure not found: HELIX 5 5 ILE A 98 ALA A 150 1
53
9610 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #23
---
Chain | Description
D | No description available
F | No description available
U | No description available
> ribbon style #9-23 width 2.5 thickness 0.6
> volume #1 color #808080
> volume #1 transparency 0.75
> material ambientReflectivity 0
> material specularReflectivity 0
> lighting intensity 2.2
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> graphics silhouettes true color black
> hide atoms
> ~ribbon
> ribbon #13/A:170-2000#17-21
> color #19 #f79400
> color #20 #f0ae51
> color #18 #9e8562
> color #17 #fcda2b
> color #21 #573a10
> color #13/A:170-2000 #FF004A
> ribbon style #17-21#13/A width 2.5 thickness 0.6
> graphics silhouettes true width 3
> volume #1 level 1.5
> set bgColor black
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!19 models
> show #!19 models
> show #1
> color #18 #f79400
> color #20 #f0ae51
> color #19 #9e8562
> color #17 #fcda2b
> color #21 #573a10
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #18 #f79400
> color #20 #f0ae51
> color #19 #9e8562
> color #17 #fcda2b
> color #21 #573a10
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #18 #f7eb00
> color #20 #f0ae51
> color #19 #9e8562
> color #17 #fcda2b
> color #21 #573a10
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #18 #f7d600
> color #20 #f0ae51
> color #19 #9e8562
> color #17 #fcda2b
> color #21 #573a10
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #18 #f7bd00
> color #18 #f7a100
> color #18 #f7a100
> color #20 #f0ae51
> color #19 #9e8562
> color #17 #fada37
> color #21 #573a10
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #18 #f78c00
> save 358_top1.png supersample 3 transparentBackground true
> color /A* #FF004A
> color /0* #0098EB
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #917db6
> color /B* #0259b0
> color /C* #005887
> color /R* #159493
> color /T* #8df245
> color /K* #0098EB
> color /N* #8df245
> color /O* yellow
> color /Q* cyan
> color /D* #FFC459
> color /F* #b4e400
> color /I* #b4e400
> color /H* violet
> color /D* #fce88b
> color /F* #8df245
> color /4* #45f248
> color /K* purple
> color /E* #159493
> color /J* purple
> color /V* #adf245
> color /U* magenta
> color /W* #00b5a3
> volume #1 level 2.5
> ~ribbon
> ribbon #14/A:94-155/C
> view 205_CRinner_side1
> save 205_side1.png supersample 3 transparentBackground true
> view 205_CRinner_side2
> save 205_side2.png supersample 3 transparentBackground true
> volume #1 level 2.4
> ~ribbon
> ribbon #12/B
> ~ribbon /B:1515-1535
> view 188_NRouter_side1
Expected an objects specifier or a view name or a keyword
> save 188_NRouter_side1.png supersample 3 transparentBackground true
> ~ribbon
> ribbon #13/R/M/P/N/O/Q/S/L
> view hub_side1
> ui mousemode right zoom
> view name hub_side2
> color /M #533c8c
> color /R #126b6a
> color /N #6fa638
> color /P #ad4e36
> volume #1 level 2.5
> color /M #533c8c
> color /R #126b6a
> color /N #6fa638
> color /P #ad4e36
> ~ribbon
> ribbon #13/R/M/P/N/O/Q/S/L
> set bgColor black
> view hub_side1
> save hub_side1.png supersample 3 transparentBackground true
> view hub_side2
> save hub_side2.png supersample 3 transparentBackground true
> color /R #1b6970
> view hub_side1
> save hub_side1.png supersample 3 transparentBackground true
> view hub_side2
> save hub_side2.png supersample 3 transparentBackground true
> volume #1 level 2.5
> ~ribbon
> ribbon #14/A:94-155/C
> view 205_CRinner_side1
> color /C* #005887
> ~ribbon
> ribbon #14/A:94-155/C
> view 205_CRinner_side1
> save 205_side1.png supersample 3 transparentBackground true
> color /C* #0259b0
> color /C* #04496e
> color /M* #917db6
> color /B* #0259b0
> color /C* #004970
> color /R* #159493
> view 205_CRinner_side2
> view 205_CRinner_side1
> view 205_CRinner_side2
> view 205_CRinner_side1
> save 205_side1.png supersample 3 transparentBackground true
> view 205_CRinner_side2
> save 205_side2.png supersample 3 transparentBackground true
> volume #1 level 2.4
> ~ribbon
> ribbon #12/B
> ~ribbon /B:1515-1535
> view 188_NRouter_side1
Expected an objects specifier or a view name or a keyword
> save 188_NRouter_side1.png supersample 3 transparentBackground true
> view 188_NRouter_side1
Expected an objects specifier or a view name or a keyword
> view 188_NRouter_side
Expected an objects specifier or a view name or a keyword
> view list
Named views: 205_CRinner_side1, 205_CRinner_side2, 214_side1, 214_side2,
214_top1, 358_side1, 358_side2, 358_top, Y_side1, hub_side1, hub_side2,
ouside, side1, side3, side_cut, side_ouside, side_outside, tilt, top
> view #12/B
> ribbon #12/A:94-155/C
> ui tool show "Side View"
> volume #1 level 2.8
> volume #1 level 2
> volume #1 level 1.5
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #1 level 2
> volume #1 level 2.5
> set bgColor white
> volume zone #1 nearAtoms #12/B
> volume unzone #1
> volume zone #1 nearAtoms #12/B range 10
> volume unzone #1
> volume zone #1 nearAtoms #12/B range 20
> volume zone #1 nearAtoms #12/B range 30
> volume zone #1 nearAtoms #12/B range 40
> volume zone #1 nearAtoms #12/B range 15
> volume zone #1 nearAtoms #12/B range 20
> volume zone #1 nearAtoms #12/B range 40
> volume zone #1 nearAtoms #12/B range 50
> volume zone #1 nearAtoms #12/B range 20 newMap true
> volume zone #1 nearAtoms #12/B range 20 newMap true
> volume #25 transparency 0.7
> volume #25 transparency 70
> volume #25 transparency 0.7
> show #!1 models
> hide #!1 models
> hide #!1 models
> show #!1 models
> volume unzone #1
> hide #!1 models
> show #!1 models
> view name 188_IRnuc_outer_side1
> volume #1 level 2.4
> ~ribbon
> ribbon #12/B
> ~ribbon /B:1515-1535
> set bgColor black
> view 188_IRnuc_outer_side1
> save 188_IRnuc_outer_side1.png supersample 3 transparentBackground true
> volume #1 level 2.4
> ~ribbon
> ribbon #12/B/A:94-155/C
> ~ribbon /B:1515-1535
> set bgColor black
> view 188_IRnuc_outer_side1
> save 188_IRnuc_outer_side1.png supersample 3 transparentBackground true
> color /B #0270b0
> save 188_IRnuc_outer_side1.png supersample 3 transparentBackground true
> view name 188_IRnuc_outer_side1
> save 188_IRnuc_outer_side1.png supersample 3 transparentBackground true
> view name 188_IRnuc_outer_side1
> save 188_IRnuc_outer_side1.png supersample 3 transparentBackground true
> ~ribbon
> ribbon #13/A:170-2000#17-21
> color #13/A:170-2000 #FF004A
> ribbon style #17-21#13/A width 2.5 thickness 0.6
> graphics silhouettes true width 3
> volume #1 level 1.5
> set bgColor black
> color #18 #f77c00
> color #20 #f5fc68
> color #19 #d0fc68
> color #17 #fada37
> color #21 #f7ff57
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #19 #ff8957
> color #17 #bcfa37
> color #18 #e7fa3e
> color #20 #ffc182
> color #19 #ff8a66
> color #21 #f7ff57
> color #17 #bcfa37
> color #18 #e7fa3e
> color #20 #ffc182
> color #19 #ff8a66
> color #21 #fad000
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #17 #a9fa37
> color #20 #ff8a82
> save 358_top1.png supersample 3 transparentBackground true
> surface dust #1 size 100
> save 358_top1.png supersample 3 transparentBackground true
> hide #!20 models
> show #!20 models
> color #17 #a9fa37
> color #18 #e7fa3e
> color #20 #ffcf82
> color #19 #ff8a66
> color #21 #fad000
> view 358_top
> save 358_top1.png supersample 3 transparentBackground true
> color #20 #5c3400
> color #19 #5c3400
> color #20 #b86800
> color #20 #c9780e
> color #21 #ffff00
> color #18 #a3b500
> save 358_top1.png supersample 3 transparentBackground true
> color #18 #606b00
> save 358_top1.png supersample 3 transparentBackground true
> color #17 #a9fa37
> color #18 #e7fa3e
> color #19 #5c3400
> color #20 #c9780e
> color #21 #ffff00
> color #20 #c9780e
> color #20 #b86800
> color #18 #a3b500
> color #18 #606b00
> color #17 #a9fa37
> color #18 #606b00
> color #19 #5c3400
> color #20 #c9780e
> color #21 #ffff00
> save 358_top.png supersample 3 transparentBackground true
> hide #1
> measure symmetry #1
Symmetry pore_whole_resample.mrc: C8, center 288 288 294
> sym #9-23 symmetry #1 copies true
> graphics silhouettes false
> color #9-24 white
> ribbon #9-24
> ribbon style #9-24 width 2.5 thickness 0.6
> transparency #9-24 50 target r
> set bgColor white
> view hub_side1
> save hub_side1_back.png supersample 3 transparentBackground true
> view hub_side2
> save hub_side2_back.png supersample 3 transparentBackground true
> view 205_side1
Expected an objects specifier or a view name or a keyword
> save 205_side1_back.png supersample 3 transparentBackground true
> view 205_CRinner_side2
> save 205_side2_back.png supersample 3 transparentBackground true
> view 358_top
> save 358_top_back.png supersample 3 transparentBackground true
> view 188_IRnuc_outer_side1
> save 188_IRnuc_outer_side1_back.png supersample 3 transparentBackground true
> close #24-26#26.1-8
> hide #1
> measure symmetry #1
Symmetry pore_whole_resample.mrc: C8, center 288 288 294
> sym #9-23 symmetry #1 copies true
> graphics silhouettes false
> color #9-24 white
> ribbon #9-24
> ribbon style #9-24 width 2.5 thickness 0.6
> transparency #9-24 50 target r
> set bgColor white
> view hub_side1
> save hub_side1_back.png supersample 3 transparentBackground true
> view hub_side2
> save hub_side2_back.png supersample 3 transparentBackground true
> view 205_side1
Expected an objects specifier or a view name or a keyword
> save 205_side1_back.png supersample 3 transparentBackground true
> view 205_CRinner_side2
> save 205_side2_back.png supersample 3 transparentBackground true
> view 358_top
> save 358_top_back.png supersample 3 transparentBackground true
> view 188_IRnuc_outer_side1
> save 188_IRnuc_outer_side1_back.png supersample 3 transparentBackground true
> close #9-24#24.1-8
> save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview4.cxs
opened ChimeraX session
> close #5
> volume gaussian #6 sDev 15
> view tilt
> close #7
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/christian/Hek_wt_Membrane_m.mrc
Opened Hek_wt_Membrane_m.mrc, grid size 144,144,144, pixel 1, shown at level
0.132, step 1, values float32
> volume #7 voxelSize 13.8
> volume #5 level 0.009225
> hide #!7 models
> volume #5 level 0.008414
> view side_cut
> volume #5 level 0.008077
> volume #5 level 0.006118
> show #!7 models
> hide #!5 models
> volume #7 level 0.06322
> surface dust #7 size 100
> lighting intensity 1
> show #7
> volume #7 transparency 0
> volume #7 color #595b5e
> hide #!7 models
> show #!7 models
> material ambientReflectivity 0
> material specularReflectivity 0
> lighting intensity 2.2
> lighting fillDirection 1,-1,-1
> lighting direction 1,-1,-2
> volume #7 level 0.0269
> volume #7 level 0.0148
> save /Users/agnieszka/NPC/human/NPC_AF/figures/maps_and_models_overview5.cxs
opened ChimeraX session
> close #7
> close #5
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/membrane_masked_r200_resample_clean3.mrc
Opened membrane_masked_r200_resample_clean3.mrc, grid size 576,576,576, pixel
3.37, shown at level 0.011, step 4, values float32
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/christian/Hek_wt_Membrane_m_resample_noGp210_clean1.mrc
Opened Hek_wt_Membrane_m_resample_noGp210_clean1.mrc, grid size 576,576,576,
pixel 3.37, shown at level 0.127, step 4, values float32
> save /Users/agnieszka/NPC/human/NPC_AF/figures/NPC_overview_7.cxs
> hide #!7 models
> show #!7 models
> hide #!5 models
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRcyt_outer.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRcyt_outer.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
10231 messages similar to the above omitted
Chain information for IRcyt_outer.pdb #9
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRcyt_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRcyt_inner.pdb
---
warnings | Duplicate atom serial number found: 10365
Duplicate atom serial number found: 10366
Duplicate atom serial number found: 10367
Duplicate atom serial number found: 10368
Duplicate atom serial number found: 10369
2770 messages similar to the above omitted
Chain information for IRcyt_inner.pdb #10
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRnuc_inner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRnuc_inner.pdb
---
warnings | Duplicate atom serial number found: 22040
Duplicate atom serial number found: 22041
Duplicate atom serial number found: 22042
Duplicate atom serial number found: 22043
Duplicate atom serial number found: 22044
5869 messages similar to the above omitted
Chain information for IRnuc_inner.pdb #11
---
Chain | Description
A | No description available
C | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/IRnuc_outer.pdb
Chain information for IRnuc_outer.pdb #12
---
Chain | Description
4 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/Y.CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/Y.CRouter.pdb
---
warnings | Duplicate atom serial number found: 119573
Duplicate atom serial number found: 119574
Duplicate atom serial number found: 119575
Duplicate atom serial number found: 119576
Duplicate atom serial number found: 119577
18192 messages similar to the above omitted
Chain information for Y.CRouter.pdb #13
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
V | No description available
W | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/Y.CRinner.pdb
Chain information for Y.CRinner.pdb #14
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/Y.NRinner.pdb
Chain information for Y.NRinner.pdb #15
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/Y.NRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/Y.NRouter.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
11687 messages similar to the above omitted
Chain information for Y.NRouter.pdb #16
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_1_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_1_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN S 29
ASP S 31 1 3
Start residue of secondary structure not found: HELIX 2 2 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 4 4 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 5 5 THR R 273 ILE R 275
1 3
1238 messages similar to the above omitted
Chain information for hNup358_1_CRouter.pdb #17
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_2_CRouter.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_2_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN S 29
ASP S 31 1 3
Start residue of secondary structure not found: HELIX 2 2 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 4 4 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 5 5 THR R 273 ILE R 275
1 3
1238 messages similar to the above omitted
Chain information for hNup358_2_CRouter.pdb #18
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_1_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_1_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN S 29
ASP S 31 1 3
Start residue of secondary structure not found: HELIX 2 2 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 4 4 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 5 5 THR R 273 ILE R 275
1 3
1238 messages similar to the above omitted
Chain information for hNup358_1_CRinner.pdb #19
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_2_CRinner.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_2_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN S 29
ASP S 31 1 3
Start residue of secondary structure not found: HELIX 2 2 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 4 4 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 5 5 THR R 273 ILE R 275
1 3
1238 messages similar to the above omitted
Chain information for hNup358_2_CRinner.pdb #20
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_CRmiddle.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup358_CRmiddle.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN S 29
ASP S 31 1 3
Start residue of secondary structure not found: HELIX 2 2 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 4 4 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 5 5 THR R 273 ILE R 275
1 3
1238 messages similar to the above omitted
Chain information for hNup358_CRmiddle.pdb #21
---
Chain | Description
0 | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup155_CRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup155_CRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN S 29
ASP S 31 1 3
Start residue of secondary structure not found: HELIX 2 2 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 3 3 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 4 4 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 5 5 THR R 273 ILE R 275
1 3
1344 messages similar to the above omitted
Chain information for hNup155_CRconnector.pdb #22
---
Chain | Description
D | No description available
> open
> /g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup155_NRconnector.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/Hek_AF_complex/models_figures/hNup155_NRconnector.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO R 169
MET R 172 1 4
Start residue of secondary structure not found: HELIX 2 2 ILE R 190 LYS R 192
1 3
Start residue of secondary structure not found: HELIX 3 3 VAL R 262 LEU R 266
1 5
Start residue of secondary structure not found: HELIX 4 4 THR R 273 ILE R 275
1 3
Start residue of secondary structure not found: HELIX 5 5 PRO R 281 ASP R 283
1 3
1051 messages similar to the above omitted
Chain information for hNup155_NRconnector.pdb #23
---
Chain | Description
D | No description available
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_fit/Gp210/Gp210_0984_8mer_1.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_fit/Gp210/Gp210_0984_8mer_1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 12
ALA A 18 1 7
Start residue of secondary structure not found: HELIX 2 2 SER A 165 ALA A 167
1 3
Start residue of secondary structure not found: HELIX 3 3 SER A 191 LYS A 198
1 8
Start residue of secondary structure not found: HELIX 4 4 ALA A 225 TYR A 227
1 3
Start residue of secondary structure not found: HELIX 5 5 ILE A 327 MET A 329
1 3
1267 messages similar to the above omitted
Chain information for Gp210_0984_8mer_1.pdb
---
Chain | Description
24.1/1 24.2/1 24.3/1 24.4/1 24.5/1 24.6/1 24.7/1 24.8/1 | No description
available
> color /A* #FF004A
> color /0* #104a8e
> color /L* #FF8853
> color /P* #FF5851
> color /R* #45f248
> color /M* #533c8c
> color /B* #5F84A2
> color /C #1b3e5c
> color /R* #1b6970
> color /T* #8df245
> color /N* #8df245
> color /O* #104a8e
> color /Q* cyan
> color /D* #ff8c69
> color /F* #b4e400
> color /I #195d6b
> color /J #aeff00
> color /D* #FA8072
> color /F* #8df245
> color /4* #45f248
> color /K* purple
> color /E* #159493
> color /H #00C9CA
> color /W* #1d5a8f
> color /U* magenta
> color /V #00d948
> color /1 #002a45
> color /W* #1787e8
> color /D* #FA8072
> color /F* #b4e400
> color /S* magenta
> color /O* #FFE800
> color /U* magentapdb
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> ~ribbon
> show #9-24
> delete @H
> style #9-24 sphere
Changed 658589 atom styles
> size #9-24 atomRadius 3
Changed 658589 atom radii
> measure symmetry #8
Symmetry Hek_wt_fullm_resample_onConstricted.mrc: C8, center 285 288 293
> sym #9-24 symmetry #8
> hide /V:1-700
> volume #7 level 0.0253
> ui tool show "Side View"
> view name side_cut1
> material ambientReflectivity 1.2
> graphics silhouettes true width 1.5
> lighting ambientIntensity 2
> volume #7 color #8d9094
> lighting soft
> lighting ambientIntensity 2
> material ambientReflectivity 0.8
> lighting shadows false
> graphics silhouettes true color black
> graphics silhouettes true width 3
> material ambientReflectivity 1.2
> graphics silhouettes true width 1.5
> lighting ambientIntensity 2
> volume #7 color #8d9094
> view tilt
> save NPC_dilated_ambient_tilt_map4.png supersample 3 transparentBackground
> true
> view side_cut1
> save NPC_dilate_ambient_cut_map4.png supersample 3 transparentBackground
> true
> graphics quality atomTriangles default colorDepth 16
> view tilt
> save NPC_dilated_ambient_tilt_map4.png supersample 3 transparentBackground
> true
> view side_cut1
> save NPC_dilate_ambient_cut_map4.png supersample 3 transparentBackground
> true
> view tilt
> save NPC_dilated_ambient_tilt_Gp210_map4.png supersample 3
> transparentBackground true
> view side_cut1
> save NPC_dilate_ambient_cut_Gp210_map4.png supersample 3
> transparentBackground true
> save NPC_dilate_ambient_cut_Gp210_map4.png supersample 3
> transparentBackground false
> save NPC_dilated_ambient_cut_Gp210_map4.png supersample 3
> transparentBackground true
> volume #5 level 0.015
> hide #!7 models
> show #!7 models
> volume #5 level 0.025
> volume #5 level 0.5
> volume #7 level 0.03
> volume #8 level 0.2
> view side_cut1
> save NPC_dilated_ambient_cut_Gp210_map4.png supersample 3
> transparentBackground true
> volume #6 level -0.03578
> volume #7 level 0.05443
> hide #!5 models
> hide #!6 models
> volume #7 level 0.06
> volume #7 level 0.05
> hide #!7 models
> show #!7 models
> save NPC_dilated_ambient_cut_Gp210_map4.png supersample 3
> transparentBackground true
> close #17-21#9-16,22-24#24.1-8
> save /Users/agnieszka/NPC/human/NPC_AF/figures/NPC_overview_8.cxs
opened ChimeraX session
> hide #7
> show #5
> close #5
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/membrane_masked_r200_resample_clean3.mrc
Opened membrane_masked_r200_resample_clean3.mrc, grid size 576,576,576, pixel
3.37, shown at level 0.011, step 4, values float32
> close #6
> open
> /Users/agnieszka/NPC/human/NPC2.0/maps04/npc_rings/membrane_masked_r200_resample_clean3.mrc
Opened membrane_masked_r200_resample_clean3.mrc, grid size 576,576,576, pixel
3.37, shown at level 0.011, step 4, values float32
> close #5
> volume gaussian #6 sDev 5
> hide #!5 models
> show #!5 models
> volume #5 level 0.005
> show #5
> volume #5 color #8d9094
> save /Users/agnieszka/NPC/human/NPC_AF/figures/NPC_overview_9.cxs
opened ChimeraX session
> open
> /g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/*1.pdb
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_1_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_2_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_3_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_4_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_5_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_6_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_7_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/Gp210_8_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup155_CRconnector_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup155_NRconnector_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup358_1_CRinner_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup358_1_CRouter_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup358_2_CRinner_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup358_2_CRouter_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup358_CRmiddle_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup98_CRconnector_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup98_IRcyt_inner_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup98_IRcyt_outer_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup98_IRnuc_inner_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup98_IRnuc_outer_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Summary of feedback from opening
/g/kosinski/agnieszka/NPC_human/const_AF_complex/PDBs_final/spokes/hNup98_NRconnector_1.pdb
---
warning | Ignored bad PDB record found on line 42
REMARK THIS IS A SIMULATION BOX
Gp210_1_1.pdb title:
Gromacs Runs On Most of All Computer Systems [more info...]
Chain information for Gp210_1_1.pdb #9
---
Chain | Description
1 | No description available
Gp210_2_1.pdb title:
Great Red Oystrich Makes All Chemists Sane [more info...]
Chain information for Gp210_2_1.pdb #10
---
Chain | Description
1 | No description available
Gp210_3_1.pdb title:
Gromacs Runs One Microsecond At Cannonball Speeds [more info...]
Chain information for Gp210_3_1.pdb #11
---
Chain | Description
1 | No description available
Gp210_4_1.pdb title:
S C A M O R G [more info...]
Chain information for Gp210_4_1.pdb #12
---
Chain | Description
1 | No description available
Gp210_5_1.pdb title:
GROwing Monsters And Cloning Shrimps [more info...]
Chain information for Gp210_5_1.pdb #13
---
Chain | Description
1 | No description available
Gp210_6_1.pdb title:
God Rules Over Mankind, Animals, Cosmos and Such [more info...]
Chain information for Gp210_6_1.pdb #14
---
Chain | Description
1 | No description available
Gp210_7_1.pdb title:
Great Red Owns Many ACres of Sand [more info...]
Chain information for Gp210_7_1.pdb #15
---
Chain | Description
1 | No description available
Gp210_8_1.pdb title:
GRowing Old MAkes el Chrono Sweat [more info...]
Chain information for Gp210_8_1.pdb #16
---
Chain | Description
1 | No description available
Chain information for IR_cyt_inner_1.pdb #17
---
Chain | Description
4 | No description available
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
Chain information for IR_cyt_outer_1.pdb #18
---
Chain | Description
A | No description available
B | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
Chain information for IR_nuc_inner_1.pdb #19
---
Chain | Description
4 | No description available
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
Chain information for IR_nuc_outer_1.pdb #20
---
Chain | Description
A | No description available
B | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
Chain information for Y_CRinner_1.pdb #21
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
Chain information for Y_CRouter_1.pdb #22
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
Chain information for Y_NRinner_1.pdb #23
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
Chain information for Y_NRouter_1.pdb #24
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
hNup155_CRconnector_1.pdb title:
GROningen MAchine for Chemical Simulation [more info...]
Chain information for hNup155_CRconnector_1.pdb #25
---
Chain | Description
D | No description available
hNup155_NRconnector_1.pdb title:
GROwing Monsters And Cloning Shrimps [more info...]
Chain information for hNup155_NRconnector_1.pdb #26
---
Chain | Description
D | No description available
hNup358_1_CRinner_1.pdb title:
GROwing Monsters And Cloning Shrimps [more info...]
Chain information for hNup358_1_CRinner_1.pdb #27
---
Chain | Description
0 | No description available
hNup358_1_CRouter_1.pdb title:
GROwing Monsters And Cloning Shrimps [more info...]
Chain information for hNup358_1_CRouter_1.pdb #28
---
Chain | Description
0 | No description available
hNup358_2_CRinner_1.pdb title:
Gyas ROwers Mature At Cryogenic Speed [more info...]
Chain information for hNup358_2_CRinner_1.pdb #29
---
Chain | Description
0 | No description available
hNup358_2_CRouter_1.pdb title:
Gromacs Runs One Microsecond At Cannonball Speeds [more info...]
Chain information for hNup358_2_CRouter_1.pdb #30
---
Chain | Description
0 | No description available
hNup358_CRmiddle_1.pdb title:
GRowing Old MAkes el Chrono Sweat [more info...]
Chain information for hNup358_CRmiddle_1.pdb #31
---
Chain | Description
0 | No description available
hNup98_CRconnector_1.pdb title:
Gyas ROwers Mature At Cryogenic Speed [more info...]
Chain information for hNup98_CRconnector_1.pdb #32
---
Chain | Description
U | No description available
hNup98_IRcyt_inner_1.pdb title:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon [more info...]
Chain information for hNup98_IRcyt_inner_1.pdb #33
---
Chain | Description
U | No description available
hNup98_IRcyt_outer_1.pdb title:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon [more info...]
Chain information for hNup98_IRcyt_outer_1.pdb #34
---
Chain | Description
U | No description available
hNup98_IRnuc_inner_1.pdb title:
GRowing Old MAkes el Chrono Sweat [more info...]
Chain information for hNup98_IRnuc_inner_1.pdb #35
---
Chain | Description
U | No description available
hNup98_IRnuc_outer_1.pdb title:
GRowing Old MAkes el Chrono Sweat [more info...]
Chain information for hNup98_IRnuc_outer_1.pdb #36
---
Chain | Description
U | No description available
hNup98_NRconnector_1.pdb title:
Giant Rising Ordinary Mutants for A Clerical Setup [more info...]
Chain information for hNup98_NRconnector_1.pdb #37
---
Chain | Description
U | No description available
> delete #9-16
> view
> ui tool show "Side View"
> show #1
> volume #1 level 5.61
> volume #1 level 2.5
> ui mousemode right zoom
> view name spoke1_zoom
> delete #17-37
> save
> /Users/agnieszka/NPC/human/NPC_AF/figures.bk/NPC_overview_9_flowchart.cxs
opened ChimeraX session
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H15)
Kernel Version: Darwin 19.6.0
Time since boot: 128 days 12:25
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.01.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
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