![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#6855 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4rc202205111743 (2022-05-11 17:43:38 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001093d6dc0 (most recent call first):
File "/private/var/folders/q2/np9_t13j7kx8thf4hlvz4v_cw_ps5b/T/AppTranslocation/547E7D52-6E38-4D67-B0D3-758866724250/d/ChimeraX-1.4-rc2022.05.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/private/var/folders/q2/np9_t13j7kx8thf4hlvz4v_cw_ps5b/T/AppTranslocation/547E7D52-6E38-4D67-B0D3-758866724250/d/ChimeraX-1.4-rc2022.05.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/private/var/folders/q2/np9_t13j7kx8thf4hlvz4v_cw_ps5b/T/AppTranslocation/547E7D52-6E38-4D67-B0D3-758866724250/d/ChimeraX-1.4-rc2022.05.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/private/var/folders/q2/np9_t13j7kx8thf4hlvz4v_cw_ps5b/T/AppTranslocation/547E7D52-6E38-4D67-B0D3-758866724250/d/ChimeraX-1.4-rc2022.05.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/q2/np9_t13j7kx8thf4hlvz4v_cw_ps5b/T/AppTranslocation/547E7D52-6E38-4D67-B0D3-758866724250/d/ChimeraX-1.4-rc2022.05.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [11002]
Path: /private/var/folders/*/ChimeraX-1.4-rc2022.05.11.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.4.0 (1.4.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [11002]
User ID: 950756523
Date/Time: 2022-05-13 16:36:37.498 -0400
OS Version: Mac OS X 10.15.7 (19H1715)
Report Version: 12
Bridge OS Version: 6.2 (19P744)
Anonymous UUID: C781CD8B-2CBB-B3BB-02BC-F06C86629184
Sleep/Wake UUID: 922C2619-CB63-4C90-8212-5B21862FA86F
Time Awake Since Boot: 1200000 seconds
Time Since Wake: 27000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain
Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_MEMORY_ERROR at 0x0000000128f52690
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x128f52690:
shared memory 0000000128f30000-0000000128f38000 [ 32K] r--/r-- SM=SHM
--> mapped file 0000000128f38000-0000000128fd8000 [ 640K] r-x/rwx SM=COW Object_id=39fa9909
mapped file 0000000128fd8000-0000000128fe8000 [ 64K] rw-/rwx SM=COW Object_id=cecbc309
Thread 0 Crashed:: CrBrowserMain
0 ??? 0x00007fff6c76e33a 0 + 140735013118778
1 ??? 0x00007fff6c68593e 0 + 140735012165950
2 ??? 0x00007fff6c81f5fd 0 + 140735013844477
3 ChimeraX 000000000000000000 0 + 0
4 ??? 0x00007fff32888b97 0 + 140734041197463
5 ??? 0x00007fff3288842d 0 + 140734041195565
6 ??? 0x00007fff3288776e 0 + 140734041192302
7 ??? 0x00007fff314b3aad 0 + 140734020401837
8 ??? 0x00007fff314b37c5 0 + 140734020401093
9 ??? 0x00007fff314b3569 0 + 140734020400489
10 ??? 0x00007fff2fafc659 0 + 140733993436761
11 ??? 0x00007fff2fafaea0 0 + 140733993430688
12 ??? 0x00007fff2faecbae 0 + 140733993372590
13 ??? 0x0000000128f5148c 0 + 4982117516
14 ??? 0x0000000119b05516 0 + 4725953814
15 ??? 0x0000000119afc3e5 0 + 4725916645
16 ??? 0x000000011be2990a 0 + 4762802442
17 ??? 0x000000010829771d 0 + 4431902493
18 ??? 0x00000001082585b7 0 + 4431644087
19 ??? 0x0000000108330e9c 0 + 4432531100
20 ??? 0x000000010832e2a2 0 + 4432519842
21 ??? 0x0000000108258d28 0 + 4431645992
22 ??? 0x000000010825ad6a 0 + 4431654250
23 ??? 0x0000000108330e0c 0 + 4432530956
24 ??? 0x000000010832e2a2 0 + 4432519842
25 ??? 0x0000000108331b03 0 + 4432534275
26 ??? 0x0000000108258cb1 0 + 4431645873
27 ??? 0x0000000108330e0c 0 + 4432530956
28 ??? 0x000000010832e34b 0 + 4432520011
29 ??? 0x0000000108331b03 0 + 4432534275
30 ??? 0x0000000108327dab 0 + 4432493995
31 ??? 0x0000000108324c12 0 + 4432481298
32 ??? 0x0000000108297023 0 + 4431900707
33 ??? 0x0000000108330e0c 0 + 4432530956
34 ??? 0x000000010832e34b 0 + 4432520011
35 ??? 0x0000000108331b03 0 + 4432534275
36 ??? 0x0000000108258cb1 0 + 4431645873
37 ??? 0x0000000108330e0c 0 + 4432530956
38 ??? 0x000000010832e34b 0 + 4432520011
39 ??? 0x0000000108331b03 0 + 4432534275
40 ??? 0x0000000108258cb1 0 + 4431645873
41 ??? 0x0000000108397870 0 + 4432951408
42 ??? 0x0000000108396f87 0 + 4432949127
43 ??? 0x000000010839758f 0 + 4432950671
44 ??? 0x000000010839749b 0 + 4432950427
45 ??? 0x000000010820ddc8 0 + 4431338952
46 ??? 0x00007fff6c626cc9 0 + 140735011777737
Thread 1:
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x000000010974249f 0 + 4453573791
2 ??? 0x00007fff6c82b109 0 + 140735013892361
3 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 2:
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x000000010974249f 0 + 4453573791
2 ??? 0x00007fff6c82b109 0 + 140735013892361
3 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 3:
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x000000010974249f 0 + 4453573791
2 ??? 0x00007fff6c82b109 0 + 140735013892361
3 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 4:
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x000000010974249f 0 + 4453573791
2 ??? 0x00007fff6c82b109 0 + 140735013892361
3 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 5:
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x000000010974249f 0 + 4453573791
2 ??? 0x00007fff6c82b109 0 + 140735013892361
3 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 6:: ThreadPoolServiceThread
0 ??? 0x00007fff6c770b96 0 + 140735013129110
1 ??? 0x00000001213ec4c7 0 + 4852729031
2 ??? 0x000000012136919c 0 + 4852191644
3 ??? 0x0000000121320ff8 0 + 4851896312
4 ??? 0x000000012138b458 0 + 4852331608
5 ??? 0x000000012137284d 0 + 4852230221
6 ??? 0x000000012138b5ea 0 + 4852332010
7 ??? 0x00000001213b34a8 0 + 4852495528
8 ??? 0x00007fff6c82b109 0 + 140735013892361
9 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 7:: ThreadPoolBackgroundWorker
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x000000012137ed5f 0 + 4852280671
4 ??? 0x000000012137f80c 0 + 4852283404
5 ??? 0x000000012137f37d 0 + 4852282237
6 ??? 0x00000001213b34a8 0 + 4852495528
7 ??? 0x00007fff6c82b109 0 + 140735013892361
8 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 8:: Chrome_IOThread
0 ??? 0x00007fff6c770b96 0 + 140735013129110
1 ??? 0x00000001213ec4c7 0 + 4852729031
2 ??? 0x000000012136919c 0 + 4852191644
3 ??? 0x0000000121320ff8 0 + 4851896312
4 ??? 0x000000012138b458 0 + 4852331608
5 ??? 0x00000001202b1e32 0 + 4834663986
6 ??? 0x000000012138b5ea 0 + 4852332010
7 ??? 0x00000001213b34a8 0 + 4852495528
8 ??? 0x00007fff6c82b109 0 + 140735013892361
9 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 9:: NetworkConfigWatcher
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 10:: CompositorTileWorker1
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x00000001213b28bb 0 + 4852492475
2 ??? 0x000000012348355d 0 + 4886902109
3 ??? 0x00000001213b34a8 0 + 4852495528
4 ??? 0x00007fff6c82b109 0 + 140735013892361
5 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 11:: Chrome_InProcGpuThread
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 12:: Chrome_ChildIOThread
0 ??? 0x00007fff6c770b96 0 + 140735013129110
1 ??? 0x00000001213ec4c7 0 + 4852729031
2 ??? 0x000000012136919c 0 + 4852191644
3 ??? 0x0000000121320ff8 0 + 4851896312
4 ??? 0x000000012138b458 0 + 4852331608
5 ??? 0x000000012138b5ea 0 + 4852332010
6 ??? 0x00000001213b34a8 0 + 4852495528
7 ??? 0x00007fff6c82b109 0 + 140735013892361
8 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 13:: NetworkConfigWatcher
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 14:: VizCompositorThread
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 15:: NetworkService
0 ??? 0x00007fff6c770b96 0 + 140735013129110
1 ??? 0x00000001213ec4c7 0 + 4852729031
2 ??? 0x000000012136919c 0 + 4852191644
3 ??? 0x0000000121320ff8 0 + 4851896312
4 ??? 0x000000012138b458 0 + 4852331608
5 ??? 0x000000012138b5ea 0 + 4852332010
6 ??? 0x00000001213b34a8 0 + 4852495528
7 ??? 0x00007fff6c82b109 0 + 140735013892361
8 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 16:: NetworkConfigWatcher
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 17:: ThreadPoolSingleThreadForegroundBlocking0
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x000000012137ed5f 0 + 4852280671
4 ??? 0x000000012137f80c 0 + 4852283404
5 ??? 0x000000012137f46d 0 + 4852282477
6 ??? 0x00000001213b34a8 0 + 4852495528
7 ??? 0x00007fff6c82b109 0 + 140735013892361
8 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 18:: NetworkConfigWatcher
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 19:: com.apple.NSEventThread
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00007fff32889825 0 + 140734041200677
3 ??? 0x00007fff328882f2 0 + 140734041195250
4 ??? 0x00007fff3288776e 0 + 140734041192302
5 ??? 0x00007fff2fc9dea4 0 + 140733995146916
6 ??? 0x00007fff6c82b109 0 + 140735013892361
7 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 20:: MemoryInfra
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x00000001213ba78f 0 + 4852524943
4 ??? 0x00000001212f0089 0 + 4851695753
5 ??? 0x000000012136919c 0 + 4852191644
6 ??? 0x0000000121320ff8 0 + 4851896312
7 ??? 0x000000012138b458 0 + 4852331608
8 ??? 0x000000012138b5ea 0 + 4852332010
9 ??? 0x00000001213b34a8 0 + 4852495528
10 ??? 0x00007fff6c82b109 0 + 140735013892361
11 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 21:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x000000012137ed5f 0 + 4852280671
4 ??? 0x000000012137f53a 0 + 4852282682
5 ??? 0x000000012137f3ad 0 + 4852282285
6 ??? 0x00000001213b34a8 0 + 4852495528
7 ??? 0x00007fff6c82b109 0 + 140735013892361
8 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 22:: QFileInfoGatherer
0 ??? 0x00007fff6c76a882 0 + 140735013103746
1 ??? 0x0000000119c931ab 0 + 4727583147
2 ??? 0x0000000119c9311e 0 + 4727583006
3 ??? 0x000000011cc7ed7d 0 + 4777831805
4 ??? 0x0000000119c88b43 0 + 4727540547
5 ??? 0x00007fff6c82b109 0 + 140735013892361
6 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 23:: ThreadPoolForegroundWorker
0 ??? 0x00007fff6c767dfa 0 + 140735013092858
1 ??? 0x00007fff6c768170 0 + 140735013093744
2 ??? 0x00000001213ba9c6 0 + 4852525510
3 ??? 0x000000012137ed5f 0 + 4852280671
4 ??? 0x000000012137f80c 0 + 4852283404
5 ??? 0x000000012137f40d 0 + 4852282381
6 ??? 0x00000001213b34a8 0 + 4852495528
7 ??? 0x00007fff6c82b109 0 + 140735013892361
8 ??? 0x00007fff6c826b8b 0 + 140735013874571
Thread 24:
0 ??? 0x00007fff6c826b68 0 + 140735013874536
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000001093d6dc0 rcx: 0x00007fd2ef455a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000a rbp: 0x00007fd2ef455a80 rsp: 0x00007fd2ef455a58
r8: 0x00007fd2ef455f48 r9: 0x659f163393486cb1 r10: 0x00000001093d6dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000000000040 r14: 0x000000000000000a r15: 0x0000000000000016
rip: 0x00007fff6c76e33a rfl: 0x0000000000000246 cr2: 0x00000001093a9188
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
0 - 0xffffffffffffffff +ChimeraX (???) /private/var/folders/*/ChimeraX-1.4-rc2022.05.11.app/Contents/MacOS/ChimeraX
0x10930b000 - 0x10939d267 dyld (750.7) /usr/lib/dyld
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 62
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: 3848838
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=812K resident=0K(0%) swapped_out_or_unallocated=812K(100%)
Writable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 640K 5
Activity Tracing 256K 1
CG backing stores 2552K 4
CG image 1244K 26
CoreAnimation 1716K 64
CoreGraphics 8K 1
CoreImage 24K 2
CoreUI image data 3612K 32
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 565.9M 709
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Mach message 16K 2
OpenGL GLSL 384K 4
STACK GUARD 96K 24
Stack 140.2M 25
Stack Guard 56.0M 1
VM_ALLOCATE 171.2M 167
VM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)
__DATA 216K 2
__DATA_CONST 20K 1
__LINKEDIT 224K 1
__TEXT 588K 1
dylib 3676K 18
dylib (reserved) 256K 36 reserved VM address space (unallocated)
mapped file 434.8M 475
shared memory 4308K 40
=========== ======= =======
TOTAL 1.8G 1653
TOTAL, minus reserved VM space 1.4G 1653
===== Log before crash start =====
UCSF ChimeraX version: 1.4rc202205111743 (2022-05-11)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/skeparniasi3/Downloads/drive-
> download-20220513T155017Z-001/cryosparc_P10_J29_001_volume_map_sharp.mrc
Opened cryosparc_P10_J29_001_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.93, shown at level 0.0436, step 2, values float32
> open /Users/skeparniasi3/Downloads/drive-
> download-20220513T155017Z-001/3dhs.pdb
3dhs.pdb title:
Mapping metal-binding sites In the catalytic domain of bacterial RNAse P RNA
[more info...]
Chain information for 3dhs.pdb #2
---
Chain | Description
A | RNAse P RNA
Non-standard residues in 3dhs.pdb #2
---
OS — osmium ion
> select add #2
4628 atoms, 5167 bonds, 3 pseudobonds, 230 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,103.65,0,1,0,45.386,0,0,1,0
> view matrix models #2,1,0,0,79.402,0,1,0,38.248,0,0,1,14.122
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.44765,-0.66244,-0.60065,209.03,0.65253,-0.70127,0.2871,173.31,-0.61141,-0.26342,0.74618,67.286
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.44765,-0.66244,-0.60065,244.02,0.65253,-0.70127,0.2871,170.11,-0.61141,-0.26342,0.74618,81.96
> fitmap #2 inMap #1
Fit molecule 3dhs.pdb (#2) to map cryosparc_P10_J29_001_volume_map_sharp.mrc
(#1) using 4628 atoms
average map value = 0.2116, steps = 428
shifted from previous position = 87.3
rotated from previous position = 38.2 degrees
atoms outside contour = 1102, contour level = 0.043616
Position of 3dhs.pdb (#2) relative to
cryosparc_P10_J29_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.50545901 -0.86096540 -0.05700679 241.42068629
0.63867195 -0.41774149 0.64621218 140.51175970
-0.58018043 0.29022513 0.76102565 113.78747412
Axis -0.21870795 0.32142246 0.92133297
Axis point 103.69219871 123.78495282 -0.00000000
Rotation angle (degrees) 125.52706285
Shift along axis 97.19916387
> transparency 50
> volume #1 level 0.0558
> fitmap #2 inMap #1
Fit molecule 3dhs.pdb (#2) to map cryosparc_P10_J29_001_volume_map_sharp.mrc
(#1) using 4628 atoms
average map value = 0.2116, steps = 44
shifted from previous position = 0.0102
rotated from previous position = 0.02 degrees
atoms outside contour = 1210, contour level = 0.055802
Position of 3dhs.pdb (#2) relative to
cryosparc_P10_J29_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.50550357 -0.86092791 -0.05717749 241.43165576
0.63842032 -0.41778765 0.64643094 140.51782093
-0.58041849 0.29026988 0.76082703 113.80061695
Axis -0.21884264 0.32150466 0.92127230
Axis point 103.71219223 123.77383906 0.00000000
Rotation angle (degrees) 125.53724869
Shift along axis 97.18294976
> view orient
> volume #1 level 0.03752
> color (#!2 & sel) blue
> color (#!2 & sel) byhetero
> color (#!2 & sel) medium blue
> select subtract #2
Nothing selected
> set bgColor white
> save /Users/skeparniasi3/Desktop/M1_RNA_J29.tif width 792 height 645
> supersample 3
> open /Users/skeparniasi3/Downloads/drive-
> download-20220513T164226Z-001/cryosparc_P10_J28_class_00_00062_volume_sharp.mrc
Opened cryosparc_P10_J28_class_00_00062_volume_sharp.mrc as #3, grid size
128,128,128, pixel 2.18, shown at level 0.177, step 1, values float32
> open /Users/skeparniasi3/Downloads/drive-
> download-20220513T164226Z-001/cryosparc_P10_J28_class_01_00062_volume_sharp.mrc
Opened cryosparc_P10_J28_class_01_00062_volume_sharp.mrc as #4, grid size
128,128,128, pixel 2.18, shown at level 0.447, step 1, values float32
> open /Users/skeparniasi3/Downloads/drive-
> download-20220513T164226Z-001/cryosparc_P10_J28_class_02_00062_volume_sharp.mrc
Opened cryosparc_P10_J28_class_02_00062_volume_sharp.mrc as #5, grid size
128,128,128, pixel 2.18, shown at level 0.299, step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #2.1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!3 models
> volume #1 level 0.05948
> volume #3 level 0.2299
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!3 models
> hide #!4 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4rc202205111743 (2022-05-11)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1715)
Kernel Version: Darwin 19.6.0
Time since boot: 37 days 22:39
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: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
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
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4rc202205111743
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.2.0
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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