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#7282 feedback defect

Crash in event loop

Reported by:	richard_walsh@…	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:        Linux-3.10.0-1160.66.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f5b5cb8d700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1284 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f5ebbbe1740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /nfs/userdocs/sch/walsh/Documents/preholo/RealSpaceRefine_102/beta2-propetide-
> figurepanels-final.cxs format session

Opened preholo_3A_J319_C2_sharp.mrc as #2, grid size 360,360,360, pixel 1.06,
shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #6.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #6.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #6.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #6.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #6.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #6.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #6.8, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #4.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #4.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #4.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #4.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #4.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #4.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #4.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #4.8, grid size 360,360,360, pixel
1.06, shown at level 0.4, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #5.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #5.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #5.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #5.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #5.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #5.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #5.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #5.8, grid size 360,360,360, pixel
1.06, shown at level 0.4, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #9.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #9.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #9.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #9.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #9.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #9.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #9.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #9.8, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
opened ChimeraX session  

> hide #!9.8 models

> hide #!9.4 models

> hide #!9.2 models

> hide #!9 models

> hide #!8 models

> show #!8 models

> select add #8/H:58

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select up

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select up

54 atoms, 51 bonds, 7 residues, 1 model selected  

> select up

2716 atoms, 2764 bonds, 351 residues, 1 model selected  

> select up

55160 atoms, 56176 bonds, 7050 residues, 1 model selected  

> show sel cartoons

> select #8/I:13

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #8/I:92

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #8/N:70

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

177 atoms, 180 bonds, 22 residues, 1 model selected  

> select up

1550 atoms, 1579 bonds, 202 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel papaya whip

> select #8/N:14

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #8/I:116

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add #8/H:60

26 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #8/N:72

35 atoms, 33 bonds, 4 residues, 1 model selected  

> select add #8/H:56

42 atoms, 39 bonds, 5 residues, 1 model selected  

> select up

550 atoms, 556 bonds, 66 residues, 1 model selected  

> select up

4266 atoms, 4343 bonds, 553 residues, 1 model selected  

> select ~sel

163026 atoms, 165514 bonds, 127 pseudobonds, 17198 residues, 74 models
selected  

> hide sel & #!8 cartoons

> select #8/I:136

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #8/I:40

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select add #8/N:14

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #8/N:15

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #8/N:16

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select add #8/N:17

26 atoms, 22 bonds, 4 residues, 1 model selected  

> select add #8/N:18

34 atoms, 29 bonds, 5 residues, 1 model selected  

> select add #8/N:19

38 atoms, 32 bonds, 6 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium violet red

> select clear

> select #8/H:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #8/H:67

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select up

202 atoms, 204 bonds, 22 residues, 1 model selected  

> select up

977 atoms, 993 bonds, 122 residues, 1 model selected  

> select up

55160 atoms, 56176 bonds, 7050 residues, 1 model selected  

> select down

977 atoms, 993 bonds, 122 residues, 1 model selected  

> hide sel cartoons

> select #8/I:12

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

81 atoms, 82 bonds, 9 residues, 1 model selected  

> select up

1739 atoms, 1771 bonds, 229 residues, 1 model selected  

> select down

81 atoms, 82 bonds, 9 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #8/I:18

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> select add #8/I:2

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #8/I:3

17 atoms, 14 bonds, 3 residues, 1 model selected  

> select add #8/I:4

25 atoms, 21 bonds, 4 residues, 1 model selected  

> select add #8/I:5

31 atoms, 26 bonds, 5 residues, 1 model selected  

> select add #8/I:7

39 atoms, 33 bonds, 6 residues, 1 model selected  

> select add #8/I:6

50 atoms, 44 bonds, 7 residues, 1 model selected  

> select add #8/I:8

58 atoms, 51 bonds, 8 residues, 1 model selected  

> hide sel cartoons

> select add #8/I:30@CB

59 atoms, 51 bonds, 9 residues, 1 model selected  

> select up

65 atoms, 63 bonds, 9 residues, 1 model selected  

> hide sel atoms

> ui tool show "Color Actions"

> select add #8/I:249

74 atoms, 71 bonds, 10 residues, 1 model selected  

> select add #8/I:247

81 atoms, 77 bonds, 11 residues, 1 model selected  

> select add #8/I:248

89 atoms, 84 bonds, 12 residues, 1 model selected  

> select add #8/I:246

97 atoms, 91 bonds, 13 residues, 1 model selected  

> select add #8/I:244

106 atoms, 99 bonds, 14 residues, 1 model selected  

> select add #8/I:242

114 atoms, 106 bonds, 15 residues, 1 model selected  

> select add #8/I:243

123 atoms, 114 bonds, 16 residues, 1 model selected  

> hide sel cartoons

> select #8/I:245

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select subtract #8/I:245

Nothing selected  

> select add #8/I:245

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select add #8/I:232

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select add #8/I:233

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #8/I:231

33 atoms, 30 bonds, 4 residues, 1 model selected  

> select add #8/I:234

44 atoms, 41 bonds, 5 residues, 1 model selected  

> select add #8/I:235

51 atoms, 48 bonds, 6 residues, 1 model selected  

> select add #8/I:236

62 atoms, 58 bonds, 7 residues, 1 model selected  

> select add #8/I:237

66 atoms, 61 bonds, 8 residues, 1 model selected  

> select add #8/I:238

73 atoms, 67 bonds, 9 residues, 1 model selected  

> select add #8/I:239

80 atoms, 73 bonds, 10 residues, 1 model selected  

> select add #8/I:240

85 atoms, 77 bonds, 11 residues, 1 model selected  

> select add #8/I:241

92 atoms, 83 bonds, 12 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select add #8/N:14

96 atoms, 86 bonds, 13 residues, 1 model selected  

> select up

231 atoms, 233 bonds, 30 residues, 1 model selected  

> select up

3289 atoms, 3350 bonds, 431 residues, 1 model selected  

> select down

231 atoms, 233 bonds, 30 residues, 1 model selected  

> select up

3289 atoms, 3350 bonds, 431 residues, 1 model selected  

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #8 distance 1.06

> color zone #2 near #8 distance 4

> color zone #2 near sel distance 4

> volume splitbyzone #2

Opened preholo_3A_J319_C2_sharp.mrc 0 as #7.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #7.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #7.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #7.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #7.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #7.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #7.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  

> hide #!7.6 models

> show #!7.6 models

> hide #!7.5 models

> hide #!7.4 models

> hide #!7.3 models

> hide #!7.2 models

> hide #!7.1 models

> hide #!8 models

> show #!8 models

> select clear

> select #8/I:83

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

164 atoms, 165 bonds, 22 residues, 1 model selected  

> select up

1739 atoms, 1771 bonds, 229 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel peach puff

> select clear

> hide #!7.6 models

> hide #!7.7 models

> hide #!8 models

> show #!8 models

> select add #8/N:14

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add #8/I:149

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select up

67 atoms, 65 bonds, 10 residues, 1 model selected  

> select up

3289 atoms, 3350 bonds, 431 residues, 1 model selected  

> color zone #2 near sel distance 4

> volume splitbyzone #2

Opened preholo_3A_J319_C2_sharp.mrc 0 as #10.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #10.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #10.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #10.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  

> hide #!10.1 models

> hide #!10.2 models

> show #!10.2 models

> hide #!10 models

> select clear

> select #8/I:82

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

164 atoms, 165 bonds, 22 residues, 1 model selected  

> select up

1739 atoms, 1771 bonds, 229 residues, 1 model selected  

> show sel cartoons

> select clear

> select add #8/I:231

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #8/I:232

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select add #8/I:233

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #8/I:234

38 atoms, 36 bonds, 4 residues, 1 model selected  

> select add #8/I:235

45 atoms, 43 bonds, 5 residues, 1 model selected  

> select add #8/I:238

52 atoms, 49 bonds, 6 residues, 1 model selected  

> select add #8/I:237

56 atoms, 52 bonds, 7 residues, 1 model selected  

> select add #8/I:236

67 atoms, 62 bonds, 8 residues, 1 model selected  

> select add #8/I:239

74 atoms, 68 bonds, 9 residues, 1 model selected  

> select add #8/I:240

79 atoms, 72 bonds, 10 residues, 1 model selected  

> select add #8/I:241

86 atoms, 78 bonds, 11 residues, 1 model selected  

> select add #8/I:242

94 atoms, 85 bonds, 12 residues, 1 model selected  

> select add #8/I:243

103 atoms, 93 bonds, 13 residues, 1 model selected  

> select add #8/I:244

112 atoms, 101 bonds, 14 residues, 1 model selected  

> select add #8/I:246

120 atoms, 108 bonds, 15 residues, 1 model selected  

> select add #8/I:247

127 atoms, 114 bonds, 16 residues, 1 model selected  

> select add #8/I:245

133 atoms, 119 bonds, 17 residues, 1 model selected  

> select add #8/I:248

141 atoms, 126 bonds, 18 residues, 1 model selected  

> select add #8/I:249

150 atoms, 134 bonds, 19 residues, 1 model selected  

> color sel lime

> select clear

> select add #8/I:83

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #8/N:70

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select up

341 atoms, 345 bonds, 44 residues, 1 model selected  

> select up

3289 atoms, 3350 bonds, 431 residues, 1 model selected  

> color zone #2 near sel distance 4

> volume splitbyzone #2

Opened preholo_3A_J319_C2_sharp.mrc 0 as #11.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #11.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #11.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #11.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #11.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  

> hide #!11.1 models

> select subtract #8/I:231

3283 atoms, 3345 bonds, 430 residues, 1 model selected  

> select clear

> select #8/I:231

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #8/I:232

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #8/I:233

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #8/I:232

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select add #8/I:231

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #8/I:234

38 atoms, 36 bonds, 4 residues, 1 model selected  

> select add #8/I:235

45 atoms, 43 bonds, 5 residues, 1 model selected  

> select add #8/I:236

56 atoms, 53 bonds, 6 residues, 1 model selected  

> select add #8/I:237

60 atoms, 56 bonds, 7 residues, 1 model selected  

> select add #8/I:238

67 atoms, 62 bonds, 8 residues, 1 model selected  

> select add #8/I:239

74 atoms, 68 bonds, 9 residues, 1 model selected  

> select add #8/I:240

79 atoms, 72 bonds, 10 residues, 1 model selected  

> select add #8/I:241

86 atoms, 78 bonds, 11 residues, 1 model selected  

> hide sel cartoons

> select add #8/I:242

94 atoms, 85 bonds, 12 residues, 1 model selected  

> select add #8/I:244

103 atoms, 93 bonds, 13 residues, 1 model selected  

> select add #8/I:245

109 atoms, 98 bonds, 14 residues, 1 model selected  

> select add #8/I:247

116 atoms, 104 bonds, 15 residues, 1 model selected  

> select add #8/I:246

124 atoms, 111 bonds, 16 residues, 1 model selected  

> select add #8/I:248

132 atoms, 118 bonds, 17 residues, 1 model selected  

> select add #8/I:249

141 atoms, 126 bonds, 18 residues, 1 model selected  

> select add #8/I:243

150 atoms, 134 bonds, 19 residues, 1 model selected  

> hide sel cartoons

> volume #11.4 level 0.3297

> volume #11.4 level 0.3913

> volume #11.4 level 0.4

> select clear

> select #8/N:20

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 7 atom styles  

> show sel target ab

> color sel yellow

> color sel byhetero

> select clear

> volume #11.2 level 0.4

> volume #11.5 level 0.4

> volume #11.4 level 0.5

> volume #11.5 level 0.5

> volume #11.2 level 0.5

> select #11.5

2 models selected  

> transparency #11.5.1 70

> select #11.4

2 models selected  

> transparency #11.4.1 70

> select #11.2

2 models selected  

> transparency #11.2.1 70

> select clear

> ui tool show "Hide Dust"

> surface dust #11.5 size 6.36

> surface dust #11.4 size 6.36

> select #10.2

2 models selected  

> surface dust #11.4 size 6.36

> select #10.3

2 models selected  

> surface dust #11.4 size 6.36

> select #10.4

2 models selected  

> surface dust #11.3 size 6.36

> surface dust #11.2 size 6.36

> volume #11.4 level 0.4

> volume #11.5 level 0.4

> volume #11.2 level 0.4

> volume #11.2 level 0.45

> volume #11.4 level 0.45

> volume #11.5 level 0.45

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting soft

> surface dust #11.4 size 6.36

> surface dust #11.4 size 6.4

> surface dust #11.4 size 6.44

> surface dust #11.4 size 6.48

> surface dust #11.4 size 6.53

> surface dust #11.4 size 6.58

> surface dust #11.4 size 6.63

> surface dust #11.4 size 6.68

> surface dust #11.4 size 6.73

> surface dust #11.4 size 6.78

> surface dust #11.4 size 6.83

> surface dust #11.4 size 6.88

> surface dust #11.4 size 6.93

> surface dust #11.4 size 6.98

> surface dust #11.4 size 7.03

> surface dust #11.4 size 7.08

> surface dust #11.4 size 7.13

> surface dust #11.4 size 7.18

> surface dust #11.4 size 7.23

> surface dust #11.4 size 7.28

> surface dust #11.4 size 7.33

> surface dust #11.4 size 7.38

> surface dust #11.4 size 7.43

> surface dust #11.4 size 7.48

> surface dust #11.4 size 7.63

> surface dust #11.4 size 1.66

> surface dust #11.4 size 1.67

> surface dust #11.4 size 1.68

> surface dust #11.4 size 1.69

> surface dust #11.4 size 1.7

> surface dust #11.4 size 1.71

> surface dust #11.4 size 1.72

> surface dust #11.4 size 1.73

> surface dust #11.4 size 1.74

> surface dust #11.4 size 1.75

> surface dust #11.4 size 1.06

> surface dust #11.4 size 6

> surface dust #11.5 size 7.12

> surface dust #11.2 size 6.36

> surface dust #11.2 size 8.92

> save /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide.tif width
> 1964 height 1141 supersample 4 transparentBackground true

> save /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide.cxs
> includeMaps true

> lighting full

> save /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide.tif width
> 1964 height 1141 supersample 4 transparentBackground true

> save /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide2.tif width
> 1964 height 1141 supersample 4 transparentBackground true

> surface dust #11.5 size 7.12

> surface dust #11.5 size 16.06

> surface dust #11.5 size 53.03

> surface dust #11.5 size 53.4

> surface dust #11.5 size 7.63

> surface dust #11.5 size 2

> surface dust #11.5 size 20

> turn x 135

> surface dust #11.2 size 2

> surface dust #11.2 size 20

> surface dust #11.2 size 15

> turn x 135

> undo

> surface dust #11.2 size 15

> save /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide3.tif width
> 1964 height 1141 supersample 4 transparentBackground true

> save /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide2.cxs

> open /nfs/userdocs/sch/walsh/Documents/preholo/beat1-propetide.cxs

Opened preholo_3A_J319_C2_sharp.mrc as #2, grid size 360,360,360, pixel 1.06,
shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #6.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #6.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #6.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #6.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #6.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #6.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #6.8, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #4.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #4.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #4.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #4.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #4.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #4.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #4.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #4.8, grid size 360,360,360, pixel
1.06, shown at level 0.4, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #5.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #5.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #5.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #5.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #5.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #5.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #5.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #5.8, grid size 360,360,360, pixel
1.06, shown at level 0.4, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #9.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #9.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #9.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #9.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #9.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #9.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #9.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 7 as #9.8, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #7.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #7.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #7.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #7.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #7.5, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 5 as #7.6, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 6 as #7.7, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #10.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #10.2, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #10.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #10.4, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 0 as #11.1, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 1 as #11.2, grid size 360,360,360, pixel
1.06, shown at level 0.45, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 2 as #11.3, grid size 360,360,360, pixel
1.06, shown at level 0.5, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 3 as #11.4, grid size 360,360,360, pixel
1.06, shown at level 0.45, step 1, values float32  
Opened preholo_3A_J319_C2_sharp.mrc 4 as #11.5, grid size 360,360,360, pixel
1.06, shown at level 0.45, step 1, values float32  
opened ChimeraX session  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G        3.1G         18G        199M        9.4G         27G
	Swap:          2.0G        272M        1.7G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11a3]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    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-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash in event loop

comment:2 by Eric Pettersen, 3 years ago

Status:	accepted → feedback

Hi Richard,

Thanks for reporting this problem. According to the log it looks like you had just opened a session file. Did the crash occur while that was happening, or were you doing something afterward when it crashed?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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