![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7329 closed defect (duplicate)
Volume Viewer after session restore: wrapped C/C++ object of type QScrollArea has been deleted
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/edk4001/Library/Mobile Documents/com~apple~CloudDocs/HCN pore
> figure v5.cxs"
Log from Mon Jul 25 09:14:07 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/edk4001/Desktop/HCN pore figure v3.cxs"
Log from Sun Jul 24 16:41:39 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/edk4001/Desktop/HCN pore figure v2.cxs"
Log from Sun Jul 24 15:48:35 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/edk4001/Desktop/HCN pore figure.cxs"
Log from Mon Jul 18 00:34:54 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/edk4001/Desktop/5U6O_pore.pdb
Chain information for 5U6O_pore.pdb #1
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/5U6P_pore.pdb
Chain information for 5U6P_pore.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> open /Users/edk4001/Desktop/6GYN_pore.pdb
Chain information for 6GYN_pore.pdb #3
---
Chain | Description
A B D | No description available
C | No description available
> open /Users/edk4001/Desktop/6GYO_pore.pdb
Chain information for 6GYO_pore.pdb #4
---
Chain | Description
A C D | No description available
B | No description available
> open /Users/edk4001/Desktop/7NP4_pore.pdb
Chain information for 7NP4_pore.pdb #5
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/7NP3_pore.pdb
Chain information for 7NP3_pore.pdb #6
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/7NMN_pore.pdb
Chain information for 7NMN_pore.pdb #7
---
Chain | Description
A B C D | No description available
> select add #1
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select add #2
30120 atoms, 30856 bonds, 16 pseudobonds, 4024 residues, 4 models selected
> select add #3
47052 atoms, 48136 bonds, 17 pseudobonds, 6040 residues, 6 models selected
> select add #5
63636 atoms, 65124 bonds, 17 pseudobonds, 8048 residues, 7 models selected
> select add #4
81176 atoms, 83016 bonds, 22 pseudobonds, 10100 residues, 10 models selected
> select add #6
97308 atoms, 99540 bonds, 22 pseudobonds, 12060 residues, 11 models selected
> select add #7
112744 atoms, 115352 bonds, 26 pseudobonds, 13936 residues, 13 models selected
> hide sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> select #1/A#2/A#3/A#4/A#5/A#6/A#7/A
28091 atoms, 28744 bonds, 6 pseudobonds, 3465 residues, 11 models selected
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B
28091 atoms, 28744 bonds, 7 pseudobonds, 3465 residues, 12 models selected
> hide sel cartoons
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D
28091 atoms, 28744 bonds, 6 pseudobonds, 3465 residues, 11 models selected
> hide sel cartoons
> select #2/E
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #2/F
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #2/H
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #2/G
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select clear
> set bgColor white
> graphics silhouettes true
> hide #!7 models
> hide #6 models
> hide #5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> show #5 models
> hide #!4 models
> hide #5 models
> show #!1 models
> select clear
> select #1/C:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:364
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:363
14 atoms, 12 bonds, 2 residues, 1 model selected
> select subtract #1/A:363
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:364
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #1/C:360
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #1/A:360
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #1/C:361
38 atoms, 34 bonds, 5 residues, 1 model selected
> select add #1/A:361
50 atoms, 46 bonds, 6 residues, 1 model selected
> select add #1/C:359
58 atoms, 53 bonds, 7 residues, 1 model selected
> select add #1/C:358
64 atoms, 58 bonds, 8 residues, 1 model selected
> select add #1/A:359
72 atoms, 65 bonds, 9 residues, 1 model selected
> select add #1/A:358
78 atoms, 70 bonds, 10 residues, 1 model selected
> select add #1/A:357
86 atoms, 77 bonds, 11 residues, 1 model selected
> select subtract #1/A:357
78 atoms, 70 bonds, 10 residues, 1 model selected
> show sel atoms
> select #1/C:360
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:360
8 atoms, 6 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #1/C:362
12 atoms, 9 bonds, 3 residues, 1 model selected
> select add #1/A:362
16 atoms, 12 bonds, 4 residues, 1 model selected
> select #1/C:364
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:386
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #1/A:386
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!2 models
> hide #!1 models
> select add #2/C:364
29 atoms, 28 bonds, 3 residues, 2 models selected
> select add #2/A:364
34 atoms, 32 bonds, 4 residues, 2 models selected
> select add #2/C:362
38 atoms, 35 bonds, 5 residues, 2 models selected
> select add #2/A:362
42 atoms, 38 bonds, 6 residues, 2 models selected
> select add #2/C:361
54 atoms, 50 bonds, 7 residues, 2 models selected
> select add #2/C:360
58 atoms, 53 bonds, 8 residues, 2 models selected
> select add #2/C:359
66 atoms, 60 bonds, 9 residues, 2 models selected
> select add #2/C:358
72 atoms, 65 bonds, 10 residues, 2 models selected
> select add #2/A:361
84 atoms, 77 bonds, 11 residues, 2 models selected
> select add #2/A:360
88 atoms, 80 bonds, 12 residues, 2 models selected
> select add #2/A:359
96 atoms, 87 bonds, 13 residues, 2 models selected
> select add #2/A:358
102 atoms, 92 bonds, 14 residues, 2 models selected
> select add #2/C:386
114 atoms, 104 bonds, 15 residues, 2 models selected
> select add #2/A:386
126 atoms, 116 bonds, 16 residues, 2 models selected
> show sel & #!2 atoms
> style (#!2 & sel) stick
Changed 102 atom styles
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> select add #3/C:483
137 atoms, 126 bonds, 17 residues, 3 models selected
> select add #3/C:484
142 atoms, 130 bonds, 18 residues, 3 models selected
> select subtract #3/C:483
131 atoms, 120 bonds, 17 residues, 3 models selected
> select add #3/A:484
136 atoms, 124 bonds, 18 residues, 3 models selected
> select add #3/C:482
140 atoms, 127 bonds, 19 residues, 3 models selected
> select add #3/C:481
152 atoms, 139 bonds, 20 residues, 3 models selected
> select add #3/C:480
156 atoms, 142 bonds, 21 residues, 3 models selected
> select add #3/C:479
164 atoms, 149 bonds, 22 residues, 3 models selected
> select add #3/C:478
170 atoms, 154 bonds, 23 residues, 3 models selected
> select add #3/A:482
174 atoms, 157 bonds, 24 residues, 3 models selected
> select add #3/A:481
186 atoms, 169 bonds, 25 residues, 3 models selected
> select add #3/A:480
190 atoms, 172 bonds, 26 residues, 3 models selected
> select add #3/A:479
198 atoms, 179 bonds, 27 residues, 3 models selected
> select add #3/A:478
204 atoms, 184 bonds, 28 residues, 3 models selected
> show sel & #!3 atoms
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!4 models
> select #4/C:484
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/A:483
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #4/C:482
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #4/C:481
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #4/C:480
36 atoms, 32 bonds, 5 residues, 1 model selected
> select add #4/C:479
44 atoms, 39 bonds, 6 residues, 1 model selected
> select add #4/C:478
50 atoms, 44 bonds, 7 residues, 1 model selected
> select add #4/A:482
54 atoms, 47 bonds, 8 residues, 1 model selected
> select add #4/A:481
66 atoms, 59 bonds, 9 residues, 1 model selected
> select add #4/A:480
70 atoms, 62 bonds, 10 residues, 1 model selected
> select add #4/A:479
78 atoms, 69 bonds, 11 residues, 1 model selected
> select add #4/A:478
84 atoms, 74 bonds, 12 residues, 1 model selected
> show sel atoms
> select subtract #4/A:483
73 atoms, 64 bonds, 11 residues, 1 model selected
> select #4/A:483@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:484
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!4 models
> show #5 models
> select #5/C:483
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #5/A:483
8 atoms, 6 bonds, 2 residues, 1 model selected
> select add #5/A:485
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #5/C:485
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #5/C:482
38 atoms, 34 bonds, 5 residues, 1 model selected
> select add #5/C:481
42 atoms, 37 bonds, 6 residues, 1 model selected
> select add #5/C:480
50 atoms, 44 bonds, 7 residues, 1 model selected
> select add #5/C:479
56 atoms, 49 bonds, 8 residues, 1 model selected
> select add #5/A:482
68 atoms, 61 bonds, 9 residues, 1 model selected
> select add #5/A:481
72 atoms, 64 bonds, 10 residues, 1 model selected
> select add #5/A:480
80 atoms, 71 bonds, 11 residues, 1 model selected
> select add #5/A:479
86 atoms, 76 bonds, 12 residues, 1 model selected
> show sel atoms
> hide #5 models
> show #6 models
> select #6/C:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #6/A:485
20 atoms, 18 bonds, 2 residues, 1 model selected
> select add #6/C:483
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #6/C:482
36 atoms, 33 bonds, 4 residues, 1 model selected
> select add #6/C:481
40 atoms, 36 bonds, 5 residues, 1 model selected
> select add #6/C:480
48 atoms, 43 bonds, 6 residues, 1 model selected
> select add #6/C:479
54 atoms, 48 bonds, 7 residues, 1 model selected
> select add #6/A:479
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #6/A:480
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #6/A:481
72 atoms, 63 bonds, 10 residues, 1 model selected
> select add #6/A:482
84 atoms, 75 bonds, 11 residues, 1 model selected
> select add #6/A:483
88 atoms, 78 bonds, 12 residues, 1 model selected
> select add #6/A:484
99 atoms, 88 bonds, 13 residues, 1 model selected
> show sel atoms
> select #6/C:484@CA
1 atom, 1 residue, 1 model selected
> select #6/A:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
78 atoms, 79 bonds, 11 residues, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
78 atoms, 79 bonds, 11 residues, 1 model selected
> select up
4033 atoms, 4131 bonds, 490 residues, 1 model selected
> select down
78 atoms, 79 bonds, 11 residues, 1 model selected
> select down
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/C:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/C:485
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #6 models
> show #!7 models
> select #7/C:485
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7/A:485
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #7/C:483
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #7/C:482
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #7/C:481
38 atoms, 34 bonds, 5 residues, 1 model selected
> select add #7/C:480
46 atoms, 41 bonds, 6 residues, 1 model selected
> select add #7/C:479
52 atoms, 46 bonds, 7 residues, 1 model selected
> select add #7/A:483
56 atoms, 49 bonds, 8 residues, 1 model selected
> select add #7/A:482
68 atoms, 61 bonds, 9 residues, 1 model selected
> select add #7/A:481
72 atoms, 64 bonds, 10 residues, 1 model selected
> select add #7/A:480
80 atoms, 71 bonds, 11 residues, 1 model selected
> select add #7/A:479
86 atoms, 76 bonds, 12 residues, 1 model selected
> show sel atoms
> show #6 models
> show #5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!7 models
> hide #6 models
> hide #5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> select #3/C:506
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3/A:506
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #!3 models
> show #!4 models
> select #4/C:506
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #4/A:506
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #!4 models
> show #5 models
> select #5/C:507
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5/A:507
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #5 models
> show #6 models
> select #6/C:507
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #6/A:507
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #6 models
> show #!7 models
> select #7/C:507
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #7/A:507
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> show #6 models
> show #5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> size stickRadius 0.1
Changed 114976 bond radii
> size stickRadius 0.2
Changed 114976 bond radii
> size stickRadius 0.3
Changed 114976 bond radii
> size stickRadius 0.25
Changed 114976 bond radii
> cartoon style coil thickness 0.25
> cartoon style coil thickness 0.3
> cartoon style coil thickness 0.4
> cartoon style coil thickness 0.5
> cartoon style coil thickness 0.6
> cartoon style coil thickness 0.55
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> hide #!7 models
> cartoon style coil thickness 0.5
> show #!7 models
> select add #7
15436 atoms, 15812 bonds, 4 pseudobonds, 1876 residues, 2 models selected
> select subtract #7
Nothing selected
> color #1 white transparency 0
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> hide #!7 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 2
> graphics silhouettes width 3
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> color #2 white transparency 0
> show #!4 models
> show #5 models
> select add #4
17540 atoms, 17892 bonds, 5 pseudobonds, 2052 residues, 3 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> color sel light steel blue
> select subtract #4
Nothing selected
> select add #5
16584 atoms, 16988 bonds, 2008 residues, 1 model selected
> color sel light green
> color sel dark sea green
> color sel light pink
> color sel dark sea green
> color sel lavender
> color sel plum
> color sel light green
> color sel pale green
[Repeated 1 time(s)]
> color sel dark sea green
> select clear
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #5 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> save /Users/edk4001/Desktop/image1.png supersample 3
> hide #!2 models
> show #5 models
> select add #5
16584 atoms, 16988 bonds, 2008 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light cyan
> color sel lavender
> color sel pale goldenrod
[Repeated 1 time(s)]
> color sel khaki
> color sel pale goldenrod
> color sel wheat
[Repeated 1 time(s)]
> color sel mint cream
> color sel antique white
> color sel thistle
> color sel light pink
> color sel pale goldenrod
> select clear
> save /Users/edk4001/Desktop/image2.png supersample 3
> show #6 models
> show #!7 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #5 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select add #6
16132 atoms, 16524 bonds, 1960 residues, 1 model selected
> ui tool show "Color Actions"
> color sel silver
> select add #7
31568 atoms, 32336 bonds, 4 pseudobonds, 3836 residues, 3 models selected
> select subtract #6
15436 atoms, 15812 bonds, 4 pseudobonds, 1876 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium aquamarine
> color sel cadet blue
> color sel medium aquamarine
[Repeated 1 time(s)]
> color sel turquoise
> color sel medium spring green
> color sel pale green
> color sel light green
> color sel dark sea green
> color sel pale green
> ui tool show "Color Actions"
> color sel light pink
> color sel pink
> color sel peach puff
> color sel navajo white
[Repeated 1 time(s)]
> color sel misty rose
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color sel light pink
> select clear
> hide #6 models
> show #5 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!7 models
> show #!7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #5 models
> show #5 models
> save /Users/edk4001/Desktop/image3.png supersample 3
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #6 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> color #3 #73fa79 transparency 0
> color #3 #73fcd6 transparency 0
> select add #3
16932 atoms, 17280 bonds, 1 pseudobond, 2016 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light green
> color sel pale green
[Repeated 2 time(s)]
> color sel light green
> color sel pale green
> select clear
> show #!1 models
> hide #!2 models
> hide #!4 models
> hide #5 models
> select add #1
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light steel blue
> color sel light sky blue
> color sel sky blue
> color sel light blue
> color sel powder blue
> select clear
> save /Users/edk4001/Desktop/image4.png supersample 3
> hide #!7 models
> hide #6 models
> show #5 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> save /Users/edk4001/Desktop/image5.png supersample 3
> select add #4
17540 atoms, 17892 bonds, 5 pseudobonds, 2052 residues, 3 models selected
> ui tool show "Color Actions"
> color sel white smoke
> color sel mint cream
> color sel ivory
> color sel white
> color sel seashell
> color sel honeydew
> color sel alice blue
> ui tool show "Color Actions"
> color sel light gray
> select add #5
34124 atoms, 34880 bonds, 5 pseudobonds, 4060 residues, 4 models selected
> select subtract #4
16584 atoms, 16988 bonds, 2008 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light slate gray
> color sel cadet blue
> color sel light steel blue
> color sel powder blue
> color sel light steel blue
> color sel light blue
> color sel light sky blue
> color sel sky blue
> color sel light steel blue
> color sel slate gray
> color sel light slate gray
> ui tool show "Color Actions"
> color sel steel blue
> color sel cadet blue
> select subtract #5
Nothing selected
> select add #4
17540 atoms, 17892 bonds, 5 pseudobonds, 2052 residues, 3 models selected
> ui tool show "Color Actions"
> color sel silver
> select clear
> save /Users/edk4001/Desktop/image6.png supersample 3
> hide #!4 models
> hide #5 models
> hide #!2 models
> show #!1 models
> show #!3 models
> show #6 models
> show #!7 models
> select add #1
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select add #3
31412 atoms, 32120 bonds, 9 pseudobonds, 3944 residues, 4 models selected
> select subtract #3
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> color (#!1 & sel) light gray
> select add #3
31412 atoms, 32120 bonds, 9 pseudobonds, 3944 residues, 4 models selected
> select subtract #1
16932 atoms, 17280 bonds, 1 pseudobond, 2016 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dim gray
> color sel gray
> color sel dark gray
> color sel light slate gray
> color sel slate gray
> color sel light steel blue
> color sel light blue
> color sel gainsboro
> color sel dim gray
[Repeated 1 time(s)]
> color sel gray
> color sel dark gray
> color sel light gray
> color sel light steel blue
> color sel silver
> color sel white smoke
> color sel alice blue
[Repeated 1 time(s)]
> color sel lavender blush
> color sel azure
> color sel gainsboro
> select add #6
33064 atoms, 33804 bonds, 1 pseudobond, 3976 residues, 3 models selected
> select subtract #3
16132 atoms, 16524 bonds, 1960 residues, 1 model selected
> color sel light cyan
> color sel light sky blue
> color sel sky blue
> color sel light steel blue
> color sel cornflower blue
> color sel dark turquoise
> color sel deep sky blue
> color sel sky blue
> select subtract #6
Nothing selected
> select add #7
15436 atoms, 15812 bonds, 4 pseudobonds, 1876 residues, 2 models selected
> color sel light sky blue
> color sel light steel blue
> color sel steel blue
> select subtract #7
Nothing selected
> save /Users/edk4001/Desktop/image7.png supersample 3
> hide #6 models
> hide #!7 models
> hide #!3 models
> select #1/C:360
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #1/D
Alignment identifier is 1
> select #1/A-D:359
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1/A-D:359-364
168 atoms, 168 bonds, 24 residues, 1 model selected
> select #1/A-D:358
24 atoms, 20 bonds, 4 residues, 1 model selected
> select #1/A-D:358-362
136 atoms, 136 bonds, 20 residues, 1 model selected
> select clear
> show #!3 models
> show #!7 models
> show #6 models
> save "/Users/edk4001/Desktop/apo HCN pores.png" width 3000 height 2272
> supersample 4 transparentBackground true
> graphics silhouettes false
> graphics silhouettes true
> save "/Users/edk4001/Desktop/apo HCN pores.png" width 3000 height 2272
> supersample 4 transparentBackground true
> hide #!1 models
> hide #!3 models
> hide #6 models
> hide #!7 models
> show #!2 models
> show #!4 models
> show #5 models
> save "/Users/edk4001/Desktop/camp HCN pores.png" width 3000 height 2272
> supersample 4 transparentBackground true
> hide #5 models
> hide #!2 models
> show #!1 models
> hide #!4 models
> select #1/A:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:360
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:361
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:362
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:363
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:364
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:386
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #5 models
> show #!7 models
> show #6 models
> ui mousemode right zoom
> open /Users/edk4001/Desktop/5U6O_pore.pdb
Chain information for 5U6O_pore.pdb #8
---
Chain | Description
A B C D | No description available
> close #8
> save "/Users/edk4001/Desktop/HCN pore figure.cxs"
——— End of log from Mon Jul 18 00:34:54 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in <lambda>
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
Populating font family aliases took 199 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
See log for complete Python traceback.
> hide #!7 models
> hide #6 models
> hide #!3 models
> hide #!1 models
> select #4/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/A:358
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #5/A:479@SG
13 atoms, 10 bonds, 3 residues, 3 models selected
> select #4/A:478@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark gray
> size stickRadius 0.5
Changed 114976 bond radii
> size stickRadius 0.2
Changed 114976 bond radii
> size sel stickRadius 0.4
Changed 5 bond radii
> size sel stickRadius 0.3
Changed 5 bond radii
> size sel stickRadius 0.35
Changed 5 bond radii
> select add #5/A:479@CB
7 atoms, 5 bonds, 2 residues, 2 models selected
> select add #2/A:358@CB
8 atoms, 5 bonds, 3 residues, 3 models selected
> select up
18 atoms, 15 bonds, 3 residues, 3 models selected
> size sel stickRadius 0.35
Changed 15 bond radii
> cartoon sel style coil thickness 0.9
Expected a keyword
> open /Users/edk4001/Desktop/5U6O_pore.pdb
Chain information for 5U6O_pore.pdb #8
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/5U6P_pore.pdb
Chain information for 5U6P_pore.pdb #9
---
Chain | Description
A B C D | No description available
E F G H | No description available
> open /Users/edk4001/Desktop/6GYN_pore.pdb
Chain information for 6GYN_pore.pdb #10
---
Chain | Description
A B D | No description available
C | No description available
> open /Users/edk4001/Desktop/6GYO_pore.pdb
Chain information for 6GYO_pore.pdb #11
---
Chain | Description
A C D | No description available
B | No description available
> open /Users/edk4001/Desktop/7NP4_pore.pdb
Chain information for 7NP4_pore.pdb #12
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/7NP3_pore.pdb
Chain information for 7NP3_pore.pdb #13
---
Chain | Description
A B C D | No description available
> open /Users/edk4001/Desktop/7NMN_pore.pdb
Chain information for 7NMN_pore.pdb #14
---
Chain | Description
A B C D | No description available
> size sel stickRadius 0.2
Changed 15 bond radii
> hide #!2 models
> hide #!4 models
> hide #5 models
> select add #2
15272 atoms, 15650 bonds, 8 pseudobonds, 2022 residues, 4 models selected
> select subtract #2
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #4
17546 atoms, 17897 bonds, 5 pseudobonds, 2053 residues, 4 models selected
> select subtract #4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5
16584 atoms, 16988 bonds, 2008 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #8
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select add #9
30120 atoms, 30856 bonds, 16 pseudobonds, 4024 residues, 4 models selected
> select add #10
47052 atoms, 48136 bonds, 17 pseudobonds, 6040 residues, 6 models selected
> select add #11
64592 atoms, 66028 bonds, 22 pseudobonds, 8092 residues, 9 models selected
> select add #12
81176 atoms, 83016 bonds, 22 pseudobonds, 10100 residues, 10 models selected
> select add #13
97308 atoms, 99540 bonds, 22 pseudobonds, 12060 residues, 11 models selected
> select add #14
112744 atoms, 115352 bonds, 26 pseudobonds, 13936 residues, 13 models selected
> cartoon (#12-13#!8-11,14 & sel)
> hide sel atoms
> select #9/E
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #9/F
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #9/G
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #9/H
95 atoms, 94 bonds, 19 residues, 1 model selected
> delete sel
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B
56182 atoms, 57488 bonds, 14 pseudobonds, 6930 residues, 24 models selected
> hide sel & #12-13#!8-11,14 cartoons
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D#8/D#9/D#10/D#11/D#12/D#13/D#14/D
56182 atoms, 57488 bonds, 12 pseudobonds, 6930 residues, 22 models selected
> hide sel & #12-13#!8-11,14 cartoons
> select clear
> show #!2 models
> show #!4 models
> show #5 models
> hide #!8 models
> hide #!10 models
> hide #13 models
> hide #!14 models
> select add #12
16584 atoms, 16988 bonds, 2008 residues, 1 model selected
> select add #11
34124 atoms, 34880 bonds, 5 pseudobonds, 4060 residues, 4 models selected
> select add #9
49384 atoms, 50520 bonds, 13 pseudobonds, 6080 residues, 6 models selected
> cartoon (#12#!9,11 & sel)
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B
56182 atoms, 57488 bonds, 14 pseudobonds, 6930 residues, 24 models selected
> hide sel & #5,12#!2,4,9,11 cartoons
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D#8/D#9/D#10/D#11/D#12/D#13/D#14/D
56182 atoms, 57488 bonds, 12 pseudobonds, 6930 residues, 22 models selected
> hide sel & #5,12#!2,4,9,11 cartoons
> hide #!2 models
> hide #!4 models
> hide #5 models
> show #5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #5 models
> select #11/A:479
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/A:478
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #9/A:358
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #12/A:480
20 atoms, 17 bonds, 3 residues, 3 models selected
> select subtract #12/A:480
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #12/A:479
18 atoms, 15 bonds, 3 residues, 3 models selected
> select add #11/C:478
24 atoms, 20 bonds, 4 residues, 3 models selected
> select add #12/C:479
30 atoms, 25 bonds, 5 residues, 3 models selected
> select add #9/C:358
36 atoms, 30 bonds, 6 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 36 atom styles
> size sel stickRadius 0.2
Changed 30 bond radii
> size sel stickRadius 0.4
Changed 30 bond radii
> cartoon sel style coil thickness 0.9
Expected a keyword
> cartoon style coil thickness 0.9
> cartoon style coil thickness 0.8
> select add #12/A:482
48 atoms, 42 bonds, 7 residues, 3 models selected
> select subtract #12/A:482
36 atoms, 30 bonds, 6 residues, 3 models selected
> select #9/A:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #11/A:485
10 atoms, 8 bonds, 2 residues, 2 models selected
> select add #12/A:486
15 atoms, 12 bonds, 3 residues, 3 models selected
> select add #9/A:363
20 atoms, 16 bonds, 4 residues, 3 models selected
> select add #11/A:483
31 atoms, 26 bonds, 5 residues, 3 models selected
> hide #12 models
> hide #!11 models
> select #9/C:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #9/C:363
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #9/A:363
15 atoms, 12 bonds, 3 residues, 1 model selected
> select add #9/A:365
20 atoms, 16 bonds, 4 residues, 1 model selected
> show #!10 models
> hide #!9 models
> select add #10/C:485
25 atoms, 20 bonds, 5 residues, 2 models selected
> select add #10/C:482
29 atoms, 23 bonds, 6 residues, 2 models selected
> select subtract #10/C:482
25 atoms, 20 bonds, 5 residues, 2 models selected
> select add #10/C:483
36 atoms, 30 bonds, 6 residues, 2 models selected
> select add #10/A:482
40 atoms, 33 bonds, 7 residues, 2 models selected
> select subtract #10/A:482
36 atoms, 30 bonds, 6 residues, 2 models selected
> select add #10/A:483
47 atoms, 40 bonds, 7 residues, 2 models selected
> select add #10/A:482
51 atoms, 43 bonds, 8 residues, 2 models selected
> select subtract #10/A:483
40 atoms, 33 bonds, 7 residues, 2 models selected
> select subtract #10/A:482
36 atoms, 30 bonds, 6 residues, 2 models selected
> select add #10/A:484
41 atoms, 34 bonds, 7 residues, 2 models selected
> select subtract #10/A:484
36 atoms, 30 bonds, 6 residues, 2 models selected
> select add #10/A:485
41 atoms, 34 bonds, 7 residues, 2 models selected
> select add #10/A:483
52 atoms, 44 bonds, 8 residues, 2 models selected
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!11 models
> hide #!11 models
> show #12 models
> select add #12/C:484
63 atoms, 54 bonds, 9 residues, 3 models selected
> select add #12/A:484
74 atoms, 64 bonds, 10 residues, 3 models selected
> select add #12/A:486
79 atoms, 68 bonds, 11 residues, 3 models selected
> select add #12/C:486
84 atoms, 72 bonds, 12 residues, 3 models selected
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!10 models
> select add #12/C:479@CA
85 atoms, 72 bonds, 13 residues, 3 models selected
> select add #12/A:479@CA
86 atoms, 72 bonds, 14 residues, 3 models selected
> show #!10 models
> hide #12 models
> select add #10/A:478
92 atoms, 77 bonds, 15 residues, 3 models selected
> select add #10/C:478
98 atoms, 82 bonds, 16 residues, 3 models selected
> hide #!10 models
> show #!9 models
> select add #9/A:358
104 atoms, 87 bonds, 17 residues, 3 models selected
> select add #9/C:358@CA
105 atoms, 87 bonds, 18 residues, 3 models selected
> show #!10 models
> show #12 models
> select up
120 atoms, 102 bonds, 18 residues, 3 models selected
> color sel orange red
> select ~sel
224608 atoms, 229814 bonds, 52 pseudobonds, 27702 residues, 26 models selected
> hide sel & #12#!9-10 cartoons
> show #!2 models
> show #!4 models
> show #5 models
> hide #!2 models
> hide #!4 models
> hide #5 models
> select #12/C:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #10/C:485
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #9/C:365
21 atoms, 18 bonds, 3 residues, 3 models selected
> select add #12/C:486
26 atoms, 22 bonds, 4 residues, 3 models selected
> select add #9/C:363
31 atoms, 26 bonds, 5 residues, 3 models selected
> select add #10/C:483
42 atoms, 36 bonds, 6 residues, 3 models selected
> select add #12/A:484
53 atoms, 46 bonds, 7 residues, 3 models selected
> select add #10/A:485
58 atoms, 50 bonds, 8 residues, 3 models selected
> select add #9/A:365
63 atoms, 54 bonds, 9 residues, 3 models selected
> select add #12/A:486
68 atoms, 58 bonds, 10 residues, 3 models selected
> select add #10/A:483
79 atoms, 68 bonds, 11 residues, 3 models selected
> select add #9/A:363
84 atoms, 72 bonds, 12 residues, 3 models selected
> select add #10/A:478
90 atoms, 77 bonds, 13 residues, 3 models selected
> select add #12/A:479
96 atoms, 82 bonds, 14 residues, 3 models selected
> select add #9/A:358
102 atoms, 87 bonds, 15 residues, 3 models selected
> select add #9/C:358@CB
103 atoms, 87 bonds, 16 residues, 3 models selected
> select add #10/C:478
109 atoms, 93 bonds, 17 residues, 3 models selected
> select up
111 atoms, 93 bonds, 18 residues, 3 models selected
> select up
120 atoms, 102 bonds, 18 residues, 3 models selected
> select down
111 atoms, 93 bonds, 18 residues, 3 models selected
> select up
120 atoms, 102 bonds, 18 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 120 atom styles
> size sel stickRadius 0.4
Changed 102 bond radii
> show #!2 models
> show #!4 models
> show #5 models
> hide #!2 models
> hide #!4 models
> hide #5 models
> select clear
> graphics silhouettes false
> graphics silhouettes true
> save /Users/edk4001/Desktop/background.png width 3000 height 2272
> supersample 3 transparentBackground true
> hide #12 models
> hide #!10 models
> hide #!9 models
> show #!2 models
> show #!4 models
> show #5 models
> cartoon style coil thickness 0.4
> cartoon style coil thickness 0.5
> cartoon style coil thickness 0.4
> select #4/C:485
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/C:365
10 atoms, 8 bonds, 2 residues, 2 models selected
> select add #5/C:486
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #5/C:484
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #4/C:485
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #2/C:365
21 atoms, 18 bonds, 3 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> show #!9 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> select #2/C:363
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/C:483
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #5/C:486
21 atoms, 18 bonds, 3 residues, 3 models selected
> select add #5/A:486
26 atoms, 22 bonds, 4 residues, 3 models selected
> select add #2/A:365
31 atoms, 26 bonds, 5 residues, 3 models selected
> select add #5/A:484
42 atoms, 36 bonds, 6 residues, 3 models selected
> select add #2/A:363
47 atoms, 40 bonds, 7 residues, 3 models selected
> select add #4/A:483
58 atoms, 50 bonds, 8 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 58 atom styles
> select clear
> show #!9 models
> show #!10 models
> show #12 models
> hide #12 models
> hide #!10 models
> hide #!9 models
> save /Users/edk4001/Desktop/front.png width 3000 height 2272 supersample 3
> transparentBackground true
> show #!9 models
> show #!10 models
> show #12 models
> show #!11 models
> hide #!10 models
> color #11 #ff2600 transparency 0
> hide #!2 models
> hide #!4 models
> hide #5 models
> hide #!11 models
> show #!11 models
> hide #!9 models
> hide #12 models
> select add #11/C:485
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #11/C:483
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #11/A:483
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #11/A:485
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> size sel stickRadius 0.4
Changed 28 bond radii
> select add #11/A:478
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #11/C:478
44 atoms, 38 bonds, 6 residues, 1 model selected
> size sel stickRadius 0.3
Changed 38 bond radii
> size sel stickRadius 0.35
Changed 38 bond radii
> size sel stickRadius 0.3
Changed 38 bond radii
> cartoon style coil thickness 0.4
[Repeated 1 time(s)]
> select clear
> select add #11
17540 atoms, 17892 bonds, 5 pseudobonds, 2052 residues, 3 models selected
> cartoon style coil thickness 0.4
[Repeated 2 time(s)]
> cartoon style coil thickness 0.5
> cartoon style coil thickness 0.6
> select subtract #11
Nothing selected
> show #12 models
> hide #12 models
> select add #11/A:483
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #11/A:485
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #11/C:485
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #11/C:483
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #11/C:478
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #11/A:478
44 atoms, 38 bonds, 6 residues, 1 model selected
> select ~sel
224684 atoms, 229902 bonds, 52 pseudobonds, 27714 residues, 26 models selected
> hide sel & #!11 cartoons
> show #!9 models
> show #12 models
> color #11 #ff2600 transparency 0
> color #9 #ff2600 transparency 0
> color #12 #ff2600 transparency 0
> select add #11/C:483@CG
224685 atoms, 229902 bonds, 52 pseudobonds, 27715 residues, 26 models selected
> select add #11/A:483@CG
224686 atoms, 229902 bonds, 52 pseudobonds, 27716 residues, 26 models selected
> select subtract #9/A:363@CB
224685 atoms, 229901 bonds, 52 pseudobonds, 27716 residues, 26 models selected
> select add #9/A:363@CB
224686 atoms, 229901 bonds, 52 pseudobonds, 27716 residues, 26 models selected
> select up
224706 atoms, 229925 bonds, 52 pseudobonds, 27716 residues, 26 models selected
> select up
224728 atoms, 229951 bonds, 52 pseudobonds, 27720 residues, 26 models selected
> size sel stickRadius 0.3
Changed 229952 bond radii
> select clear
> save /Users/edk4001/Desktop/background.png width 3000 height 2272
> supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!4 models
> show #5 models
> cartoon style coil thickness 0.3
> cartoon style coil thickness 0.4
> save "/Users/edk4001/Desktop/HCN pore figure v2.png" width 1154 height 874
> supersample 3
> save "/Users/edk4001/Desktop/HCN pore figure v2.cxs"
——— End of log from Sun Jul 24 15:48:35 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in <lambda>
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
Populating font family aliases took 199 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
See log for complete Python traceback.
> hide #!2 models
> hide #!4 models
> hide #5 models
> select add #9
15260 atoms, 15640 bonds, 8 pseudobonds, 2020 residues, 2 models selected
> select add #11
32800 atoms, 33532 bonds, 13 pseudobonds, 4072 residues, 5 models selected
> select add #12
49384 atoms, 50520 bonds, 13 pseudobonds, 6080 residues, 6 models selected
> cartoon style coil thickness 0.7
> size sel stickRadius 0.35
Changed 50520 bond radii
> select clear
> save /Users/edk4001/Desktop/background.png width 3000 height 2272
> supersample 3 transparentBackground true
> hide #!9 models
> hide #!11 models
> hide #12 models
> show #!2 models
> show #!4 models
> show #5 models
> select #5/C:485
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!4 models
> hide #!2 models
> select add #5/A:485
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide #5 models
> show #5 models
> cartoon style coil thickness 04
> cartoon style coil thickness 0.4
> cartoon style coil thickness 0.5
> cartoon style coil thickness 0.4
> select #5/C:482@CA
1 atom, 1 residue, 1 model selected
> select add #5/C:484
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #5/C:486
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #5/A:484
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #5/A:486
33 atoms, 28 bonds, 5 residues, 1 model selected
> select add #5/A:482
45 atoms, 40 bonds, 6 residues, 1 model selected
> select add #5/A:480
53 atoms, 47 bonds, 7 residues, 1 model selected
> select add #5/C:480
61 atoms, 54 bonds, 8 residues, 1 model selected
> select add #5/C:479
67 atoms, 59 bonds, 9 residues, 1 model selected
> select add #5/A:479
73 atoms, 64 bonds, 10 residues, 1 model selected
> select add #5/A:507
85 atoms, 76 bonds, 11 residues, 1 model selected
> select add #5/C:507
97 atoms, 88 bonds, 12 residues, 1 model selected
> size sel stickRadius 0.3
Changed 90 bond radii
> size sel stickRadius 0.3
Changed 90 bond radii
> size sel stickRadius 0.2
Changed 90 bond radii
> size sel stickRadius 0.3
Changed 90 bond radii
> size sel stickRadius 0.2
Changed 90 bond radii
> size sel stickRadius 0.25
Changed 90 bond radii
> size sel stickRadius 0.22
Changed 90 bond radii
> select subtract #5/C:482
96 atoms, 88 bonds, 11 residues, 1 model selected
> select add #5/C:482
108 atoms, 100 bonds, 12 residues, 1 model selected
> select up
572 atoms, 584 bonds, 78 residues, 1 model selected
> select down
108 atoms, 100 bonds, 12 residues, 1 model selected
> size sel stickRadius 0.25
Changed 102 bond radii
> select clear
> select add #5
16584 atoms, 16988 bonds, 2008 residues, 1 model selected
> size sel stickRadius 0.2
Changed 16988 bond radii
> size sel stickRadius 0.3
Changed 16988 bond radii
> cartoon style coil thickness 0.4
> cartoon style coil thickness 0.45
> cartoon style coil thickness 0.5
> select clear
> show #!3 models
> show #!1 models
> hide #5 models
> select #1/C:364
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3/C:484
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add #3/A:484
19 atoms, 16 bonds, 3 residues, 2 models selected
> select add #1/A:363
24 atoms, 20 bonds, 4 residues, 2 models selected
> select subtract #1/A:363
19 atoms, 16 bonds, 3 residues, 2 models selected
> select add #1/A:364
28 atoms, 24 bonds, 4 residues, 2 models selected
> hide sel atoms
> select #1/C:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #3/C:485
10 atoms, 8 bonds, 2 residues, 2 models selected
> select add #3/A:485
15 atoms, 12 bonds, 3 residues, 2 models selected
> select add #1/A:365
20 atoms, 16 bonds, 4 residues, 2 models selected
> select add #1/C:363
25 atoms, 20 bonds, 5 residues, 2 models selected
> select add #3/C:483
36 atoms, 30 bonds, 6 residues, 2 models selected
> select add #3/A:483
47 atoms, 40 bonds, 7 residues, 2 models selected
> select add #1/A:363
52 atoms, 44 bonds, 8 residues, 2 models selected
> show sel atoms
> show #5 models
> select clear
> hide #5 models
> select add #3/A:485
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #5 models
> select add #1
14485 atoms, 14844 bonds, 8 pseudobonds, 1929 residues, 3 models selected
> select add #3
31412 atoms, 32120 bonds, 9 pseudobonds, 3944 residues, 4 models selected
> select add #5
47996 atoms, 49108 bonds, 9 pseudobonds, 5952 residues, 5 models selected
> size sel stickRadius 0.3
Changed 49108 bond radii
> size sel stickRadius 0.3
Changed 49108 bond radii
> select clear
> hide #!3 models
> show #!4 models
> show #!2 models
> hide #!1 models
> select add #2
15260 atoms, 15640 bonds, 8 pseudobonds, 2020 residues, 2 models selected
> select add #4
32800 atoms, 33532 bonds, 13 pseudobonds, 4072 residues, 5 models selected
> select add #6
48932 atoms, 50056 bonds, 13 pseudobonds, 6032 residues, 6 models selected
> select subtract #6
32800 atoms, 33532 bonds, 13 pseudobonds, 4072 residues, 5 models selected
> select add #5
49384 atoms, 50520 bonds, 13 pseudobonds, 6080 residues, 6 models selected
> size sel stickRadius 0.3
Changed 50520 bond radii
> show #!9 models
> show #!11 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> hide #!11 models
> hide #!9 models
> size sel stickRadius 0.25
Changed 50520 bond radii
> select clear
> select #4/A:484
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #2/C:364
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #4
17540 atoms, 17892 bonds, 5 pseudobonds, 2052 residues, 3 models selected
> show sel cartoons
> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B
56182 atoms, 57488 bonds, 14 pseudobonds, 6930 residues, 24 models selected
> hide sel & #5#!2,4 cartoons
> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D#8/D#9/D#10/D#11/D#12/D#13/D#14/D
56182 atoms, 57488 bonds, 12 pseudobonds, 6930 residues, 22 models selected
> hide sel & #5#!2,4 cartoons
> select clear
> save /Users/edk4001/Desktop/front.png width 3000 height 2272 supersample 3
> transparentBackground true
> ui mousemode right zoom
> save /Users/edk4001/Desktop/front.png width 3000 height 2272 supersample 3
> transparentBackground true
> hide #!2 models
> hide #!4 models
> hide #5 models
> show #!9 models
> show #!11 models
> show #12 models
> select add #9
15260 atoms, 15640 bonds, 8 pseudobonds, 2020 residues, 2 models selected
> select add #11
32800 atoms, 33532 bonds, 13 pseudobonds, 4072 residues, 5 models selected
> select add #12
49384 atoms, 50520 bonds, 13 pseudobonds, 6080 residues, 6 models selected
> cartoon style coil thickness 0.5
> cartoon style coil thickness 0.7
> cartoon style coil thickness 0.75
> select clear
> save /Users/edk4001/Desktop/background.png width 3000 height 2272
> supersample 3 transparentBackground true
> hide #!9 models
> hide #!11 models
> hide #12 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> cartoon style coil thickness 0.5
> show #6 models
> show #!7 models
> select add #1
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select add #3
31412 atoms, 32120 bonds, 9 pseudobonds, 3944 residues, 4 models selected
> select add #6
47544 atoms, 48644 bonds, 9 pseudobonds, 5904 residues, 5 models selected
> select add #8
62024 atoms, 63484 bonds, 17 pseudobonds, 7832 residues, 7 models selected
> select add #7
77460 atoms, 79296 bonds, 21 pseudobonds, 9708 residues, 9 models selected
> select subtract #8
62980 atoms, 64456 bonds, 13 pseudobonds, 7780 residues, 7 models selected
> size sel stickRadius 0.25
Changed 64456 bond radii
> select clear
> hide #6 models
> hide #!7 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #6 models
> select #6/C:485
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/A:484
20 atoms, 18 bonds, 2 residues, 1 model selected
> select subtract #6/A:484
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/A:485
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #6/C:486
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #6/C:484
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #6/A:484
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #6/A:486
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> hide #6 models
> show #!7 models
> select #7/C:485
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7/A:484
20 atoms, 18 bonds, 2 residues, 1 model selected
> select subtract #7/A:484
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7/A:485
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #7/C:486
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #7/C:484
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #7/A:486
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #7/A:484
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> show #6 models
> show #!1 models
> show #!3 models
> select clear
> save "/Users/edk4001/Desktop/front sodium.png" width 3000 height 2272
> supersample 3 transparentBackground true
> color #10 #ff2600 transparency 0
> color #13 #ff7e79 transparency 0
> color #13 #ff2600 transparency 0
> color #14 #ff2600 transparency 0
> hide #!1 models
> hide #!3 models
> hide #6 models
> hide #!7 models
> color #8 #ff2600 transparency 0
> show #!8 models
> select add #8/C:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #8/A:358
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #8/C:363
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #8/C:365
22 atoms, 18 bonds, 4 residues, 1 model selected
> select add #8/A:364
31 atoms, 26 bonds, 5 residues, 1 model selected
> select subtract #8/A:364
22 atoms, 18 bonds, 4 residues, 1 model selected
> select add #8/A:365
27 atoms, 22 bonds, 5 residues, 1 model selected
> select add #8/A:363
32 atoms, 26 bonds, 6 residues, 1 model selected
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> select add #10/C:485
37 atoms, 30 bonds, 7 residues, 2 models selected
> select add #10/C:483
48 atoms, 40 bonds, 8 residues, 2 models selected
> select add #10/A:485
53 atoms, 44 bonds, 9 residues, 2 models selected
> select add #10/A:483@CA
54 atoms, 44 bonds, 10 residues, 2 models selected
> select add #10/A:478
60 atoms, 49 bonds, 11 residues, 2 models selected
> select add #10/C:478@CA
61 atoms, 49 bonds, 12 residues, 2 models selected
> select up
63 atoms, 51 bonds, 12 residues, 2 models selected
> select up
76 atoms, 64 bonds, 12 residues, 2 models selected
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #12 models
> hide #12 models
> show #13 models
> select add #13/C:479
82 atoms, 69 bonds, 13 residues, 3 models selected
> select add #13/A:479
88 atoms, 74 bonds, 14 residues, 3 models selected
> select add #13/C:486
93 atoms, 78 bonds, 15 residues, 3 models selected
> select add #13/A:486
98 atoms, 82 bonds, 16 residues, 3 models selected
> select add #13/A:484
109 atoms, 92 bonds, 17 residues, 3 models selected
> select add #13/C:484
120 atoms, 102 bonds, 18 residues, 3 models selected
> show sel & #13 atoms
> show #!14 models
> hide #13 models
> select add #14/A:479
126 atoms, 107 bonds, 19 residues, 4 models selected
> select add #14/C:479
132 atoms, 112 bonds, 20 residues, 4 models selected
> select add #14/C:484
143 atoms, 122 bonds, 21 residues, 4 models selected
> select add #14/A:484
154 atoms, 132 bonds, 22 residues, 4 models selected
> select add #14/A:486
159 atoms, 136 bonds, 23 residues, 4 models selected
> select add #14/C:486
164 atoms, 140 bonds, 24 residues, 4 models selected
> show sel & #!14 atoms
> show #13 models
> show #!8 models
> show #!10 models
> select ~sel
224564 atoms, 229764 bonds, 52 pseudobonds, 27696 residues, 26 models selected
> hide sel & #13#!8,10,14 cartoons
> hide #!8 models
> show #!8 models
> hide #!10 models
> show #!10 models
> select subtract #1
210084 atoms, 214924 bonds, 44 pseudobonds, 25768 residues, 24 models selected
> select subtract #2
194824 atoms, 199284 bonds, 36 pseudobonds, 23748 residues, 22 models selected
> select subtract #3
177892 atoms, 182004 bonds, 35 pseudobonds, 21732 residues, 20 models selected
> select subtract #4
160352 atoms, 164112 bonds, 30 pseudobonds, 19680 residues, 17 models selected
> select subtract #5
143768 atoms, 147124 bonds, 30 pseudobonds, 17672 residues, 16 models selected
> select subtract #6
127636 atoms, 130600 bonds, 30 pseudobonds, 15712 residues, 15 models selected
> select subtract #7
112200 atoms, 114788 bonds, 26 pseudobonds, 13836 residues, 13 models selected
> select subtract #9
96940 atoms, 99148 bonds, 18 pseudobonds, 11816 residues, 11 models selected
> select subtract #11
79400 atoms, 81256 bonds, 13 pseudobonds, 9764 residues, 8 models selected
> select subtract #12
62816 atoms, 64268 bonds, 13 pseudobonds, 7756 residues, 7 models selected
> hide #!10 models
> show #!10 models
> select add #8
62848 atoms, 64306 bonds, 13 pseudobonds, 7762 residues, 7 models selected
> select add #10
62892 atoms, 64356 bonds, 13 pseudobonds, 7768 residues, 7 models selected
> select add #13
62936 atoms, 64406 bonds, 13 pseudobonds, 7774 residues, 7 models selected
> select add #14
62980 atoms, 64456 bonds, 13 pseudobonds, 7780 residues, 7 models selected
> size sel stickRadius 0.3
Changed 64456 bond radii
> cartoon style coil thickness 0.75
> size sel stickRadius 0.4
Changed 64456 bond radii
> size sel stickRadius 0.35
Changed 64456 bond radii
> size sel stickRadius 0.4
Changed 64456 bond radii
> size sel stickRadius 0.35
Changed 64456 bond radii
> select clear
> save "/Users/edk4001/Desktop/background sodium.png" width 3000 height 2272
> supersample 3 transparentBackground true
> select add #8
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select add #9
29740 atoms, 30480 bonds, 16 pseudobonds, 3948 residues, 4 models selected
> select add #10
46672 atoms, 47760 bonds, 17 pseudobonds, 5964 residues, 6 models selected
> select add #11
64212 atoms, 65652 bonds, 22 pseudobonds, 8016 residues, 9 models selected
> select add #12
80796 atoms, 82640 bonds, 22 pseudobonds, 10024 residues, 10 models selected
> select add #13
96928 atoms, 99164 bonds, 22 pseudobonds, 11984 residues, 11 models selected
> select add #14
112364 atoms, 114976 bonds, 26 pseudobonds, 13860 residues, 13 models selected
> size sel stickRadius 0.4
Changed 114976 bond radii
> cartoon style coil thickness 0.8
> select clear
> save "/Users/edk4001/Desktop/background sodium.png" width 3000 height 2272
> supersample 3 transparentBackground true
> hide #!8 models
> hide #!10 models
> hide #13 models
> hide #!14 models
> show #!9 models
> show #!11 models
> show #12 models
> save /Users/edk4001/Desktop/background.png width 3000 height 2272
> supersample 3 transparentBackground true
> save "/Users/edk4001/Desktop/HCN pore figure v3.cxs"
——— End of log from Sun Jul 24 16:41:39 2022 ———
opened ChimeraX session
> hide #!9 models
> hide #!11 models
> hide #12 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #5 models
> show #6 models
> show #!7 models
> select add #1
14480 atoms, 14840 bonds, 8 pseudobonds, 1928 residues, 2 models selected
> select add #2
29740 atoms, 30480 bonds, 16 pseudobonds, 3948 residues, 4 models selected
> select add #3
46672 atoms, 47760 bonds, 17 pseudobonds, 5964 residues, 6 models selected
> select add #4
64212 atoms, 65652 bonds, 22 pseudobonds, 8016 residues, 9 models selected
> select add #6
80344 atoms, 82176 bonds, 22 pseudobonds, 9976 residues, 10 models selected
> select add #5
96928 atoms, 99164 bonds, 22 pseudobonds, 11984 residues, 11 models selected
> select add #7
112364 atoms, 114976 bonds, 26 pseudobonds, 13860 residues, 13 models selected
> show sel cartoons
> select up
112364 atoms, 114976 bonds, 26 pseudobonds, 13860 residues, 13 models selected
> select #1-2/A-D:1-341
14388 atoms, 14764 bonds, 16 pseudobonds, 1896 residues, 4 models selected
> hide sel cartoons
> select #1-2/A-D:402-800
11680 atoms, 11936 bonds, 1568 residues, 2 models selected
> hide sel cartoons
> select #3-4/A-D:1-461
16180 atoms, 16592 bonds, 1984 residues, 2 models selected
> hide sel cartoons
> select #3-4/A-D:519-1000
14868 atoms, 15060 bonds, 1628 residues, 2 models selected
> hide sel cartoons
> select #5-7/A-D:1-462
23984 atoms, 24604 bonds, 4 pseudobonds, 2876 residues, 4 models selected
> hide sel cartoons
> select #5-7/A-D:520-1000
18884 atoms, 19280 bonds, 2280 residues, 3 models selected
> hide sel cartoons
> ui mousemode right zoom
> select add #1
33364 atoms, 34120 bonds, 8 pseudobonds, 4208 residues, 5 models selected
> select add #3
50296 atoms, 51400 bonds, 9 pseudobonds, 6224 residues, 7 models selected
> select add #2
65556 atoms, 67040 bonds, 17 pseudobonds, 8244 residues, 9 models selected
> select add #4
83096 atoms, 84932 bonds, 22 pseudobonds, 10296 residues, 12 models selected
> select add #5
93188 atoms, 95296 bonds, 22 pseudobonds, 11520 residues, 12 models selected
> select add #6
103124 atoms, 105492 bonds, 22 pseudobonds, 12732 residues, 12 models selected
> select add #7
112364 atoms, 114976 bonds, 26 pseudobonds, 13860 residues, 13 models selected
> hide sel atoms
> hide #!1 models
> hide #!3 models
> hide #6 models
> hide #!7 models
> select clear
> view
[Repeated 1 time(s)]
> view orient
> ui tool show "Side View"
> save "/Users/edk4001/Desktop/pore looking down.cxs"
> save "/Users/edk4001/Desktop/pore looking down.png" width 3000 height 2272
> supersample 3 transparentBackground true
> cartoon style coil thickness 0.4
> save "/Users/edk4001/Desktop/pore looking down.png" width 3000 height 2272
> supersample 3 transparentBackground true
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> hide #5 models
> show #6 models
> show #!7 models
> save "/Users/edk4001/Desktop/pore looking down sodium.png" width 3000 height
> 2272 supersample 3 transparentBackground true
> save "/Users/edk4001/Desktop/HCN pore figure v5.cxs"
——— End of log from Mon Jul 25 09:14:07 2022 ———
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in <lambda>
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
Populating font family aliases took 198 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
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: MacBookPro18,2
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 64 GB
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 4 days 8:56
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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: 1.4
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: 1.5.1
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: 1.18.3
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: 3.7.0
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: 23.1.0
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: 5.1.1
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 → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Volume Viewer after session restore: wrapped C/C++ object of type QScrollArea has been deleted |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #7103