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Opened 9 months ago
Closed 9 months ago
#16755 closed defect (duplicate)
Crash fetching from Toolshed
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202501230202 (2025-01-23 02:02:02 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d
Thread 0x000060b0 (most recent call first):
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 324 in wait
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 622 in wait
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 1392 in run
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00002538 (most recent call first):
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\ssl.py", line 1134 in read
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\ssl.py", line 1278 in recv_into
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\socket.py", line 706 in readinto
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\http\client.py", line 279 in _read_status
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\http\client.py", line 318 in begin
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\http\client.py", line 1378 in getresponse
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 1352 in do_open
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 1391 in https_open
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 496 in _call_chain
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 536 in _open
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 519 in open
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\urllib\request.py", line 216 in urlopen
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 975 in run
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\threading.py", line 995 in _bootstrap
Current thread 0x00005780 (most recent call first):
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
File "D:\ChimeraX 1.10.dev202501230202\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\structure\\\sen\\\TRPV1_18.cxs
Log from Wed Jan 29 15:33:42 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\structure\\\sen\\\fold_v1_ar18_model_0.cif
Chain information for fold_v1_ar18_model_0.cif #1
---
Chain | Description
A B C D | .
E F G H | .
> hide #1/B,C,D,F,G,H
> select /A:78@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
Computing secondary structure
224 atoms, 224 bonds, 30 residues, 1 model selected
> select up
2714 atoms, 2768 bonds, 349 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select #1/A: 96-349
2000 atoms, 2046 bonds, 254 residues, 1 model selected
> hide sel cartoons
> select #1/E:1-114
862 atoms, 884 bonds, 114 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/E:779-839
488 atoms, 498 bonds, 61 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A: 1-95 & #1/E:115-778: style sel stick
Changed 157 atom styles
> show sel target ab
> select #1/E:115-778 & #1/A: 1-95: style sel stick
Changed 166 atom styles
> select #1/E:115-778 & #1/A: 1-95: select #1/E:115-778
5335 atoms, 5455 bonds, 664 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> hide sel target a
> select #1/E:115-778 & #1/A: 1-95: style sel stick
Changed 166 atom styles
> show sel target ab
> ui tool show Clashes
> clashes interModel false intraMol false ignoreHiddenModels true
127 clashes
> clashes interModel false intraMol false ignoreHiddenModels true
127 clashes
> select clear
> select /A:15
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /A:15
23 atoms, 22 bonds, 2 residues, 1 model selected
> select add /A:53
31 atoms, 29 bonds, 3 residues, 1 model selected
> select add /A:54
43 atoms, 41 bonds, 4 residues, 1 model selected
> select add /A:11
52 atoms, 49 bonds, 5 residues, 1 model selected
Drag select of 2 residues
> select subtract /A:4
8 atoms, 1 residue, 1 model selected
> select /E:739
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:34
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /E:739
22 atoms, 21 bonds, 2 residues, 1 model selected
> select add /E:727
30 atoms, 28 bonds, 3 residues, 1 model selected
> select subtract /E:727
22 atoms, 21 bonds, 2 residues, 1 model selected
> select add /E:726
30 atoms, 28 bonds, 3 residues, 1 model selected
> select add /E:722@CB
31 atoms, 28 bonds, 4 residues, 1 model selected
> select subtract /E:722
30 atoms, 28 bonds, 3 residues, 1 model selected
> select add /E:722
41 atoms, 38 bonds, 4 residues, 1 model selected
> select add /A:46
49 atoms, 45 bonds, 5 residues, 1 model selected
> select add /A:8
57 atoms, 52 bonds, 6 residues, 1 model selected
> select add /E:429
68 atoms, 62 bonds, 7 residues, 1 model selected
> select add /E:725
77 atoms, 70 bonds, 8 residues, 1 model selected
> select add /E:717
85 atoms, 77 bonds, 9 residues, 1 model selected
> select clear
> select add /A:62
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add /E:714
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add /E:717
28 atoms, 26 bonds, 3 residues, 1 model selected
> select add /A:49
36 atoms, 33 bonds, 4 residues, 1 model selected
> select subtract /A:49
28 atoms, 26 bonds, 3 residues, 1 model selected
> select add /E:716
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add /E:430
45 atoms, 42 bonds, 5 residues, 1 model selected
> select add /E:434
53 atoms, 49 bonds, 6 residues, 1 model selected
> select add /A:10
62 atoms, 57 bonds, 7 residues, 1 model selected
> select subtract /A:10
53 atoms, 49 bonds, 6 residues, 1 model selected
> select add /E:776
64 atoms, 60 bonds, 7 residues, 1 model selected
> select add /A:11
73 atoms, 68 bonds, 8 residues, 1 model selected
> select add /E:772
84 atoms, 78 bonds, 9 residues, 1 model selected
> select add /A:14
89 atoms, 82 bonds, 10 residues, 1 model selected
> select subtract /A:14
84 atoms, 78 bonds, 9 residues, 1 model selected
> hide sel target a
> select /A:21
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:39
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:35
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:15
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:45
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:54
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add /E:433
31 atoms, 29 bonds, 3 residues, 1 model selected
> hide sel atoms
> select add /E:722
42 atoms, 39 bonds, 4 residues, 1 model selected
> select add /E:725@CA
43 atoms, 39 bonds, 5 residues, 1 model selected
> select subtract /E:725
42 atoms, 39 bonds, 4 residues, 1 model selected
> select add /E:725@CA
43 atoms, 39 bonds, 5 residues, 1 model selected
> select subtract /E:725
42 atoms, 39 bonds, 4 residues, 1 model selected
> select add /E:725
51 atoms, 47 bonds, 5 residues, 1 model selected
> select add /E:726
59 atoms, 54 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add /E:739
70 atoms, 65 bonds, 7 residues, 1 model selected
> hide sel atoms
> select clear
> select add /E:430
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /E:429
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /E:430
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /E:430
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /E:429
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add /A:43
19 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select /A:50@CD1
1 atom, 1 residue, 1 model selected
> select add /E:721@CE1
2 atoms, 2 residues, 1 model selected
> select clear
> select /E:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
113 atoms, 115 bonds, 12 residues, 1 model selected
> select up
6685 atoms, 6839 bonds, 839 residues, 1 model selected
> color sel orange
> color sel byelement
> select add /A:50
6693 atoms, 6846 bonds, 840 residues, 1 model selected
> select add /A:46
6701 atoms, 6853 bonds, 841 residues, 1 model selected
> select add /A:2
6709 atoms, 6860 bonds, 842 residues, 1 model selected
> select subtract /A:2
6701 atoms, 6853 bonds, 841 residues, 1 model selected
> select add /A:1
6709 atoms, 6860 bonds, 842 residues, 1 model selected
> select add /A:49
6717 atoms, 6867 bonds, 843 residues, 1 model selected
> color sel byelement
> select clear
> select /E:713
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
Drag select of 138 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> select /E:554
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
77 atoms, 78 bonds, 9 residues, 1 model selected
> select up
6685 atoms, 6839 bonds, 839 residues, 1 model selected
> select clear
> select /E:554
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
77 atoms, 78 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select /E:544
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
89 atoms, 91 bonds, 12 residues, 1 model selected
> hide sel cartoons
> select /E:530
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
180 atoms, 185 bonds, 21 residues, 1 model selected
> hide sel cartoons
> select /E:537
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
30 atoms, 30 bonds, 3 residues, 1 model selected
Drag select of 6 residues
[Repeated 1 time(s)]
> hide sel cartoons
Drag select of 3 residues
> hide sel atoms
> hide sel cartoons
Drag select of 19 residues
> hide sel cartoons
> select /E:491
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
258 atoms, 265 bonds, 31 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 2 time(s)]
> select /E:466
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
124 atoms, 128 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select clear
> select /E:772
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
247 atoms, 252 bonds, 31 residues, 1 model selected
> hide sel cartoons
Drag select of 4 atoms, 3 bonds
> hide sel cartoons
> hide sel atoms
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /E:437
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add /A:1
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add /A:46
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add /A:50
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add /E:721
46 atoms, 43 bonds, 5 residues, 1 model selected
> select add /A:49
54 atoms, 50 bonds, 6 residues, 1 model selected
> select add /E:720
59 atoms, 54 bonds, 7 residues, 1 model selected
> select subtract /E:720
54 atoms, 50 bonds, 6 residues, 1 model selected
> select add /E:720
59 atoms, 54 bonds, 7 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select /E:708
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
175 atoms, 176 bonds, 21 residues, 1 model selected
> hide sel cartoons
> select /E:714
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select /E:717
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 4 residues, 1 model selected
> hide sel cartoons
Drag select of 17 residues
[Repeated 1 time(s)]Drag select of 14 residues
> hide sel cartoons
> select /E:440
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/E:115-400
2230 atoms, 2267 bonds, 286 residues, 1 model selected
> select #1/E:115-440
2584 atoms, 2633 bonds, 326 residues, 1 model selected
> surface sel
> transparency (#!1 & sel) 80
> save C:/Windows/System32/114452.cxs
——— End of log from Wed Jan 29 15:33:42 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Selection Inspector"
> ui tool show "Side View"
> ui mousemode right clip
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\structure\\\des\\\TRPV1_AR10.cxs
Log from Fri Jan 24 15:30:02 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501230202 (2025-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\zhyau\\\OneDrive\\\Desktop\\\fold_v1_ar10_model_0.cif
Chain information for fold_v1_ar10_model_0.cif #1
---
Chain | Description
A B C D | .
E F G H | .
> select #1/B,C,D,F,G,H
27810 atoms, 28446 bonds, 3501 residues, 1 model selected
> hide sel atoms
> select #1/A,E
9270 atoms, 9482 bonds, 1167 residues, 1 model selected
> hide sel atoms
> show sel atoms
> show sel cartoons
Computing secondary structure
> style sel stick
Changed 9270 atom styles
> hide sel atoms
> surface sel
> select clear
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 36547 of 936656
triangles, 21 residues
> hide sel atoms
> hide sel
> hide sel surfaces
> hide sel cartoons
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 67580 of 936656
triangles, 44 residues
> hide sel cartoons
> select /A:214@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
69 atoms, 69 bonds, 8 residues, 2 models selected
> select up
2585 atoms, 2643 bonds, 328 residues, 2 models selected
> hide sel surfaces
> hide #1/A:1-244
> select #1/A:1-244
1931 atoms, 1976 bonds, 244 residues, 1 model selected
> hide sel
> hide sel cartoons
> select clear
> select /A:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:328
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/E:1-100
756 atoms, 775 bonds, 100 residues, 1 model selected
> select #1/E:1-1100
6685 atoms, 6839 bonds, 839 residues, 1 model selected
> select #1/E:1-110
823 atoms, 844 bonds, 110 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> hide sel
> hide sel surfaces
> select /E:434@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
215 atoms, 223 bonds, 24 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> select /E:818@CA
1 atom, 1 residue, 1 model selected
> select /E:818@CZ
1 atom, 1 residue, 1 model selected
> select /E:817@CD2
1 atom, 1 residue, 1 model selected
> select /E:818@N
1 atom, 1 residue, 1 model selected
> select e
Expected an objects specifier or a keyword
> select E
Expected an objects specifier or a keyword
> select #1/E:790-818
241 atoms, 246 bonds, 29 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 103123 of 936656
triangles, 95 residues
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 57894 of 936656
triangles, 53 residues
> hide sel surfaces
> hide sel cartoons
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 87854 of 936656
triangles, 103 residues
> hide sel cartoons
> hide sel surfaces
> undo
[Repeated 7 time(s)]
> select clear
> select /E:484
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
258 atoms, 265 bonds, 31 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> select down
258 atoms, 265 bonds, 31 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> surface (#!1 & sel)
> select #1/E:790-818
241 atoms, 246 bonds, 29 residues, 1 model selected
> select clear
> transparency 80
> select /E:199@CB
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
105 atoms, 107 bonds, 13 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> color (#!1 & sel) orange
> transparency (#!1 & sel) 70
> select clear
> select /A:291
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
194 atoms, 200 bonds, 22 residues, 2 models selected
> select up
2585 atoms, 2643 bonds, 328 residues, 2 models selected
> color (#!1 & sel) light sea green
> select clear
> select /E:800@CB
1 atom, 1 residue, 1 model selected
> select #1/E:800-818
160 atoms, 163 bonds, 19 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 23784 of 936656
triangles, 14 residues
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 36115 of 936656
triangles, 21 residues
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select /E:66@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
811 atoms, 831 bonds, 108 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> select /E:672@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
139 atoms, 141 bonds, 17 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> select down
139 atoms, 141 bonds, 17 residues, 2 models selected
> select /E:550@O
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select up
89 atoms, 91 bonds, 12 residues, 2 models selected
> select /E:115
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /E /F /G /H
Alignment identifier is 1
> select /E-H:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:419-480
2160 atoms, 2232 bonds, 248 residues, 1 model selected
> select /E-H:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:419-606
6340 atoms, 6528 bonds, 752 residues, 1 model selected
> hide sel surfaces
> undo
> show sel surfaces
[Repeated 2 time(s)]
> select clear
> select /H:491@CD2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
258 atoms, 265 bonds, 31 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select /F:444@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
215 atoms, 223 bonds, 24 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> hide sel surfaces
> select /G:583@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
181 atoms, 186 bonds, 22 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> hide sel surfaces
> select clear
> select /E:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
73 atoms, 73 bonds, 9 residues, 2 models selected
> select up
6685 atoms, 6839 bonds, 839 residues, 2 models selected
> surface (#!1 & sel)
> select /E-H:1
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:1-114
3448 atoms, 3536 bonds, 456 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> select /E:825@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
298 atoms, 304 bonds, 37 residues, 2 models selected
> hide sel surfaces
> select /E:712@C
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
175 atoms, 176 bonds, 21 residues, 2 models selected
> select clear
> select
> /E-H:2-6,115-123,127-130,133-140,147-149,158-164,172-183,187-191,205-211,215-223,235-237,252-258,262-270,288-295,300-320,326-328,337-344,347-354,361-366,396-401,413-415,419-454,470-500,504-510,512-532,536-559,561-599,604-606,631-641,657-712,714-719,786-790,800-802
12808 atoms, 12948 bonds, 1572 residues, 1 model selected
> select clear
> select /E-H:162
20 atoms, 16 bonds, 4 residues, 1 model selected
> select /E-H:162-224
1988 atoms, 2008 bonds, 252 residues, 1 model selected
> select /E-H:162
20 atoms, 16 bonds, 4 residues, 1 model selected
> select /E-H:162-194
1012 atoms, 1016 bonds, 132 residues, 1 model selected
> select /E-H:195-225
992 atoms, 1004 bonds, 124 residues, 1 model selected
> select /E-H:195-222
908 atoms, 920 bonds, 112 residues, 1 model selected
> select /E-H:261-262
68 atoms, 64 bonds, 8 residues, 1 model selected
> select /E-H:261-292
988 atoms, 1004 bonds, 128 residues, 1 model selected
> select /E-H:325-326
68 atoms, 64 bonds, 8 residues, 1 model selected
> select /E-H:325-328
140 atoms, 136 bonds, 16 residues, 1 model selected
> select /E-H:413
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:413-415
96 atoms, 92 bonds, 12 residues, 1 model selected
> select /E-H:434
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:434-436
124 atoms, 128 bonds, 12 residues, 1 model selected
> select /E-H:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:419-599
6124 atoms, 6312 bonds, 724 residues, 1 model selected
> select /E-H:407
28 atoms, 24 bonds, 4 residues, 1 model selected
> select /E-H:407-408
56 atoms, 56 bonds, 8 residues, 1 model selected
> select /E-H:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:419-454
1312 atoms, 1356 bonds, 144 residues, 1 model selected
> select /E-H:433
44 atoms, 40 bonds, 4 residues, 1 model selected
> select /E-H:433-436
168 atoms, 172 bonds, 16 residues, 1 model selected
> select /E-H:459
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /E-H:459-464
188 atoms, 196 bonds, 24 residues, 1 model selected
> select /E-H:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /E-H:419-454
1312 atoms, 1356 bonds, 144 residues, 1 model selected
> select /E-H:437-438
76 atoms, 76 bonds, 8 residues, 1 model selected
> select /E-H:437-454
628 atoms, 652 bonds, 72 residues, 1 model selected
> select /E-H:432
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /E-H:432-606
5860 atoms, 6036 bonds, 700 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> select /E-H:396
28 atoms, 24 bonds, 4 residues, 1 model selected
> select /E-H:396-454
2036 atoms, 2096 bonds, 236 residues, 1 model selected
> select /E-H:470
28 atoms, 24 bonds, 4 residues, 1 model selected
> select /E-H:470-681
6904 atoms, 7084 bonds, 848 residues, 1 model selected
> select /E-H:470
28 atoms, 24 bonds, 4 residues, 1 model selected
> select /E-H:470-719
8144 atoms, 8336 bonds, 1000 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 34487 of 936656
triangles
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 38618 of 936656
triangles
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 1352 of 936656
triangles
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 39714 of 936656
triangles
> select clear
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 34130 of 936656
triangles
> select clear
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 26393 of 936656
triangles
> select clear
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 6865 of 936656
triangles
> select clear
> select /E:463@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
124 atoms, 128 bonds, 15 residues, 2 models selected
> hide sel surfaces
> select clear
Drag select of fold_v1_ar10_model_0.cif_E SES surface, 9526 of 936656
triangles
> select /E:451@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
215 atoms, 223 bonds, 24 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> set bgColor white
> select /E:427@NE1
1 atom, 1 residue, 1 model selected
> select /E:427@CH2
1 atom, 1 residue, 1 model selected
> select /E:428@CB
1 atom, 1 residue, 1 model selected
> select add /E:424@CG
2 atoms, 2 residues, 2 models selected
> select add /E:427@NE1
3 atoms, 3 residues, 2 models selected
> select add /E:427@CD1
4 atoms, 3 residues, 2 models selected
> select clear
> select /E:427@NE1
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /E:427@CZ2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /E:427@CH2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /E:125@CB
1 atom, 1 residue, 1 model selected
> select /E:427@CZ3
1 atom, 1 residue, 1 model selected
> select /E:430
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/E:115-430:<3.5 & #1/A: 245-328
132 atoms, 130 bonds, 15 residues, 1 model selected
> select #1/E:115-430:<4.0 & #1/A: 245-328
144 atoms, 142 bonds, 16 residues, 1 model selected
> select clear
> select /E:427@CZ3
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #1/E:115-430:<4.0 & #1/A: 245-328
144 atoms, 142 bonds, 16 residues, 1 model selected
> name frozen A_E sel
> select #1/A: 245-328:<4.0 & #1/E:115-430
130 atoms, 117 bonds, 16 residues, 1 model selected
> name frozen E_A sel
> show (#!1 & sel-residues & sidechain) target ab
> style (#!1 & sel) stick
Changed 130 atom styles
> color (#!1 & sel) byelement
> select A_E
2585 atoms, 142 bonds, 328 residues, 1 model selected
> style (#!1 & sel) stick
Changed 2585 atom styles
> select E_A
6685 atoms, 117 bonds, 839 residues, 1 model selected
> select A_E
2585 atoms, 142 bonds, 328 residues, 1 model selected
> style (#!1 & sel) stick
Changed 2585 atom styles
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> style (#!1 & sel) stick
Changed 2585 atom styles
> select clear
> select A_E
2585 atoms, 142 bonds, 328 residues, 1 model selected
> select #1/E:115-430:<4.0 & #1/A: 245-328
144 atoms, 142 bonds, 16 residues, 1 model selected
> name frozen A_E sel
> style (#!1 & sel) stick
Changed 144 atom styles
> hide #* target a
> show (#!1 & sel) target ab
> color (#!1 & sel) byelement
> select E_A
6685 atoms, 117 bonds, 839 residues, 1 model selected
> show (#!1 & sel) target ab
> undo
> select #1/A: 245-328:<4.0 & #1/E:115-430
130 atoms, 117 bonds, 16 residues, 1 model selected
> show (#!1 & sel) target ab
> name frozen E_A sel
> ui tool show H-Bonds
> save C:/Users/zhyau/2.cxs
> save C:/Users/zhyau/Desktop/TRPV1_AR10.cxs
——— End of log from Fri Jan 24 15:30:02 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 566.07
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: zh_CN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming F15 FX507VI_FX507VI
OS: Microsoft Windows 11 家庭版 (Build 26100)
Memory: 16,780,505,088
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i7-13620H
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.12.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.17
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501230202
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.43
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.15.4
fonttools: 4.55.4
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.2
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash fetching from Toolshed |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #16707
Again, the user did a ton of work before the crash occurred