Crash fetching from Toolshed

[chimerax-bug-report@…]

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

[Eric Pettersen]

Duplicate of #16707

Again, the user did a ton of work before the crash occurred