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 0x00003fac (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 0x00005f48 (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 =====
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

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C /D

Alignment identifier is 1  
Computing secondary structure  

> select /A-D:1

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /A-D:1-94

2840 atoms, 2868 bonds, 376 residues, 1 model selected  

> select /A-D:99-130

968 atoms, 980 bonds, 128 residues, 1 model selected  

> select /A-D:99-283

5912 atoms, 6048 bonds, 740 residues, 1 model selected  

> select /A-D:99

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /A-D:99-349

7936 atoms, 8120 bonds, 1004 residues, 1 model selected  

> hide sel atoms

> select /E:831@O

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

298 atoms, 304 bonds, 37 residues, 1 model selected  

> hide sel atoms

> select /E:47@N

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

862 atoms, 884 bonds, 114 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> select /A:71@C

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

224 atoms, 224 bonds, 30 residues, 1 model selected  

> select up

2714 atoms, 2768 bonds, 349 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select clear

Drag select of 42 atoms, 3 residues  

> select clear

> select /A:258

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

> select up

91 atoms, 92 bonds, 11 residues, 1 model selected  

> select up

2714 atoms, 2768 bonds, 349 residues, 1 model selected  

> select clear

> select /E:735@O

1 atom, 1 residue, 1 model selected  

> select clear

> select /A-D:1

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /A-D:1-97

2896 atoms, 2924 bonds, 388 residues, 1 model selected  

> select /A-D:1

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /A-D:1-95

2856 atoms, 2884 bonds, 380 residues, 1 model selected  

> select #1/A: 1-98 & #1/E:115-709: style sel stick

Changed 52 atom styles  

> show sel target ab

> select #1/E:115-709

4774 atoms, 4880 bonds, 595 residues, 1 model selected  

> select #1/E:115-740

5026 atoms, 5137 bonds, 626 residues, 1 model selected  

> select #1/E:115-760

5199 atoms, 5317 bonds, 646 residues, 1 model selected  

> select #1/E:115-772

5289 atoms, 5408 bonds, 658 residues, 1 model selected  

> select #1/A: 1-98 & #1/E:115-772: name frozen E_A sel

> select #1/E:115-772 & #1/A: 1-98: style sel stick

Changed 155 atom styles  

> select #1/E:115-772

5289 atoms, 5408 bonds, 658 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #1/E:115-782

5367 atoms, 5487 bonds, 668 residues, 1 model selected  

> select #1/E:782-802

169 atoms, 172 bonds, 21 residues, 1 model selected  

> hide sel atoms

> select #1/E:720-781

496 atoms, 508 bonds, 62 residues, 1 model selected  

> style sel stick

Changed 496 atom styles  

> hide sel target a

> cartoon sel

> select #1/E:115-782 & #1/A: 1-98: style sel stick

Changed 166 atom styles  

> show sel target ab

> name frozen A_E sel

> select #1/A: 1-98 & #1/E:115-782: style sel stick

Changed 157 atom styles  

> show sel target ab

> name frozen E_A sel

> select A_E

166 atoms, 161 bonds, 18 residues, 1 model selected  

> select add E_A

323 atoms, 309 bonds, 36 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ffff00 restrict cross interModel false intraMol false
> intraRes false reveal true

3 hydrogen bonds found  

> hbonds sel color #ffff00 restrict cross interModel false intraMol false
> intraRes false reveal true

3 hydrogen bonds found  

> select /F:153@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

60 atoms, 60 bonds, 8 residues, 1 model selected  

> select down

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

> hide sel atoms

> select /A:36

11 atoms, 10 bonds, 1 residue, 1 model selected  

> cartoon hide sel

> undo

> hide sel target a

> select A_E

166 atoms, 161 bonds, 18 residues, 1 model selected  

> ui tool show Clashes

> clashes interModel false intraMol false ignoreHiddenModels true

127 clashes  

> clashes interModel false intraMol false ignoreHiddenModels true

127 clashes  

> select #1/E:115-782 & #1/A: 1-98: select #1/A: 1-98 & #1/E:115-782: 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:21

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

> hide sel target a

> select /E:772

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel target a

> select /A:8

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

> select /A:11

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

> select add /A:8

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:62

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

> select add /A:54@CB

30 atoms, 28 bonds, 4 residues, 1 model selected  

> select add /A:54@CD2

31 atoms, 28 bonds, 4 residues, 1 model selected  

> select add /A:53

39 atoms, 37 bonds, 5 residues, 1 model selected  

> select add /A:15

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

> select add /A:43@CB

52 atoms, 49 bonds, 7 residues, 1 model selected  

> select add /E:722

63 atoms, 59 bonds, 8 residues, 1 model selected  

> select add /E:725

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

> select add /E:430

83 atoms, 78 bonds, 10 residues, 1 model selected  

> select clear

> select add /A:11

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

> select add /A:8

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:54

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

> select add /E:433

40 atoms, 37 bonds, 4 residues, 1 model selected  

> select add /A:62

52 atoms, 49 bonds, 5 residues, 1 model selected  

> select add /A:45@CB

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

> select add /A:38

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

> select add /A:15

76 atoms, 72 bonds, 8 residues, 1 model selected  

> select add /E:776

87 atoms, 83 bonds, 9 residues, 1 model selected  

> select add /E:716

93 atoms, 88 bonds, 10 residues, 1 model selected  

> select add /E:714

101 atoms, 95 bonds, 11 residues, 1 model selected  

> select add /E:434

109 atoms, 102 bonds, 12 residues, 1 model selected  

> hide sel target a

> select clear

> select add /E:717

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

> select add /E:721

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

> select clear

> select add /E:717

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

> select add /A:45@CD

9 atoms, 7 bonds, 2 residues, 1 model selected  

> hide sel target a

> select add /E:722@CA

10 atoms, 8 bonds, 3 residues, 1 model selected  

> select add /E:726

18 atoms, 15 bonds, 4 residues, 1 model selected  

> select add /E:739

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

> select add /A:45@OE2

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

> select add /A:45@OE1

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

> select add /A:45@CG

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

> select add /A:43

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

> select add /A:39

47 atoms, 39 bonds, 7 residues, 1 model selected  

> select add /A:35

52 atoms, 43 bonds, 8 residues, 1 model selected  

> select subtract /A:45@OE1

51 atoms, 43 bonds, 8 residues, 1 model selected  

> select subtract /A:45@CG

50 atoms, 43 bonds, 8 residues, 1 model selected  

> select subtract /A:45@OE2

49 atoms, 43 bonds, 8 residues, 1 model selected  

> select add /A:45@OE2

50 atoms, 43 bonds, 8 residues, 1 model selected  

> hide sel target a

> select clear

> select /A:45@OE1

1 atom, 1 residue, 1 model selected  

> select add /A:45@CG

2 atoms, 1 residue, 1 model selected  

> select add /E:722@NE

3 atoms, 2 residues, 1 model selected  

> hide sel target a

> select clear

> select add /E:722@CG

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add /E:722@CZ

2 atoms, 2 bonds, 1 residue, 1 model selected  

> select add /E:722@NH2

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select subtract /E:722@CZ

2 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select /E:722@CD

1 atom, 1 residue, 1 model selected  

> select /E:722@CB

1 atom, 1 residue, 1 model selected  

> select add /E:722@CD

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

> hide sel atoms

> hide sel target ab

> select clear

> select /E:722@CZ

1 atom, 1 residue, 1 model selected  

> select /E:722@NH1

1 atom, 1 residue, 1 model selected  

> select add /E:722@CZ

2 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select add /E:725@CA

3 atoms, 2 residues, 1 model selected  

> hide sel atoms

> hide sel target ab

> select clear

> select add /E:725@CB

1 atom, 1 residue, 1 model selected  

> select add /E:725@CG

2 atoms, 1 residue, 1 model selected  

> select add /E:725@CD

3 atoms, 1 residue, 1 model selected  

> select add /E:725@CE

4 atoms, 1 residue, 1 model selected  

> select add /E:725@NZ

5 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select add /E:429

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

> hide sel atoms

> select /E:430

11 atoms, 11 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add /E:713

22 atoms, 22 bonds, 2 residues, 1 model selected  

> select clear

> select add /E:713@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> hide sel atoms

> hide sel target b

> select add /E:713@CB

1 atom, 7 bonds, 1 residue, 1 model selected  

> select add /E:713@CG

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

> select add /E:713@CD1

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

> select add /E:713@CE1

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

> select add /E:713@CZ

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

> select add /E:713@CE2

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

> select add /E:713@CD2

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

> hide sel atoms

> select add /A:53

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

> hide sel target a

> select clear

Drag select of 61 residues  

> hide sel cartoons

> select clear

> select /A:272

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

> select up

34 atoms, 33 bonds, 5 residues, 1 model selected  

> hide sel cartoons

Drag select of 99 residues  

> hide sel cartoons

Drag select of 55 residues  

> hide sel cartoons

Drag select of 1 residues  
Drag select of 15 residues  

> hide sel atoms

> hide sel cartoons

Drag select of 16 residues  

> hide sel cartoons

Drag select of 1 residues  

> hide sel atoms

> hide sel cartoons

> select #1/E:115-782

5367 atoms, 5487 bonds, 668 residues, 1 model selected  

> color sel orange

> surface sel

> transparency (#!1 & sel) 80

> set bgColor #ffffff00

> select /E:669@CG2

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 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  
Drag select of fold_v1_ar18_model_0.cif_E SES surface, 135599 of 938626
triangles, 122 residues  

> hide sel atoms

> hide sel cartoons

> surface hidePatches (#!1 & sel)

> select /E:484@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select up

258 atoms, 265 bonds, 31 residues, 2 models selected  

> hide sel cartoons

> surface hidePatches (#!1 & sel)

> select /E:522@CB

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select up

180 atoms, 185 bonds, 21 residues, 2 models selected  

> hide sel cartoons

> surface hidePatches (#!1 & sel)

> select /E:550

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

89 atoms, 91 bonds, 12 residues, 2 models selected  

> hide sel cartoons

> surface hidePatches (#!1 & sel)

Drag select of fold_v1_ar18_model_0.cif_E SES surface, 41397 of 938626
triangles, 38 residues  

> hide sel cartoons

> surface hidePatches (#!1 & sel)

> VIEW

Unknown command: VIEW  

> view

> viewdockx

No suitable models found for ViewDockX  

> select add /E:441@CG2

322 atoms, 39 residues, 2 models selected  

> select clear

> select add /A:1

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

> select add /E:441@CG2

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select subtract /E:441@CG2

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select add /E:441@CG2

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select add /E:441@CG1

10 atoms, 7 bonds, 2 residues, 2 models selected  

> select add /E:441@O

11 atoms, 7 bonds, 2 residues, 2 models selected  
Drag select of fold_v1_ar18_model_0.cif_E SES surface, 773 of 938626
triangles, 2 residues  

> select clear

> select add /A:1

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

> select add /E:441@CG1

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select subtract /E:441@CG1

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select add /E:441@CG1

9 atoms, 7 bonds, 2 residues, 1 model selected  

> select subtract /E:441@CG1

8 atoms, 7 bonds, 1 residue, 2 models selected  

> select add /E:437

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

> select add /A:50

27 atoms, 25 bonds, 3 residues, 2 models selected  

> select add /E:721

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select add /E:720@CA

39 atoms, 36 bonds, 5 residues, 2 models selected  

> select subtract /E:720

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select add /E:720

43 atoms, 40 bonds, 5 residues, 2 models selected  

> select subtract /E:720@O

42 atoms, 38 bonds, 5 residues, 2 models selected  

> select add /E:439@CE2

43 atoms, 38 bonds, 6 residues, 2 models selected  

> select subtract /E:439@CE2

42 atoms, 38 bonds, 5 residues, 2 models selected  

> select subtract /E:721

31 atoms, 28 bonds, 4 residues, 2 models selected  

> select add /E:721

42 atoms, 39 bonds, 5 residues, 2 models selected  

> select clear

> select add /E:437

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add /A:1

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add /E:720

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select add /A:49

32 atoms, 29 bonds, 4 residues, 2 models selected  

> select add /A:50

40 atoms, 36 bonds, 5 residues, 2 models selected  

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> select add /E:721

51 atoms, 47 bonds, 6 residues, 2 models selected  

> select subtract /E:721

40 atoms, 36 bonds, 5 residues, 2 models selected  

> select clear

> select add /E:721

11 atoms, 11 bonds, 1 residue, 1 model selected  

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> color (#!1 & sel) byelement

> color (#!1 & sel) orange

> select add /A:1

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select clear

> select /A:1

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

> color sel byelement

> undo

> select add /A:50

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

> select add /A:49

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select add /A:46

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select add /E:437

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

> select add /E:721

54 atoms, 50 bonds, 6 residues, 2 models selected  

> select add /E:720

59 atoms, 54 bonds, 7 residues, 2 models selected  

> color (#!1 & sel) byelement

> select clear


===== 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\\\sen\\\TRPV1_AR041.cxs

Log from Wed Jan 29 13:35:06 2025UCSF 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_AR04.cxs

Log from Mon Jan 27 13:20:08 2025UCSF 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\\\TRPV1_AR04.cxs

Log from Mon Jan 27 12:33:51 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_ar04_model_0.cif

Chain information for fold_v1_ar04_model_0.cif #1  
---  
Chain | Description  
A B C D | .  
E F G H | .  
  

> select /B:1-363

2797 atoms, 2854 bonds, 363 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /C:1-363

2797 atoms, 2854 bonds, 363 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /D:1-363

2797 atoms, 2854 bonds, 363 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /F:1-839

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> hide sel atoms

> select /F:1-839

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> hide sel atoms

> select /G:1-839

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> hide sel atoms

> select /H:1-839

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> hide sel atoms

> select #1/A: 245-328:<4.0 & #1/E:115-430

84 atoms, 80 bonds, 11 residues, 1 model selected  

> select down

84 atoms, 80 bonds, 11 residues, 1 model selected  

> select #1/E:115-430:<4.0 & #1/A: 245-328

95 atoms, 89 bonds, 11 residues, 1 model selected  

> select /E:29@CB

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

Computing secondary structure  
811 atoms, 831 bonds, 108 residues, 1 model selected  

> hide sel atoms

> select /A:226@O

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

96 atoms, 97 bonds, 11 residues, 1 model selected  

> select up

2797 atoms, 2854 bonds, 363 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C /D

Alignment identifier is 1  

> select /A-D:1

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /A-D:1-94

2820 atoms, 2860 bonds, 376 residues, 1 model selected  

> select /A-D:123

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select /A-D:123-363

7616 atoms, 7796 bonds, 964 residues, 1 model selected  

> hide sel atoms

> select /A-D:118

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A-D:118-122

156 atoms, 156 bonds, 20 residues, 1 model selected  

> hide sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /E /F /G /H

Alignment identifier is 2  

> select /E-H:722

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:722-839

3788 atoms, 3876 bonds, 472 residues, 1 model selected  

> select /E-H:798

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:798-839

1340 atoms, 1364 bonds, 168 residues, 1 model selected  

> select /E-H:799

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /E-H:799-837

1220 atoms, 1244 bonds, 156 residues, 1 model selected  

> select /E-H:810

28 atoms, 28 bonds, 4 residues, 1 model selected  

> select /E-H:810-839

944 atoms, 964 bonds, 120 residues, 1 model selected  

> select /E-H:808

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select /E-H:808-839

1008 atoms, 1028 bonds, 128 residues, 1 model selected  

> hide sel atoms

> select /E:251@CD2

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

115 atoms, 118 bonds, 14 residues, 1 model selected  

> select up

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> save C:/Users/zhyau/4.cxs

——— End of log from Mon Jan 27 12:33:51 2025 ———

> view name session-start

opened ChimeraX session  

> select clear

> select /E:497@CD1

1 atom, 1 residue, 1 model selected  

> select /E-H:1

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /E-H:1-65

2016 atoms, 2084 bonds, 260 residues, 1 model selected  

> select /A-D:1

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /A-D:1-106

3132 atoms, 3172 bonds, 424 residues, 1 model selected  

> select /A-D:111

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select /A-D:111-112

40 atoms, 36 bonds, 8 residues, 1 model selected  

> select /A-D:117

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A-D:1-117

3416 atoms, 3456 bonds, 468 residues, 1 model selected  

> select /A-D:117

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A-D:116-117

52 atoms, 48 bonds, 8 residues, 1 model selected  

> select /A-D:107-117

284 atoms, 280 bonds, 44 residues, 1 model selected  

> select /A-D:117

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A-D:98-117

488 atoms, 484 bonds, 80 residues, 1 model selected  

> select /A-D:100

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /A-D:100-117

448 atoms, 444 bonds, 72 residues, 1 model selected  

> select /A-D:103

16 atoms, 12 bonds, 4 residues, 1 model selected  

> select /A-D:103-117

364 atoms, 360 bonds, 60 residues, 1 model selected  

> select /A-D:102

20 atoms, 16 bonds, 4 residues, 1 model selected  

> select /A-D:1-102

3052 atoms, 3092 bonds, 408 residues, 1 model selected  

> select #1/E:115-430:<4.0 & #1/A: 1-102

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select /E-H:66

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select /E-H:66-114

1432 atoms, 1448 bonds, 196 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-119

188 atoms, 188 bonds, 20 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-149

1140 atoms, 1148 bonds, 140 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-295

5632 atoms, 5716 bonds, 724 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-354

7404 atoms, 7512 bonds, 960 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-390

8612 atoms, 8760 bonds, 1104 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-390

8612 atoms, 8760 bonds, 1104 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-360

7628 atoms, 7740 bonds, 984 residues, 1 model selected  

> select /E-H:384

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /E-H:142-384

7576 atoms, 7716 bonds, 972 residues, 1 model selected  

> select /E-H:114

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select /E-H:114-293

5600 atoms, 5684 bonds, 720 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-325

6568 atoms, 6668 bonds, 844 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-388

8552 atoms, 8700 bonds, 1096 residues, 1 model selected  

> select /E-H:455

48 atoms, 48 bonds, 4 residues, 1 model selected  

> select /E-H:231-455

7204 atoms, 7380 bonds, 900 residues, 1 model selected  

> select /E-H:439-440

88 atoms, 92 bonds, 8 residues, 1 model selected  

> select /E-H:376-440

2168 atoms, 2224 bonds, 260 residues, 1 model selected  

> select /E-H:375-376

64 atoms, 64 bonds, 8 residues, 1 model selected  

> select /E-H:312-376

2048 atoms, 2088 bonds, 260 residues, 1 model selected  

> select /E-H:415-416

60 atoms, 56 bonds, 8 residues, 1 model selected  

> select /E-H:289-416

4008 atoms, 4084 bonds, 512 residues, 1 model selected  

> select /E-H:441

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select /E-H:417-441

940 atoms, 972 bonds, 100 residues, 1 model selected  

> select /E-H:115

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:115-289

5448 atoms, 5528 bonds, 700 residues, 1 model selected  

> select /E-H:430

44 atoms, 44 bonds, 4 residues, 1 model selected  

> select /E-H:287-430

4580 atoms, 4672 bonds, 576 residues, 1 model selected  

> select /E-H:430

44 atoms, 44 bonds, 4 residues, 1 model selected  

> select /E-H:115-430

9940 atoms, 10116 bonds, 1264 residues, 1 model selected  

> select /E-H:103-104

52 atoms, 48 bonds, 8 residues, 1 model selected  

> select /E-H:103

24 atoms, 20 bonds, 4 residues, 1 model selected  

> select /E-H:101

24 atoms, 20 bonds, 4 residues, 1 model selected  

> select /E-H:101-344

7536 atoms, 7652 bonds, 976 residues, 1 model selected  

> select /E-H:364

44 atoms, 40 bonds, 4 residues, 1 model selected  

> select /E-H:101-364

8184 atoms, 8312 bonds, 1056 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> undo

[Repeated 1 time(s)]

> select clear

> select /E-H:101

24 atoms, 20 bonds, 4 residues, 1 model selected  

> select /E-H:101-366

8256 atoms, 8388 bonds, 1064 residues, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> select /E-H:101

24 atoms, 20 bonds, 4 residues, 1 model selected  

> select /E-H:101-366

8256 atoms, 8388 bonds, 1064 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> hide sel atoms

> select clear

Drag select of 448 residues  

> select up

5032 atoms, 5124 bonds, 655 residues, 1 model selected  

> hide sel cartoons

Drag select of 63 residues  

> hide sel cartoons

> select /F:190

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

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

> select up

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> hide sel cartoons

> save C:/Users/zhyau/OneDrive/Desktop/TRPV1_AR04.cxs

——— End of log from Mon Jan 27 13:20:08 2025 ———

> view name session-start

opened ChimeraX session  

> select /E:574@CG2

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

139 atoms, 139 bonds, 17 residues, 1 model selected  

> select up

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> surface hidePatches sel

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> show sel cartoons

> select clear

> select /E:3

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

> select up

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

> select up

6685 atoms, 6839 bonds, 839 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 31 residues  

> hide sel cartoons

Drag select of 7 residues  

> hide sel cartoons

Drag select of 2 residues  

> hide sel cartoons

> select clear

Drag select of 10 residues  

> hide sel cartoons

Drag select of 3 residues  
Drag select of 16 residues  

> hide sel atoms

> hide sel cartoons

Drag select of 28 residues  

> select up

811 atoms, 831 bonds, 108 residues, 1 model selected  

> hide sel cartoons

> select /E:836

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

> select up

252 atoms, 257 bonds, 32 residues, 1 model selected  

> hide sel cartoons

> select /A:46@OG

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

21 atoms, 21 bonds, 3 residues, 1 model selected  

> select up

2797 atoms, 2854 bonds, 363 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

Drag select of 14 residues  

> select up

345 atoms, 348 bonds, 44 residues, 1 model selected  

> select up

2797 atoms, 2854 bonds, 363 residues, 1 model selected  

> select clear

Drag select of 179 residues  

> hide sel cartoons

Drag select of 12 residues  

> hide sel cartoons

Drag select of 13 residues  

> select clear

Drag select of 30 residues  

> hide sel cartoons

> select clear

[Repeated 1 time(s)]

> select /A:285

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

> select up

34 atoms, 33 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> select /A:282

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

> select add /A:288

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

> hide sel cartoons

> select /A:260

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add /A:259

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:258

24 atoms, 22 bonds, 3 residues, 1 model selected  

> hide sel cartoons

Drag select of 2 residues  
Drag select of 14 residues  

> select up

393 atoms, 401 bonds, 49 residues, 1 model selected  

> hide sel cartoons

> select add /A:362

399 atoms, 406 bonds, 50 residues, 1 model selected  

> select up

407 atoms, 415 bonds, 51 residues, 1 model selected  

> hide sel cartoons

> select #1/A: 1-108 & #1/E:115-709:<4.0

42 atoms, 42 bonds, 4 residues, 1 model selected  

> show sel target ab

> hide sel target a

> show sel cartoons

> style sel stick

Changed 42 atom styles  

> show sel atoms

> select #1/A: 1-105& #1/E:115-709:<4.0

42 atoms, 42 bonds, 4 residues, 1 model selected  

> select #1/E:115-709& #1/A: 1-105:<4.0

33 atoms, 31 bonds, 3 residues, 1 model selected  

> show sel target ab

> style sel stick

Changed 33 atom styles  

> name frozen E_A sel

> select #1/A: 1-108 & #1/E:115-709:<4.0

42 atoms, 42 bonds, 4 residues, 1 model selected  

> name frozen A_E sel

[Repeated 1 time(s)]

> select add E_A

75 atoms, 73 bonds, 7 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ffff00 restrict cross interModel false intraMol false
> intraRes false reveal true

0 hydrogen bonds found  

> ui tool show Clashes

> clashes interModel false intraMol false ignoreHiddenModels true

70 clashes  

> clashes interModel false intraMol false ignoreHiddenModels true

70 clashes  

> save C:/Users/zhyau/OneDrive/Desktop/structure/sen/TRPV1_AR041.cxs

——— End of log from Wed Jan 29 13:35:06 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: 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
    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
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
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