Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202509052054 (2025-09-05 20:54:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Current thread 0x000083b0 (most recent call first):
  File "D:\APP\For work\ChimeraX 1.11.dev202509052054\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "D:\APP\For work\ChimeraX 1.11.dev202509052054\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
  File "D:\APP\For work\ChimeraX 1.11.dev202509052054\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open "E:/202509-文章/毕业文章及论文/论文/图6/DS1-D25 fab/DS1-D25 fab-trimer.cxs"

Opened cryosparc_P16_J3315_005_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.73, shown at level 0.08, step 2, values float32  

> view name session-start

opened ChimeraX session  

> show #!3 models

> hide #!1 models

> hide #!5 models

> select #3/F:67

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

> show #!5 models

> select #5/F:67

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

> select #5/C:67

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

> show sel target ab

> style sel stick

Changed 8 atom styles  

> show #!4 models

> hide #!3 models

> ui tool show Matchmaker

> matchmaker #!4 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CL-73-ON1-20230927-coot-0.pdb, chain C (#2) with 7uja, chain A
(#4), sequence alignment score = 1723.5  
RMSD between 346 pruned atom pairs is 1.026 angstroms; (across all 372 pairs:
1.396)  
  

> select #4/P:67

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

> style sel stick

Changed 8 atom styles  

> show sel target ab

> select #4/P:80-84

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

> show sel atoms

> select #5/C:80-84

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

> show sel atoms

> style sel stick

Changed 43 atom styles  

> show sel atoms

> select #5/C:67,190,289,90,486

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

> show sel atoms

> style sel stick

Changed 45 atom styles  

> color sel red

> select #5/C:67,83

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

> distance sel

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects  

QDxgiVSyncService: DXGI Factory is no longer Current  

> open "C:/Users/prote/Desktop/structure/DS2-D25 fab/RVF-L88B-D25-fab-a.cxs"

Opened cryosparc_P45_J805_006_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.73, shown at level 0.06, step 2, values float32  

> view name session-start

opened ChimeraX session  

> open "C:/Users/prote/Desktop/structure/DS1-D25 fab/DS1-D25 fab trimer.pdb"

Chain information for DS1-D25 fab trimer.pdb #3  
---  
Chain | Description  
A D E | No description available  
B F G | No description available  
C H I | No description available  
  

> open "C:/Users/prote/Desktop/structure/DS1-D25 fab/DS1-D25 fab-trimer.cxs"

Error opening map "E:\202509-文章\毕业文章及论文\论文\图6\DS1-D25 fab\DS1-D25 fab-
trimer.cxs": File DS1-D25 fab-trimer.cxs, format mrc  
MRC header value nsymbt (909388076) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "VolumeImage" returned None  

> set bgColor transparent

restore_snapshot for "Redust" returned None  

> view name session-start

opened ChimeraX session  

> show #!2 models

> hide #!2 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> hide #!2 models

> show #!2 models

> hide #!2 models

> open "E:/202509-文章/毕业文章及论文/论文/图6/DS1-D25
> fab/cryosparc_P16_J3315_005_volume_map_sharp.mrc"

Opened cryosparc_P16_J3315_005_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.73, shown at level 0.0732, step 2, values float32  

> open "E:/202509-文章/毕业文章及论文/论文/图6/DS1-D25 fab/DS1-D25 fab.cxs"

Opened cryosparc_P16_J3315_005_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.73, shown at level 0.1, step 2, values float32  

> set bgColor transparent

> view name session-start

opened ChimeraX session  

> open "C:/Users/prote/Desktop/structure/DS1-D25 fab/DS1-D25 fab-trimer.cxs"

Error opening map "E:\202509-文章\毕业文章及论文\论文\图6\DS1-D25 fab\DS1-D25 fab-
trimer.cxs": File DS1-D25 fab-trimer.cxs, format mrc  
MRC header value nsymbt (909388076) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "VolumeImage" returned None  

restore_snapshot for "Redust" returned None  

> view name session-start

opened ChimeraX session  

> open "C:/Users/prote/Desktop/structure/DS1-D25
> fab/cryosparc_P16_J3315_005_volume_map_sharp.mrc"

Opened cryosparc_P16_J3315_005_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.73, shown at level 0.0732, step 2, values float32  

> volume #1 level 0.08

> volume #1 level 0.1

> volume #1 level 0.15

> volume #1 level 0.12

> surface dust #1 size 7.3

> transparency 80

> open "E:/202509-文章/毕业文章及论文/论文/图6/DS1-D25 fab/DS1-D25 fab-trimer.cxs"

Opened cryosparc_P16_J3315_005_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.73, shown at level 0.08, step 2, values float32  

> set bgColor #ffffff00

> view name session-start

opened ChimeraX session  

> open "C:/Users/prote/Desktop/structure/DS2-D25
> fab/DS2_D25_FAB_TRIMER_new-0930.pdb"

Chain information for DS2_D25_FAB_TRIMER_new-0930.pdb #6  
---  
Chain | Description  
A D E | No description available  
B F G | No description available  
C H I | No description available  
  

> select add #6

20358 atoms, 20772 bonds, 3 pseudobonds, 2658 residues, 2 models selected  

> style sel stick

Changed 20358 atom styles  

> hide (#!6 & sel) target a

> cartoon (#!6 & sel)

> ui tool show Matchmaker

> matchmaker #!6 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CL-73-ON1-20230927-coot-0.pdb, chain C (#2) with
DS2_D25_FAB_TRIMER_new-0930.pdb, chain C (#6), sequence alignment score =
2292.9  
RMSD between 449 pruned atom pairs is 0.001 angstroms; (across all 449 pairs:
0.001)  
  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> ui tool show "Show Sequence Viewer"

> open "C:/Users/prote/Desktop/structure/DS2-D25
> fab/cryosparc_P45_J805_006_volume_map.mrc"

Opened cryosparc_P45_J805_006_volume_map.mrc as #7, grid size 384,384,384,
pixel 0.73, shown at level 0.032, step 2, values float32  

> volume #7 level 0.08

> volume #7 color #b2b2b2

> hide #!6 models

> hide #!7 models

> hide #!1 models

> show #!6 models

> select add #7

20358 atoms, 20772 bonds, 3 pseudobonds, 2658 residues, 4 models selected  

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> close #1-3,5

> undo

QDxgiVSyncService: DXGI Factory is no longer Current  

> transparency 80

> transparency 70

> transparency sel 0

> transparency sel 50

> transparency 75

> transparency 80

> lighting soft

> set bgColor white

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> volume sel region all imageMode "full region"

> volume unzone sel

> mousemode rightMode "crop volume"

> volume sel region all imageMode "full region"

> volume unzone sel

> mousemode rightMode "crop volume"

> undo

> show #!6 models

> show #!7 models

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #7 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 140.2 tiltedSlabSpacing 0.73 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #7 orthoplanes xyz positionPlanes 192,192,192 style image region all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume showOutlineBox false

> volume style surface

> surface dust #7 size 7.3

> volume style mesh

> volume style surface

> volume style image

> volume style surface

> volume showOutlineBox true

> volume showOutlineBox false

> transparency 0

> volume style surface

> transparency 90

> transparency 60

> select subtract #6

Nothing selected  

> lighting soft

> lighting simple

> lighting soft

> lighting full

> transparency 90

> lighting soft

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> transparency 80

> ui tool show "Fit in Map"

> fitmap #6 inMap #7

Fit molecule DS2_D25_FAB_TRIMER_new-0930.pdb (#6) to map
cryosparc_P45_J805_006_volume_map.mrc (#7) using 20358 atoms  
average map value = 0.04292, steps = 204  
shifted from previous position = 7.13  
rotated from previous position = 15.2 degrees  
atoms outside contour = 16908, contour level = 0.08  
  
Position of DS2_D25_FAB_TRIMER_new-0930.pdb (#6) relative to
cryosparc_P45_J805_006_volume_map.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99925932 -0.03848136 -0.00001871 5.51041592  
0.03848136 0.99925928 -0.00027913 -5.25573963  
0.00002944 0.00027820 0.99999996 5.17161863  
Axis 0.00724130 -0.00062552 0.99997359  
Axis point 139.18000988 139.53681331 0.00000000  
Rotation angle (degrees) 2.20542229  
Shift along axis 5.21467220  
  
Average map value = 0.04292 for 20358 atoms, 16908 outside contour  

> fitmap #6 inMap #7

Fit molecule DS2_D25_FAB_TRIMER_new-0930.pdb (#6) to map
cryosparc_P45_J805_006_volume_map.mrc (#7) using 20358 atoms  
average map value = 0.04292, steps = 60  
shifted from previous position = 0.00415  
rotated from previous position = 0.00789 degrees  
atoms outside contour = 16906, contour level = 0.08  
  
Position of DS2_D25_FAB_TRIMER_new-0930.pdb (#6) relative to
cryosparc_P45_J805_006_volume_map.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99926169 -0.03841965 0.00010254 5.48943272  
0.03841968 0.99926165 -0.00029996 -5.24417544  
-0.00009094 0.00030368 0.99999995 5.18245532  
Axis 0.00785553 0.00251796 0.99996597  
Axis point 139.51259297 139.13410365 0.00000000  
Rotation angle (degrees) 2.20190176  
Shift along axis 5.21219679  
  

> close #6-7

> open "C:/Users/prote/Desktop/structure/DS2-D25 fab/RVF-L88B-D25-fab-a.cxs"

Opened cryosparc_P45_J805_006_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.73, shown at level 0.06, step 2, values float32  

> view name session-start

opened ChimeraX session  

> open "C:/Users/prote/Desktop/structure/DS1-D25 fab/DS1-D25 fab trimer.pdb"

Chain information for DS1-D25 fab trimer.pdb #3  
---  
Chain | Description  
A D E | No description available  
B F G | No description available  
C H I | No description available  
  

> select add #3

25407 atoms, 25956 bonds, 3 pseudobonds, 3336 residues, 3 models selected  

> select add #2

40794 atoms, 41619 bonds, 6 pseudobonds, 5322 residues, 4 models selected  

> select subtract #2

20358 atoms, 20772 bonds, 3 pseudobonds, 2658 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select add #3

20358 atoms, 20772 bonds, 3 pseudobonds, 2658 residues, 2 models selected  

> hide sel atoms

> cartoon (#!3 & sel)

> ui tool show Matchmaker

> matchmaker #!3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker DS2_D25_FAB_TRIMER.pdb, chain F (#2) with DS1-D25 fab trimer.pdb,
chain C (#3), sequence alignment score = 2114.3  
RMSD between 445 pruned atom pairs is 0.481 angstroms; (across all 449 pairs:
0.525)  
  

> select subtract #3

Nothing selected  

> select #2/F

10530 atoms, 10701 bonds, 3 pseudobonds, 1353 residues, 2 models selected  

> select #2/L

4857 atoms, 4962 bonds, 633 residues, 1 model selected  

> delete sel

> select #2/F

10530 atoms, 10701 bonds, 3 pseudobonds, 1353 residues, 2 models selected  

> select #2/H

5049 atoms, 5184 bonds, 678 residues, 1 model selected  

> delete sel

> ui tool show "Show Sequence Viewer"

> select #3/A

1683 atoms, 1728 bonds, 226 residues, 1 model selected  

> select #3/F

1619 atoms, 1654 bonds, 211 residues, 1 model selected  

> select #3/G

1619 atoms, 1654 bonds, 211 residues, 1 model selected  

> select #3/H

3484 atoms, 3542 bonds, 1 pseudobond, 449 residues, 2 models selected  

> delete sel

> select #3/G

1619 atoms, 1654 bonds, 211 residues, 1 model selected  

> select #3/I

3484 atoms, 3542 bonds, 1 pseudobond, 449 residues, 2 models selected  

> delete sel

> select #3/E

1683 atoms, 1728 bonds, 226 residues, 1 model selected  

> select #3/A

1683 atoms, 1728 bonds, 226 residues, 1 model selected  

> select #3/B

1619 atoms, 1654 bonds, 211 residues, 1 model selected  

> select #3/C

3484 atoms, 3542 bonds, 1 pseudobond, 449 residues, 2 models selected  

> select #3/C

3484 atoms, 3542 bonds, 1 pseudobond, 449 residues, 2 models selected  

> delete sel

> surface dust #1 size 7.3

> volume #1 level 0.08

> volume #1 level 0.07

> volume #1 level 0.08

> volume #1 level 0.06

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A #3/D #3/E

Alignment identifier is 1  

> sequence chain #3/B #3/F #3/G

Alignment identifier is 2  

> select #3/B,F-G:113

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

> select #3/B,F-G:113-114

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

> select #3/A,D-E:100I

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

> select #3/A,D-E:100I-101

57 atoms, 57 bonds, 6 residues, 1 model selected  

> select
> #3/A,D-E:3-5,10-12,18-25,32-39,45-52,56-59,67-72,77-82,88-96,107-111,120-124,136-145,176-184,195-200,205-210

2253 atoms, 2265 bonds, 288 residues, 1 model selected  

> select #3/A,D-E:102

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

> select #3/A,D-E:102

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

> select #3/A,D-E:82A

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

> select #3/A,D-E:82A-82C

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

> select #3/A,D-E:114

15 atoms, 12 bonds, 3 residues, 1 model selected  

> select #3/A,D-E:114-115

33 atoms, 30 bonds, 6 residues, 1 model selected  

> select #3/A,D-E:113

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select #3/A,D-E:113-114

33 atoms, 30 bonds, 6 residues, 1 model selected  

> select #3/A,D-E:112

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select #3/A,D-E:112-213

2199 atoms, 2256 bonds, 306 residues, 1 model selected  

> delete sel

> undo

Undo failed, probably because structures have been modified.  

> select #3/B,F-G:108

33 atoms, 30 bonds, 3 residues, 1 model selected  

> select #3/B,F-G:108-110

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

> select #3/B,F-G:109

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select #3/B,F-G:109-211

2388 atoms, 2439 bonds, 309 residues, 1 model selected  

> delete sel

QDxgiVSyncService: DXGI Factory is no longer Current  

> hide #!3 models

> show #!3 models

> select #3/A

950 atoms, 975 bonds, 124 residues, 1 model selected  

> select #3/A

950 atoms, 975 bonds, 124 residues, 1 model selected  

> select #3/A,D-E:1

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

> select #3/A,D-E

2850 atoms, 2925 bonds, 372 residues, 1 model selected  

> color sel yellow

> ui tool show "Color Actions"

> color sel yellow

> color sel orange

> color sel coral

> select #2/F

10530 atoms, 10701 bonds, 3 pseudobonds, 1353 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel orchid

> color sel medium orchid

> color sel medium purple

> color sel thistle

> color sel medium slate blue

> color sel slate blue

> color sel dark slate blue

> color sel rebecca purple

> color sel violet

> color sel plum

> color sel lavender

> color sel medium purple

> color sel plum

> color sel violet

> color sel medium purple

> color sel dark orchid

> color sel dark magenta

> color sel purple

> color sel medium purple

> color sel thistle

> color sel medium slate blue

> color sel slate blue

> color sel rebecca purple

> color sel magenta

> color sel deep pink

> color sel dark violet

> color sel pale violet red

> color sel medium purple

> color sel blue violet

> color sel orchid

> color sel plum

> select #3/B,F-G:1

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

> select #3/B,F-G

2469 atoms, 2520 bonds, 324 residues, 1 model selected  

> color sel lime

> color sel forest green

> color sel coral

> color sel crimson

> color sel light salmon

> color sel dark khaki

> color sel teal

> color sel steel blue

> color sel cadet blue

> color sel spring green

> color sel sea green

> color sel medium sea green

> color sel cyan

> color sel sea green

> color sel peru

> color sel dark goldenrod

> color sel crimson

> color sel tomato

> color sel coral

> color sel gold

> color sel orange

> select #3/B,F-G:1

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

> select #3/B,F-G:1

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

> select #2/F

10530 atoms, 10701 bonds, 3 pseudobonds, 1353 residues, 2 models selected  

> color sel teal

> color sel light sea green

> color sel medium turquoise

> color sel turquoise

> color sel dark turquoise

> color sel medium spring green

> color sel deep sky blue

> color sel green

> color sel lime

> color sel chartreuse

> color sel lawn green

> color sel lime green

> color sel spring green

> color sel forest green

> color sel lime green

> color sel light green

> color sel dark sea green

> color sel light green

> color sel dark cyan

> color sel green

> color sel lime

> color sel chartreuse

> color sel lawn green

> color sel lime green

> color sel medium sea green

> color sel sea green

> color sel olive drab

> color sel medium spring green

> color sel dark turquoise

> color sel dodger blue

> color sel turquoise

> color sel dodger blue

> color sel medium turquoise

> color sel light green

> color sel dark sea green

> color sel pale green

> color sel light green

> color sel pale green

> color sel light green

> color sel pale green

> color sel light green

> volume #1 level 0.07

> volume #1 level 0.06

> save "E:/202509-文章/毕业文章及论文/论文/图6/DS2-D25 fab/RVF-L88B-D25-fab-trimer.cxs"

> save "E:/202509-文章/毕业文章及论文/论文/图6/DS2-D25 fab/RVF-L88B-D25-fab-trimer.tif"
> width 729 height 868 supersample 3 transparentBackground true

> select clear

> save "E:/202509-文章/毕业文章及论文/论文/图6/DS2-D25 fab/RVF-L88B-D25-fab-trimer.tif"
> width 729 height 868 supersample 3 transparentBackground true

> transparency 70

> save "E:/202509-文章/毕业文章及论文/论文/图6/DS2-D25 fab/RVF-L88B-D25-fab-trimer.tif"
> width 729 height 868 supersample 3 transparentBackground true

> lighting soft

> transparency 60

> save "E:/202509-文章/毕业文章及论文/论文/图6/DS2-D25 fab/RVF-L88B-D25-fab-trimer.tif"
> width 729 height 868 supersample 3 transparentBackground true

> graphics silhouettes true

> graphics silhouettes false

> ui tool show "Color Actions"


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

Log:
UCSF ChimeraX version: 1.11.dev202509052054 (2025-09-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 3060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows

Manufacturer: Gigabyte Technology Co., Ltd.
Model: A620M S2H
OS: Microsoft Windows 11 专业版 (Build 26100)
Memory: 33,444,216,832
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 7600 6-Core Processor              
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.7.2
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.16
    ChimeraX-AtomicLibrary: 14.1.23
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202509052054
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.5.1
    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: 1.0.1
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.3.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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: 1.5.2
    ChimeraX-Scenes: 0.2.1
    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: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 2.5.2
    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: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.3.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.6
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.16
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.59.2
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.1
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.1
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.0.2
    qtconsole: 5.6.1
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1