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Opened 24 hours ago
Closed 16 hours ago
#20812 closed defect (fixed)
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | MD/Ensemble Analysis | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.12.dev202605021840 (2026-05-02 18:40:35 UTC)
Description
When trying to save the CXS file, I got this error message
Log:
UCSF ChimeraX version: 1.12.dev202605021840 (2026-05-02)
© 2016-2026 Regents of the University of California. All rights reserved.
> open
> J:/Publications/In_preparation/Cagalinec_wolframin_F/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_8/hwFS1delta_4.cxs
Log from Tue Oct 15 17:45:55 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "J:/Publications/In_preparation/Cagalinec
> wolframin/AlphaFold3/WFS1_movement.py"
> close session
Chain information for C-hWFS1delta_tetramer3_0.pdb #4
---
Chain | Description
A B C D | No description available
Chain information for O-hWFS1delta_tetramer1_0.pdb #5
---
Chain | Description
A B C D | No description available
Chain information for Morph - C-hWFS1delta_tetramer3_0.pdb #6
---
Chain | Description
A B C D | No description available
Traceback (most recent call last):
File "J:/Publications/In_preparation/Cagalinec
wolframin/AlphaFold3/WFS1_movement.py", line 437, in <module>
restore_window_size(1505, 916)
File "J:/Publications/In_preparation/Cagalinec
wolframin/AlphaFold3/WFS1_movement.py", line 255, in restore_window_size
window_size(session, w/scaling, h/scaling)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\graphics\windowsize.py", line 48, in window_size
ui.main_window.adjust_size(width-w, height-h)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py",
line 742, in adjust_size
self.resize(ww, wh)
TypeError: arguments did not match any overloaded call:
resize(self, a0: QSize): argument 1 has unexpected type 'float'
resize(self, w: int, h: int): argument 1 has unexpected type 'float'
Error opening python file J:/Publications/In_preparation/Cagalinec
wolframin/AlphaFold3/WFS1_movement.py
> hide #!7 models
> hide #7.1 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> close session
> help help:user
> open "J:/Publications/In_preparation/Cagalinec
> wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4/wfs1delta_human_4_1.pdb"
Chain information for wfs1delta_human_4_1.pdb #1
---
Chain | Description
A B C D | No description available
> close session
> open "J:/Publications/In_preparation/Cagalinec
> wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1_delta_4_13/hWFS1delta_4_13_2.pdb"
Chain information for hWFS1delta_4_13_2.pdb #1
---
Chain | Description
A B C D | No description available
> open "J:/Publications/In_preparation/Cagalinec
> wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_7/hWFS1delta_4_7_3.pdb"
Chain information for hWFS1delta_4_7_3.pdb #2
---
Chain | Description
A B C D | No description available
> open "J:/Publications/In_preparation/Cagalinec
> wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_8/hWFS1delta_4_8_3.pdb"
Chain information for hWFS1delta_4_8_3.pdb #3
---
Chain | Description
A B C D | No description available
> select #1/A#2/A#3/A
19434 atoms, 19926 bonds, 2424 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #2-3 & sel to #1 & sel
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 hWFS1delta_4_13_2.pdb, chain A (#1) with hWFS1delta_4_7_3.pdb,
chain A (#2), sequence alignment score = 4163
RMSD between 222 pruned atom pairs is 1.114 angstroms; (across all 808 pairs:
9.089)
Matchmaker hWFS1delta_4_13_2.pdb, chain A (#1) with hWFS1delta_4_8_3.pdb,
chain A (#3), sequence alignment score = 4173.2
RMSD between 217 pruned atom pairs is 0.496 angstroms; (across all 808 pairs:
10.053)
> morph #1,2,3 frames 40
Computed 81 frame morph #4
> coordset #4 1,81
> close #4
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
> show #3 models
> show #2 models
> show #1 models
> morph #1,2,3 frames 40
Computed 81 frame morph #4
> coordset #4 1,81
> morph #1,2 frames 40
Computed 41 frame morph #5
> coordset #5 1,41
> select /a
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> show #3 models
> show #2 models
> show #1 models
> hide #4 models
> hide #5 models
> color (#1-3 & sel) red
> select /b
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> color (#1-3 & sel) lime
> select /c
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> color (#1-3 & sel) cornflower blue
> select /d
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> color (#1-3 & sel) magenta
> hide #3 models
> select clear
> hide #2 models
> show #2 models
> hide #2 models
> hide #1 models
> show #2 models
> ui tool show "Change Chain IDs"
> select 1/C
Expected an objects specifier or a keyword
> select #1/C#2/C#3/C#4/C#5/C
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> select #2/C
6478 atoms, 6642 bonds, 808 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel x
Chain IDs of 808 residues changed
> select #2/D:869
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
148 atoms, 155 bonds, 17 residues, 1 model selected
> select up
6478 atoms, 6642 bonds, 808 residues, 1 model selected
> changechains sel C
Chain IDs of 808 residues changed
> select #2/x:703
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
118 atoms, 121 bonds, 13 residues, 1 model selected
> select up
6478 atoms, 6642 bonds, 808 residues, 1 model selected
> changechains sel D
Chain IDs of 808 residues changed
> changechains sel D
Chain IDs of 0 residues changed
> select /C
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> color (#2 & sel) cornflower blue
> select /D
32390 atoms, 33210 bonds, 4040 residues, 5 models selected
> color (#2 & sel) magenta
> show #1 models
> hide #2 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> morph #1,2,3 frames 40
Computed 81 frame morph #6
> coordset #6 1,81
> close #4-5
> rainbow #6
> select 323
Expected an objects specifier or a keyword
> select clear
> select #6/A:323
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #6/B:323
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #6/C:323
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #6/D:323
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select
103648 atoms, 106272 bonds, 12928 residues, 4 models selected
> color (#6 & sel) byelement
> select clear
> movie record
> movie encode C:\Users\zahradsa\Desktop\movie1.mp4 framerate 25.0
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> help help:user
[Repeated 1 time(s)]
> hide #6 models
> show #1 models
> select
103648 atoms, 106272 bonds, 12928 residues, 4 models selected
> rainbow sel & #1
> help help:user
> select :323
160 atoms, 160 bonds, 16 residues, 4 models selected
> show (#1 & sel) target ab
> color (#1 & sel) byelement
> select clear
Drag select of 28 atoms, 3232 residues, 28 bonds
> select clear
> show #2 models
> hide #1 models
> select
103648 atoms, 106272 bonds, 12928 residues, 4 models selected
> rainbow sel & #2
> select
103648 atoms, 106272 bonds, 12928 residues, 4 models selected
> select : 323
160 atoms, 160 bonds, 16 residues, 4 models selected
> select : 323
160 atoms, 160 bonds, 16 residues, 4 models selected
> show (#2 & sel) target ab
> color (#2 & sel) byelement
> select clear
> hide #2 models
> show #3 models
> select
103648 atoms, 106272 bonds, 12928 residues, 4 models selected
> rainbow sel & #3
> select : 323
160 atoms, 160 bonds, 16 residues, 4 models selected
> show (#3 & sel) target ab
> color (#3 & sel) byelement
> show #2 models
> hide #3 models
> hide #2 models
> show #1 models
> save "J:/Publications/In_preparation/Cagalinec
> wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_8/hwFS1delta_4.cxs"
——— End of log from Tue Oct 15 17:45:55 2024 ———
> view name session-start
opened ChimeraX session
> set bgColor white
> set bgColor #ffffff00
> select :495@ca
16 atoms, 16 residues, 4 models selected
> ui tool show Distances
> define plane sel
Plane 'plane' placed at [14.02659405 5.02568451 13.04378863] with normal
[-0.56352809 -0.45910395 -0.68677483] and radius 63.2
> select :520@ca
16 atoms, 16 residues, 4 models selected
> define plane sel
Plane 'plane' placed at [ -6.32991413 -11.04642078 -11.33529048] with normal
[-0.56372023 -0.45874217 -0.68685888] and radius 65.6
plane #4 to plane #5: distance: 0.000Å; angle: 0.0°
> define centroid sel
plane #4 to plane #5: distance: 0.000Å; angle: 0.0°
Centroid 'centroid' placed at [ -6.32991413 -11.04642078 -11.33529048]
> select #7
1 atom, 1 residue, 1 model selected
> select add #4
1 atom, 1 residue, 2 models selected
> show #2 models
> show #3 models
> hide #7 models
> show #7 models
> close #4-5,7
> select #1:520@ca
4 atoms, 4 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [ -9.44399977 -9.36074984 -12.15899968]
> select #1 :495@ca
4 atoms, 4 residues, 1 model selected
> define plane sel
Plane 'plane' placed at [ 9.50050068 7.8262496 13.08074975] with normal
[-0.5251556 -0.48131221 -0.70181917] and radius 58.9
centroid #1.1 to plane #1.2: distance: 35.935Å
> define plane sel
plane #1.2 to centroid #1.1: distance: 35.935Å
Plane 'plane' placed at [ 9.50050068 7.8262496 13.08074975] with normal
[-0.5251556 -0.48131221 -0.70181917] and radius 58.9
> close #1.3
> select #1:520@ca
4 atoms, 4 residues, 1 model selected
> define plane sel
Plane 'plane' placed at [ -9.44399977 -9.36074984 -12.15899968] with normal
[0.52506974 0.48178442 0.70155936] and radius 62.7
> color sel dark gray
> select clear
> color #1-3 dark gray
> graphics silhouettes true
> select #1:870-900
684 atoms, 716 bonds, 84 residues, 1 model selected
> select #1:871-900
656 atoms, 688 bonds, 80 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium violet red
> select #1:870-900
684 atoms, 716 bonds, 84 residues, 1 model selected
> color sel medium violet red
> hide #3 models
> hide #2 models
> select #1:520@ca
4 atoms, 4 residues, 1 model selected
> close #1.2
> close #1.3
> define plane sel padding 20
Plane 'plane' placed at [ -9.44399977 -9.36074984 -12.15899968] with normal
[0.52506974 0.48178442 0.70155936] and radius 82.7
> color sel slate blue
> select #1 :495@ca
4 atoms, 4 residues, 1 model selected
> define plane sel padding 20
Plane 'plane' placed at [ 9.50050068 7.8262496 13.08074975] with normal
[-0.5251556 -0.48131221 -0.70181917] and radius 78.9
> select #1 :37-339
8184 atoms, 8320 bonds, 1028 residues, 1 model selected
> select #1 :337-339
92 atoms, 88 bonds, 12 residues, 1 model selected
> select #1 :338
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1 :654-869
6900 atoms, 7060 bonds, 864 residues, 1 model selected
> color sel yellow
> select #1 :338-339
64 atoms, 60 bonds, 8 residues, 1 model selected
> color sel yellow
> select #1 :494-496
88 atoms, 88 bonds, 12 residues, 1 model selected
> color sel yellow
> select #1 :590-596
216 atoms, 212 bonds, 28 residues, 1 model selected
> color sel yellow
> ui tool show "Side View"
> select #1 :83-290
6580 atoms, 6664 bonds, 832 residues, 1 model selected
> color sel lime
> select #1 :520-530
388 atoms, 396 bonds, 44 residues, 1 model selected
> color sel lime
> select #1 :365-402
1304 atoms, 1340 bonds, 152 residues, 1 model selected
> color sel lime
> select #1 :448-453
176 atoms, 180 bonds, 24 residues, 1 model selected
> color sel lime
> color sel dark gray
> select #1 :448-450
92 atoms, 92 bonds, 12 residues, 1 model selected
> color sel lime
> select #1 :448-451
112 atoms, 112 bonds, 16 residues, 1 model selected
> color sel lime
> select #1 :448-451
112 atoms, 112 bonds, 16 residues, 1 model selected
> color sel orange
> select #1 :448-450
92 atoms, 92 bonds, 12 residues, 1 model selected
> select #1 :448-451
112 atoms, 112 bonds, 16 residues, 1 model selected
> color sel lime
> select #1 :365
44 atoms, 44 bonds, 4 residues, 1 model selected
> color sel dark gray
> select #!1/A:520
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1 :520
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel dark gray
> select #1 :288-230
Nothing selected
> select #1:288-230
Nothing selected
> select #1:288
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #1:288-230
Nothing selected
> select #1:288-290
92 atoms, 88 bonds, 12 residues, 1 model selected
> color sel gray
> select #1:287
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel dark gray
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> select #1:403-494
2860 atoms, 2952 bonds, 368 residues, 1 model selected
> color sel blue
> undo
> select #1:403-494
2860 atoms, 2952 bonds, 368 residues, 1 model selected
> select #1:403-447
1420 atoms, 1468 bonds, 180 residues, 1 model selected
> color sel turquoise
> select #1:452-494
1328 atoms, 1364 bonds, 172 residues, 1 model selected
> color sel turquoise
> select #1:496-520
836 atoms, 856 bonds, 100 residues, 1 model selected
> color sel turquoise
> select #1:448-451
112 atoms, 112 bonds, 16 residues, 1 model selected
> color sel red
> color sel lime
> select #1:289-337
1604 atoms, 1652 bonds, 196 residues, 1 model selected
> color sel medium slate blue
> color sel turquoise
> select #1:588-653
2160 atoms, 2224 bonds, 264 residues, 1 model selected
> color sel dodger blue
> color sel dark slate blue
> undo
[Repeated 1 time(s)]
> select #1:530-587
1804 atoms, 1848 bonds, 232 residues, 1 model selected
> color sel dark slate blue
> select #1:530-589
1904 atoms, 1960 bonds, 240 residues, 1 model selected
> color sel turquoise
> select #1:340-365
880 atoms, 912 bonds, 104 residues, 1 model selected
> color sel turquoise
> select #1:653-654
68 atoms, 64 bonds, 8 residues, 1 model selected
> select #1:530-589
1904 atoms, 1960 bonds, 240 residues, 1 model selected
> select #1:597-600
108 atoms, 104 bonds, 16 residues, 1 model selected
> select #1:597-653
1844 atoms, 1896 bonds, 228 residues, 1 model selected
> color sel turquoise
> hide #!1 models
> show #2 models
> show #!1 models
> select #1:1-900
25913 atoms, 26568 bonds, 3233 residues, 2 models selected
> hide sel cartoons
> select clear
> mlp #2#1.1#!1
Map values for surface "hWFS1delta_4_13_2.pdb_A SES surface": minimum -28.87,
mean -1.748, maximum 23.58
Map values for surface "hWFS1delta_4_13_2.pdb_B SES surface": minimum -28.9,
mean -1.758, maximum 23.58
Map values for surface "hWFS1delta_4_13_2.pdb_C SES surface": minimum -28.27,
mean -1.752, maximum 23.72
Map values for surface "hWFS1delta_4_13_2.pdb_D SES surface": minimum -29.12,
mean -1.742, maximum 23.69
Map values for surface "hWFS1delta_4_7_3.pdb_A SES surface": minimum -29.11,
mean -1.883, maximum 24.86
Map values for surface "hWFS1delta_4_7_3.pdb_B SES surface": minimum -30.12,
mean -1.866, maximum 24.25
Map values for surface "hWFS1delta_4_7_3.pdb_C SES surface": minimum -27.57,
mean -1.893, maximum 25.26
Map values for surface "hWFS1delta_4_7_3.pdb_D SES surface": minimum -27.98,
mean -1.865, maximum 24.56
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide #1.1#!1-2 surfaces
> select #2:1-900
25912 atoms, 26568 bonds, 3232 residues, 1 model selected
> ui tool show "Render/Select by Attribute"
> select clear
> show #1.1#!1-2 surfaces
> mlp #1.1#!1-2
Map values for surface "hWFS1delta_4_13_2.pdb_A SES surface": minimum -28.87,
mean -1.748, maximum 23.58
Map values for surface "hWFS1delta_4_13_2.pdb_B SES surface": minimum -28.9,
mean -1.758, maximum 23.58
Map values for surface "hWFS1delta_4_13_2.pdb_C SES surface": minimum -28.27,
mean -1.752, maximum 23.72
Map values for surface "hWFS1delta_4_13_2.pdb_D SES surface": minimum -29.12,
mean -1.742, maximum 23.69
Map values for surface "hWFS1delta_4_7_3.pdb_A SES surface": minimum -29.11,
mean -1.883, maximum 24.86
Map values for surface "hWFS1delta_4_7_3.pdb_B SES surface": minimum -30.12,
mean -1.866, maximum 24.25
Map values for surface "hWFS1delta_4_7_3.pdb_C SES surface": minimum -27.57,
mean -1.893, maximum 25.26
Map values for surface "hWFS1delta_4_7_3.pdb_D SES surface": minimum -27.98,
mean -1.865, maximum 24.56
To also show corresponding color key, enter the above mlp command and add key
true
> hide #1.1#!1-2 surfaces
> select #1:444@ca
4 atoms, 4 residues, 1 model selected
> define plane sel padding 20
Plane 'plane' placed at [-6.42999983 -6.60575038 -8.30600023] with normal
[-0.5247485 -0.48135945 -0.70209123] and radius 73.6
plane #1.3 to plane #1.8: distance: 0.000Å; angle: 0.0°
centroid #1.1 to plane #1.8: distance: 5.613Å
> select #1:444@ca
4 atoms, 4 residues, 1 model selected
> define centroid sel
plane #1.8 to centroid #1.1: distance: 5.613Å
Centroid 'centroid' placed at [-6.42999983 -6.60575038 -8.30600023]
centroid #1.9 to plane #1.3: distance: 30.322Å
centroid #1.9 to plane #1.8: distance: 0.000Å
> close #1.8-9
> select #1:614@ca
4 atoms, 4 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [-2.87699986 -3.66000009 -3.78324984]
> select #2/C:614
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1:615@ca
4 atoms, 4 residues, 1 model selected
> close #1.8
> select #1:615@ca
4 atoms, 4 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [-3.90049994 -4.59249985 -5.18324989]
centroid #1.8 to plane #1.3: distance: 25.833Å
> select #1:519@ca
4 atoms, 4 residues, 1 model selected
> close #1.8
> define centroid sel
Centroid 'centroid' placed at [ -8.28574944 -8.31650072 -10.65049994]
centroid #1.8 to plane #1.3: distance: 33.765Å
> select #2/C:619
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1.2
1 model selected
> select #1.2
1 model selected
> select #2/D:307
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/C:630
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #1.1,8#!1 cartoons
> select #1:425
32 atoms, 28 bonds, 4 residues, 1 model selected
> color (#!1 & sel) red
> show #!2 models
> hide #!1 models
> show #!1 models
> select #2:425
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel surfaces
> select clear
> show #1.1,8#!1-2 surfaces
> hide #1.1,8#!1-2 surfaces
[Repeated 1 time(s)]
> show #1.1,8#!1-2 surfaces
> set bgColor black
> set bgColor transparent
> select #1:425
32 atoms, 28 bonds, 4 residues, 1 model selected
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> select #1:550-560
304 atoms, 300 bonds, 44 residues, 1 model selected
> hide sel surfaces
[Repeated 1 time(s)]
> select clear
> hide #1.1,8#!1-2 surfaces
> show #1.1,8#!1-2 cartoons
> select #1:550-560
304 atoms, 300 bonds, 44 residues, 1 model selected
> color sel magenta
> show sel atoms
> style sel sphere
Changed 304 atom styles
> style sel stick
Changed 304 atom styles
> hide sel atoms
> color sel turquoise
> select #1:550
36 atoms, 32 bonds, 4 residues, 1 model selected
> hide #!2 models
> select #!1/B:552
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 3 residues
> select #1:552@ca
4 atoms, 4 residues, 1 model selected
> color sel red
> show sel surfaces
[Repeated 1 time(s)]
> select clear
> show #1.1,8#!1 surfaces
> hide #1.1,8#!1 surfaces
> select #!1/B:552
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #!1/B:550
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color sel red
> show sel surfaces
> select #1:475-500
828 atoms, 856 bonds, 104 residues, 1 model selected
> undo
[Repeated 9 time(s)]
> redo
> color sel turquoise
> show sel surfaces
> select clear
> show #1.1,8#!1 surfaces
> hide #1.1,8#!1 surfaces
> show #1.1,8#!1 surfaces
> hide #1.1,8#!1 surfaces
> show #1.1,8#!1 surfaces
> select #1:477
32 atoms, 28 bonds, 4 residues, 1 model selected
> hide sel surfaces
> color sel red
> show sel surfaces
> hide sel surfaces
> select clear
> hide #1.1,8#!1 surfaces
> show #1.1,8#!1 surfaces
> select #!1/B:495@CE1
1 atom, 1 residue, 1 model selected
> select #1:495
40 atoms, 40 bonds, 4 residues, 1 model selected
> color sel red
> hide sel surfaces
> select clear
> hide #1.1,8#!1 surfaces
> select #1:619-630
344 atoms, 340 bonds, 48 residues, 1 model selected
> color sel red
> show sel surfaces
> select #1:550-570
648 atoms, 660 bonds, 84 residues, 1 model selected
> select #1:425
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1:300-370
2332 atoms, 2404 bonds, 284 residues, 1 model selected
> select clear
> show #1.1,8#!1 surfaces
Non-native QFileDialog supports only local files
[Repeated 1 time(s)]
> save
> J:/Publications/In_preparation/Cagalinec_wolframin_F/Wolframin_clanok/Transmembrane.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\std_commands\coordset_gui.py", line 112, in take_snapshot
from chimerax.md_crds.gui import get_session_info
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
(C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\md_crds\gui.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001D2AD0E7650>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at
0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at
0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at
0x000001D2DBD59590>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at
0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at
0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at
0x000001D2DBD59590>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001D2AD0E7650>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at
0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at
0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at
0x000001D2DBD59590>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\std_commands\coordset_gui.py", line 112, in take_snapshot
from chimerax.md_crds.gui import get_session_info
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
(C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\md_crds\gui.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001D2AD0E7650>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at
0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at
0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at
0x000001D2DBD59590>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at
0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at
0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at
0x000001D2DBD59590>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001D2AD0E7650>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at
0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at
0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at
0x000001D2DBD59590>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D2D18CA4D0>
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->
File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 369.09
OpenGL renderer: Quadro 600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: en_US.cp1250
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision T1500
OS: Microsoft Windows 10 Pro (Build 19045.6466)
Memory: 17,136,992,256
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7 CPU 870 @ 2.93GHz
OSLanguage: en-GB
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.1.2
bs4: 0.0.2
build: 1.3.0
certifi: 2026.4.22
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202605021840
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: 1.2.1
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: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
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: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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
click: 8.3.3
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.62.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.13
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.20.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.3
pydantic-settings: 2.14.0
pydantic_core: 2.46.3
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.27
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
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: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.1
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.2
Unidecode: 1.4.0
urllib3: 2.6.3
uvicorn: 0.46.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
WMI: 1.5.1
yarl: 1.23.0
Change History (3)
comment:1 by , 20 hours ago
comment:2 by , 16 hours ago
| Cc: | added |
|---|---|
| Component: | Unassigned → MD/Ensemble Analysis |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' |
This bug was fixed in May 2026 and the fix is in the ChimeraX 1.12 release. Saving a session with an MD coordinate set slider was broken for a few daily builds including your May 2, 2026 ChimeraX daily build. Sorry about that.
comment:3 by , 16 hours ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
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for help on using tickets.
Hi All I found out that the error was caused by having both a morph between models and a model with surface . when I deleted the morph, the errorstopped occurring. Best regards Sasha -----Original Message----- From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] Sent: Monday, August 3, 2026 18:23 To: alexandra.zahradnikova@savba.sk Cc: pett@cgl.ucsf.edu Subject: [ChimeraX] #20812: ChimeraX bug report submission #20812: ChimeraX bug report submission --------------------------------------+----------------------------- Reporter: alexandra.zahradnikova@… | Type: defect Status: new | Priority: normal Component: Unassigned | Blocked By: Blocking: | Notify when closed: --------------------------------------+----------------------------- {{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.12.dev202605021840 (2026-05-02 18:40:35 UTC) Description When trying to save the CXS file, I got this error message Log: UCSF ChimeraX version: 1.12.dev202605021840 (2026-05-02) © 2016-2026 Regents of the University of California. All rights reserved. > open > J:/Publications/In_preparation/Cagalinec_wolframin_F/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_8/hwFS1delta_4.cxs Log from Tue Oct 15 17:45:55 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "J:/Publications/In_preparation/Cagalinec > wolframin/AlphaFold3/WFS1_movement.py" > close session Chain information for C-hWFS1delta_tetramer3_0.pdb #4 --- Chain | Description A B C D | No description available Chain information for O-hWFS1delta_tetramer1_0.pdb #5 --- Chain | Description A B C D | No description available Chain information for Morph - C-hWFS1delta_tetramer3_0.pdb #6 --- Chain | Description A B C D | No description available Traceback (most recent call last): File "J:/Publications/In_preparation/Cagalinec wolframin/AlphaFold3/WFS1_movement.py", line 437, in <module> restore_window_size(1505, 916) File "J:/Publications/In_preparation/Cagalinec wolframin/AlphaFold3/WFS1_movement.py", line 255, in restore_window_size window_size(session, w/scaling, h/scaling) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\graphics\windowsize.py", line 48, in window_size ui.main_window.adjust_size(width-w, height-h) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\gui.py", line 742, in adjust_size self.resize(ww, wh) TypeError: arguments did not match any overloaded call: resize(self, a0: QSize): argument 1 has unexpected type 'float' resize(self, w: int, h: int): argument 1 has unexpected type 'float' Error opening python file J:/Publications/In_preparation/Cagalinec wolframin/AlphaFold3/WFS1_movement.py > hide #!7 models > hide #7.1 models > hide #6 models > show #5 models > hide #5 models > show #4 models > close session > help help:user > open "J:/Publications/In_preparation/Cagalinec > wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4/wfs1delta_human_4_1.pdb" Chain information for wfs1delta_human_4_1.pdb #1 --- Chain | Description A B C D | No description available > close session > open "J:/Publications/In_preparation/Cagalinec > wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1_delta_4_13/hWFS1delta_4_13_2.pdb" Chain information for hWFS1delta_4_13_2.pdb #1 --- Chain | Description A B C D | No description available > open "J:/Publications/In_preparation/Cagalinec > wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_7/hWFS1delta_4_7_3.pdb" Chain information for hWFS1delta_4_7_3.pdb #2 --- Chain | Description A B C D | No description available > open "J:/Publications/In_preparation/Cagalinec > wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_8/hWFS1delta_4_8_3.pdb" Chain information for hWFS1delta_4_8_3.pdb #3 --- Chain | Description A B C D | No description available > select #1/A#2/A#3/A 19434 atoms, 19926 bonds, 2424 residues, 3 models selected > ui tool show Matchmaker > matchmaker #2-3 & sel to #1 & sel 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 hWFS1delta_4_13_2.pdb, chain A (#1) with hWFS1delta_4_7_3.pdb, chain A (#2), sequence alignment score = 4163 RMSD between 222 pruned atom pairs is 1.114 angstroms; (across all 808 pairs: 9.089) Matchmaker hWFS1delta_4_13_2.pdb, chain A (#1) with hWFS1delta_4_8_3.pdb, chain A (#3), sequence alignment score = 4173.2 RMSD between 217 pruned atom pairs is 0.496 angstroms; (across all 808 pairs: 10.053) > morph #1,2,3 frames 40 Computed 81 frame morph #4 > coordset #4 1,81 > close #4 > show #1 models > show #2 models > hide #1 models > hide #2 models > show #3 models > show #2 models > show #1 models > morph #1,2,3 frames 40 Computed 81 frame morph #4 > coordset #4 1,81 > morph #1,2 frames 40 Computed 41 frame morph #5 > coordset #5 1,41 > select /a 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > show #3 models > show #2 models > show #1 models > hide #4 models > hide #5 models > color (#1-3 & sel) red > select /b 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > color (#1-3 & sel) lime > select /c 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > color (#1-3 & sel) cornflower blue > select /d 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > color (#1-3 & sel) magenta > hide #3 models > select clear > hide #2 models > show #2 models > hide #2 models > hide #1 models > show #2 models > ui tool show "Change Chain IDs" > select 1/C Expected an objects specifier or a keyword > select #1/C#2/C#3/C#4/C#5/C 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > select #2/C 6478 atoms, 6642 bonds, 808 residues, 1 model selected > ui tool show "Change Chain IDs" > changechains sel x Chain IDs of 808 residues changed > select #2/D:869 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 148 atoms, 155 bonds, 17 residues, 1 model selected > select up 6478 atoms, 6642 bonds, 808 residues, 1 model selected > changechains sel C Chain IDs of 808 residues changed > select #2/x:703 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 118 atoms, 121 bonds, 13 residues, 1 model selected > select up 6478 atoms, 6642 bonds, 808 residues, 1 model selected > changechains sel D Chain IDs of 808 residues changed > changechains sel D Chain IDs of 0 residues changed > select /C 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > color (#2 & sel) cornflower blue > select /D 32390 atoms, 33210 bonds, 4040 residues, 5 models selected > color (#2 & sel) magenta > show #1 models > hide #2 models > hide #1 models > show #2 models > hide #2 models > show #3 models > hide #3 models > morph #1,2,3 frames 40 Computed 81 frame morph #6 > coordset #6 1,81 > close #4-5 > rainbow #6 > select 323 Expected an objects specifier or a keyword > select clear > select #6/A:323 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #6/B:323 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #6/C:323 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #6/D:323 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select 103648 atoms, 106272 bonds, 12928 residues, 4 models selected > color (#6 & sel) byelement > select clear > movie record > movie encode C:\Users\zahradsa\Desktop\movie1.mp4 framerate 25.0 Movie saved to \C:Users\\...\Desktop\movie1.mp4 > help help:user [Repeated 1 time(s)] > hide #6 models > show #1 models > select 103648 atoms, 106272 bonds, 12928 residues, 4 models selected > rainbow sel & #1 > help help:user > select :323 160 atoms, 160 bonds, 16 residues, 4 models selected > show (#1 & sel) target ab > color (#1 & sel) byelement > select clear Drag select of 28 atoms, 3232 residues, 28 bonds > select clear > show #2 models > hide #1 models > select 103648 atoms, 106272 bonds, 12928 residues, 4 models selected > rainbow sel & #2 > select 103648 atoms, 106272 bonds, 12928 residues, 4 models selected > select : 323 160 atoms, 160 bonds, 16 residues, 4 models selected > select : 323 160 atoms, 160 bonds, 16 residues, 4 models selected > show (#2 & sel) target ab > color (#2 & sel) byelement > select clear > hide #2 models > show #3 models > select 103648 atoms, 106272 bonds, 12928 residues, 4 models selected > rainbow sel & #3 > select : 323 160 atoms, 160 bonds, 16 residues, 4 models selected > show (#3 & sel) target ab > color (#3 & sel) byelement > show #2 models > hide #3 models > hide #2 models > show #1 models > save "J:/Publications/In_preparation/Cagalinec > wolframin/AlphaFold3/hWFS1delta_tetramer/fold_hwfs1delta_4_8/hwFS1delta_4.cxs" ——— End of log from Tue Oct 15 17:45:55 2024 ——— > view name session-start opened ChimeraX session > set bgColor white > set bgColor #ffffff00 > select :495@ca 16 atoms, 16 residues, 4 models selected > ui tool show Distances > define plane sel Plane 'plane' placed at [14.02659405 5.02568451 13.04378863] with normal [-0.56352809 -0.45910395 -0.68677483] and radius 63.2 > select :520@ca 16 atoms, 16 residues, 4 models selected > define plane sel Plane 'plane' placed at [ -6.32991413 -11.04642078 -11.33529048] with normal [-0.56372023 -0.45874217 -0.68685888] and radius 65.6 plane #4 to plane #5: distance: 0.000Å; angle: 0.0° > define centroid sel plane #4 to plane #5: distance: 0.000Å; angle: 0.0° Centroid 'centroid' placed at [ -6.32991413 -11.04642078 -11.33529048] > select #7 1 atom, 1 residue, 1 model selected > select add #4 1 atom, 1 residue, 2 models selected > show #2 models > show #3 models > hide #7 models > show #7 models > close #4-5,7 > select #1:520@ca 4 atoms, 4 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [ -9.44399977 -9.36074984 -12.15899968] > select #1 :495@ca 4 atoms, 4 residues, 1 model selected > define plane sel Plane 'plane' placed at [ 9.50050068 7.8262496 13.08074975] with normal [-0.5251556 -0.48131221 -0.70181917] and radius 58.9 centroid #1.1 to plane #1.2: distance: 35.935Å > define plane sel plane #1.2 to centroid #1.1: distance: 35.935Å Plane 'plane' placed at [ 9.50050068 7.8262496 13.08074975] with normal [-0.5251556 -0.48131221 -0.70181917] and radius 58.9 > close #1.3 > select #1:520@ca 4 atoms, 4 residues, 1 model selected > define plane sel Plane 'plane' placed at [ -9.44399977 -9.36074984 -12.15899968] with normal [0.52506974 0.48178442 0.70155936] and radius 62.7 > color sel dark gray > select clear > color #1-3 dark gray > graphics silhouettes true > select #1:870-900 684 atoms, 716 bonds, 84 residues, 1 model selected > select #1:871-900 656 atoms, 688 bonds, 80 residues, 1 model selected > ui tool show "Color Actions" > color sel medium violet red > select #1:870-900 684 atoms, 716 bonds, 84 residues, 1 model selected > color sel medium violet red > hide #3 models > hide #2 models > select #1:520@ca 4 atoms, 4 residues, 1 model selected > close #1.2 > close #1.3 > define plane sel padding 20 Plane 'plane' placed at [ -9.44399977 -9.36074984 -12.15899968] with normal [0.52506974 0.48178442 0.70155936] and radius 82.7 > color sel slate blue > select #1 :495@ca 4 atoms, 4 residues, 1 model selected > define plane sel padding 20 Plane 'plane' placed at [ 9.50050068 7.8262496 13.08074975] with normal [-0.5251556 -0.48131221 -0.70181917] and radius 78.9 > select #1 :37-339 8184 atoms, 8320 bonds, 1028 residues, 1 model selected > select #1 :337-339 92 atoms, 88 bonds, 12 residues, 1 model selected > select #1 :338 32 atoms, 28 bonds, 4 residues, 1 model selected > select #1 :654-869 6900 atoms, 7060 bonds, 864 residues, 1 model selected > color sel yellow > select #1 :338-339 64 atoms, 60 bonds, 8 residues, 1 model selected > color sel yellow > select #1 :494-496 88 atoms, 88 bonds, 12 residues, 1 model selected > color sel yellow > select #1 :590-596 216 atoms, 212 bonds, 28 residues, 1 model selected > color sel yellow > ui tool show "Side View" > select #1 :83-290 6580 atoms, 6664 bonds, 832 residues, 1 model selected > color sel lime > select #1 :520-530 388 atoms, 396 bonds, 44 residues, 1 model selected > color sel lime > select #1 :365-402 1304 atoms, 1340 bonds, 152 residues, 1 model selected > color sel lime > select #1 :448-453 176 atoms, 180 bonds, 24 residues, 1 model selected > color sel lime > color sel dark gray > select #1 :448-450 92 atoms, 92 bonds, 12 residues, 1 model selected > color sel lime > select #1 :448-451 112 atoms, 112 bonds, 16 residues, 1 model selected > color sel lime > select #1 :448-451 112 atoms, 112 bonds, 16 residues, 1 model selected > color sel orange > select #1 :448-450 92 atoms, 92 bonds, 12 residues, 1 model selected > select #1 :448-451 112 atoms, 112 bonds, 16 residues, 1 model selected > color sel lime > select #1 :365 44 atoms, 44 bonds, 4 residues, 1 model selected > color sel dark gray > select #!1/A:520 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1 :520 36 atoms, 32 bonds, 4 residues, 1 model selected > color sel dark gray > select #1 :288-230 Nothing selected > select #1:288-230 Nothing selected > select #1:288 28 atoms, 24 bonds, 4 residues, 1 model selected > select #1:288-230 Nothing selected > select #1:288-290 92 atoms, 88 bonds, 12 residues, 1 model selected > color sel gray > select #1:287 36 atoms, 32 bonds, 4 residues, 1 model selected > color sel dark gray > show #2 models > hide #2 models > show #2 models > hide #2 models > select #1:403-494 2860 atoms, 2952 bonds, 368 residues, 1 model selected > color sel blue > undo > select #1:403-494 2860 atoms, 2952 bonds, 368 residues, 1 model selected > select #1:403-447 1420 atoms, 1468 bonds, 180 residues, 1 model selected > color sel turquoise > select #1:452-494 1328 atoms, 1364 bonds, 172 residues, 1 model selected > color sel turquoise > select #1:496-520 836 atoms, 856 bonds, 100 residues, 1 model selected > color sel turquoise > select #1:448-451 112 atoms, 112 bonds, 16 residues, 1 model selected > color sel red > color sel lime > select #1:289-337 1604 atoms, 1652 bonds, 196 residues, 1 model selected > color sel medium slate blue > color sel turquoise > select #1:588-653 2160 atoms, 2224 bonds, 264 residues, 1 model selected > color sel dodger blue > color sel dark slate blue > undo [Repeated 1 time(s)] > select #1:530-587 1804 atoms, 1848 bonds, 232 residues, 1 model selected > color sel dark slate blue > select #1:530-589 1904 atoms, 1960 bonds, 240 residues, 1 model selected > color sel turquoise > select #1:340-365 880 atoms, 912 bonds, 104 residues, 1 model selected > color sel turquoise > select #1:653-654 68 atoms, 64 bonds, 8 residues, 1 model selected > select #1:530-589 1904 atoms, 1960 bonds, 240 residues, 1 model selected > select #1:597-600 108 atoms, 104 bonds, 16 residues, 1 model selected > select #1:597-653 1844 atoms, 1896 bonds, 228 residues, 1 model selected > color sel turquoise > hide #!1 models > show #2 models > show #!1 models > select #1:1-900 25913 atoms, 26568 bonds, 3233 residues, 2 models selected > hide sel cartoons > select clear > mlp #2#1.1#!1 Map values for surface "hWFS1delta_4_13_2.pdb_A SES surface": minimum -28.87, mean -1.748, maximum 23.58 Map values for surface "hWFS1delta_4_13_2.pdb_B SES surface": minimum -28.9, mean -1.758, maximum 23.58 Map values for surface "hWFS1delta_4_13_2.pdb_C SES surface": minimum -28.27, mean -1.752, maximum 23.72 Map values for surface "hWFS1delta_4_13_2.pdb_D SES surface": minimum -29.12, mean -1.742, maximum 23.69 Map values for surface "hWFS1delta_4_7_3.pdb_A SES surface": minimum -29.11, mean -1.883, maximum 24.86 Map values for surface "hWFS1delta_4_7_3.pdb_B SES surface": minimum -30.12, mean -1.866, maximum 24.25 Map values for surface "hWFS1delta_4_7_3.pdb_C SES surface": minimum -27.57, mean -1.893, maximum 25.26 Map values for surface "hWFS1delta_4_7_3.pdb_D SES surface": minimum -27.98, mean -1.865, maximum 24.56 To also show corresponding color key, enter the above mlp command and add key true > undo > hide #1.1#!1-2 surfaces > select #2:1-900 25912 atoms, 26568 bonds, 3232 residues, 1 model selected > ui tool show "Render/Select by Attribute" > select clear > show #1.1#!1-2 surfaces > mlp #1.1#!1-2 Map values for surface "hWFS1delta_4_13_2.pdb_A SES surface": minimum -28.87, mean -1.748, maximum 23.58 Map values for surface "hWFS1delta_4_13_2.pdb_B SES surface": minimum -28.9, mean -1.758, maximum 23.58 Map values for surface "hWFS1delta_4_13_2.pdb_C SES surface": minimum -28.27, mean -1.752, maximum 23.72 Map values for surface "hWFS1delta_4_13_2.pdb_D SES surface": minimum -29.12, mean -1.742, maximum 23.69 Map values for surface "hWFS1delta_4_7_3.pdb_A SES surface": minimum -29.11, mean -1.883, maximum 24.86 Map values for surface "hWFS1delta_4_7_3.pdb_B SES surface": minimum -30.12, mean -1.866, maximum 24.25 Map values for surface "hWFS1delta_4_7_3.pdb_C SES surface": minimum -27.57, mean -1.893, maximum 25.26 Map values for surface "hWFS1delta_4_7_3.pdb_D SES surface": minimum -27.98, mean -1.865, maximum 24.56 To also show corresponding color key, enter the above mlp command and add key true > hide #1.1#!1-2 surfaces > select #1:444@ca 4 atoms, 4 residues, 1 model selected > define plane sel padding 20 Plane 'plane' placed at [-6.42999983 -6.60575038 -8.30600023] with normal [-0.5247485 -0.48135945 -0.70209123] and radius 73.6 plane #1.3 to plane #1.8: distance: 0.000Å; angle: 0.0° centroid #1.1 to plane #1.8: distance: 5.613Å > select #1:444@ca 4 atoms, 4 residues, 1 model selected > define centroid sel plane #1.8 to centroid #1.1: distance: 5.613Å Centroid 'centroid' placed at [-6.42999983 -6.60575038 -8.30600023] centroid #1.9 to plane #1.3: distance: 30.322Å centroid #1.9 to plane #1.8: distance: 0.000Å > close #1.8-9 > select #1:614@ca 4 atoms, 4 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [-2.87699986 -3.66000009 -3.78324984] > select #2/C:614 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1:615@ca 4 atoms, 4 residues, 1 model selected > close #1.8 > select #1:615@ca 4 atoms, 4 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [-3.90049994 -4.59249985 -5.18324989] centroid #1.8 to plane #1.3: distance: 25.833Å > select #1:519@ca 4 atoms, 4 residues, 1 model selected > close #1.8 > define centroid sel Centroid 'centroid' placed at [ -8.28574944 -8.31650072 -10.65049994] centroid #1.8 to plane #1.3: distance: 33.765Å > select #2/C:619 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1.2 1 model selected > select #1.2 1 model selected > select #2/D:307 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/C:630 6 atoms, 5 bonds, 1 residue, 1 model selected > hide #!2 models > show #1.1,8#!1 cartoons > select #1:425 32 atoms, 28 bonds, 4 residues, 1 model selected > color (#!1 & sel) red > show #!2 models > hide #!1 models > show #!1 models > select #2:425 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel surfaces > select clear > show #1.1,8#!1-2 surfaces > hide #1.1,8#!1-2 surfaces [Repeated 1 time(s)] > show #1.1,8#!1-2 surfaces > set bgColor black > set bgColor transparent > select #1:425 32 atoms, 28 bonds, 4 residues, 1 model selected > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > select #1:550-560 304 atoms, 300 bonds, 44 residues, 1 model selected > hide sel surfaces [Repeated 1 time(s)] > select clear > hide #1.1,8#!1-2 surfaces > show #1.1,8#!1-2 cartoons > select #1:550-560 304 atoms, 300 bonds, 44 residues, 1 model selected > color sel magenta > show sel atoms > style sel sphere Changed 304 atom styles > style sel stick Changed 304 atom styles > hide sel atoms > color sel turquoise > select #1:550 36 atoms, 32 bonds, 4 residues, 1 model selected > hide #!2 models > select #!1/B:552 7 atoms, 6 bonds, 1 residue, 1 model selected Drag select of 3 residues > select #1:552@ca 4 atoms, 4 residues, 1 model selected > color sel red > show sel surfaces [Repeated 1 time(s)] > select clear > show #1.1,8#!1 surfaces > hide #1.1,8#!1 surfaces > select #!1/B:552 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #!1/B:550 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > color sel red > show sel surfaces > select #1:475-500 828 atoms, 856 bonds, 104 residues, 1 model selected > undo [Repeated 9 time(s)] > redo > color sel turquoise > show sel surfaces > select clear > show #1.1,8#!1 surfaces > hide #1.1,8#!1 surfaces > show #1.1,8#!1 surfaces > hide #1.1,8#!1 surfaces > show #1.1,8#!1 surfaces > select #1:477 32 atoms, 28 bonds, 4 residues, 1 model selected > hide sel surfaces > color sel red > show sel surfaces > hide sel surfaces > select clear > hide #1.1,8#!1 surfaces > show #1.1,8#!1 surfaces > select #!1/B:495@CE1 1 atom, 1 residue, 1 model selected > select #1:495 40 atoms, 40 bonds, 4 residues, 1 model selected > color sel red > hide sel surfaces > select clear > hide #1.1,8#!1 surfaces > select #1:619-630 344 atoms, 340 bonds, 48 residues, 1 model selected > color sel red > show sel surfaces > select #1:550-570 648 atoms, 660 bonds, 84 residues, 1 model selected > select #1:425 32 atoms, 28 bonds, 4 residues, 1 model selected > select #1:300-370 2332 atoms, 2404 bonds, 284 residues, 1 model selected > select clear > show #1.1,8#!1 surfaces Non-native QFileDialog supports only local files [Repeated 1 time(s)] > save > J:/Publications/In_preparation/Cagalinec_wolframin_F/Wolframin_clanok/Transmembrane.cxs Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\std_commands\coordset_gui.py", line 112, in take_snapshot from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\md_crds\gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [<chimerax.log.tool.Log object at 0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at 0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at 0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at 0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at 0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x000001D2DBD59590>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 1048, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 731, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at 0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at 0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at 0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at 0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at 0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x000001D2DBD59590>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>: Error while saving session data for 'tools' -> [<chimerax.log.tool.Log object at 0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at 0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at 0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at 0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at 0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x000001D2DBD59590>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 301, in discovery raise ValueError( See log for complete Python traceback. Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\std_commands\coordset_gui.py", line 112, in take_snapshot from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\md_crds\gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [<chimerax.log.tool.Log object at 0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at 0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at 0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at 0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at 0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x000001D2DBD59590>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 133, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog _dlg.display(session, **kw) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 68, in display run(session, cmd) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 1048, in save session.save(output, version=version, include_maps=include_maps) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 731, in save mgr.discovery(self._state_containers) File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at 0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at 0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at 0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at 0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at 0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x000001D2DBD59590>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>: Error while saving session data for 'tools' -> [<chimerax.log.tool.Log object at 0x000001D2AD0E7650>, <chimerax.cmd_line.tool.CommandLine object at 0x000001D2D67B6650>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0>, <chimerax.toolbar.tool.ToolbarTool object at 0x000001D2AD0EED10>, <chimerax.sideview.tool.SideViewUI object at 0x000001D2D1B4FF10>, <chimerax.model_panel.tool.ModelPanel object at 0x000001D299EF0950>, <chimerax.color_actions.tool.ColorActions object at 0x000001D2D1569550>, <chimerax.struct_measure.tool.StructMeasureTool object at 0x000001D2DBD59590>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x000001D2D18CA4D0> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> File "C:\Program Files\ChimeraX 1.12.dev202605021840\bin\Lib\site- packages\chimerax\core\session.py", line 301, in discovery raise ValueError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 369.09 OpenGL renderer: Quadro 600/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.9 Locale: en_US.cp1250 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: windows Manufacturer: Dell Inc. Model: Precision T1500 OS: Microsoft Windows 10 Pro (Build 19045.6466) Memory: 17,136,992,256 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7 CPU 870 @ 2.93GHz OSLanguage: en-GB Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 bs4: 0.0.2 build: 1.3.0 certifi: 2026.4.22 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202605021840 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: 1.2.1 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: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 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: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.6 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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 click: 8.3.3 colorama: 0.4.6 comm: 0.2.3 comtypes: 1.4.11 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.13 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.20.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.4.0 OpenMM-CUDA-12: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.9.6 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.3 pydantic-settings: 2.14.0 pydantic_core: 2.46.3 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.27 pywin32: 311 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 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: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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 sse-starlette: 3.4.1 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2026.2 Unidecode: 1.4.0 urllib3: 2.6.3 uvicorn: 0.46.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 WMI: 1.5.1 yarl: 1.23.0 }}}