id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20812 ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' alexandra.zahradnikova@… Tom Goddard "{{{ 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 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' -> [, , , , , , , ] -> 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' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> 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' -> [, , , , , , , ] -> 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 *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' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> 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 }}} " defect closed normal MD/Ensemble Analysis fixed Eric Pettersen all ChimeraX