'ArrayGridData' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/mariehelmke/Desktop/Mount1/hd_wi279-morphological_analysis_P_urativorans/coldshock3_10Å/defocus_6/Deconvolution/coldshock3_12_rec_deconv_BM.mrc

Opened coldshock3_12_rec_deconv_BM.mrc as #1, grid size 1024,1440,624, pixel
1, shown at step 1, values int8  

> open
> /Users/mariehelmke/Desktop/Mount1/hd_wi279-morphological_analysis_P_urativorans/coldshock3_10Å/defocus_6/Deconvolution/MemBrain/Thresholds/Components/coldshock3_12_rec_deconv_scores_threshold_2.5_components_106.mrc

Opened coldshock3_12_rec_deconv_scores_threshold_2.5_components_106.mrc as #2,
grid size 1024,1440,624, pixel 1, shown at step 1, values int16  

> volume #2 region 0,0,0,1023,1439,623 step 4

[Repeated 1 time(s)]

> volume #1 region 0,0,0,1023,1439,623 step 4

[Repeated 1 time(s)]

> volume #1 change image level 0,0 level 0.1,0.8 level 1,1

> volume #1 level 1

> volume onesmask #2 invertMask true

Opened mask masked as #3, grid size 52,101,23, pixel 12, shown at step 1,
values int8  

> volume #2 change image level 0,0 level 10.6,0.8 level 106,1

> volume #2 level 61.33

> volume #2 level 1

> volume onesmask #2 invertMask true

Opened mask masked as #4, grid size 52,101,23, pixel 12, shown at step 1,
values int8  

> close #3

> volume #4 level 1

> vop multiply #4,1

Opened volume product as #3, grid size 88,122,54, pixel 12, shown at step 1,
values int8  

> volume #3 step 4

> volume #3 step 2

> volume #3 step 1

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> segmentations create #3

Opened segmentation 1 of volume product as #8, grid size 88,122,54, pixel 12,
shown at level 0.501, step 1, values float64  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 521, in
_on_axis_changed  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 521, in
_on_axis_changed  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Segment Map"

Segmenting volume product, density threshold 1.000000  
Showing 4 region surfaces  
66124 watershed regions, grouped to 4 regions  
Showing volume product.seg - 4 regions, 4 surfaces  

> select #5.3

1 model selected  
Deleted 1 regions  

> hide #!3 models

> hide #!5 models

> show #!5 models

> hide #!8 models

> select #5.2

1 model selected  

> select add #5.1

2 models selected  

> select add #5.4

3 models selected  

> select subtract #5.4

2 models selected  
Grouped 2 regions  
Grouped 1 regions  

> select clear

> select add #5.4

1 model selected  

> select add #5.1

2 models selected  
Grouped 2 regions  

> show #!2 models

> select clear

> select #5.1

1 model selected  
Ungrouped to 2 regions  
Ungrouped to 1057 regions, but did not show all surfaces, see Options  
Grouped 62 regions  
Grouped 1 regions  
[Repeated 1 time(s)]

> select clear

Smoothing and grouping, standard deviation 5 voxels  
Showing 2 region surfaces  
Got 2 regions after smoothing 5 voxels.  

> select #5.1

1 model selected  
Ungrouped to 974 regions, but did not show all surfaces, see Options  
Only showing 60 of 975 regions.  
Showing 60 of 975 region surfaces  

> select #5.1

1 model selected  
Drag select of 70973, 1081 of 3084 triangles, 66779, 454 of 496 triangles,
66786, 213 of 748 triangles, 66839, 355 of 404 triangles, 66936, 66970, 70971,
2756 of 6156 triangles, 67595, 191 of 688 triangles, 68035, 102 of 592
triangles, 70898, 70853, 70816, 70736, 494 of 496 triangles, 70662, 268 of 496
triangles, 68730, 67981, 66566, 67114, 70884, 70737, 260 of 404 triangles,
67982, 70531, 68354, 2
coldshock3_12_rec_deconv_scores_threshold_2.5_components_106.mrc  
Grouped 23 regions  
Grouped 1 regions  

> select clear

> hide #!2 models

Drag select of 66729, 66755, 66782, 67028, 67038, 67601, 68099, 66348, 66437,
67118, 67122, 67532, 67592, 67715, 68496, 68332, 70561, 70308, 70167, 69863,
69401, 69180, 68920, 68425, 70549, 70137, 69403, 70886, 69192, 67379, 70112,
69872, 69791, 68856, 68424, 66366, 70975  
Grouped 37 regions  
Only showing 60 of 917 regions.  
Showing 60 of 917 region surfaces  

> select #5.1

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #5.61

1 model selected  
Ungrouped to 3 regions, but did not show all surfaces, see Options  

> show #!2 models

> hide #!2 models

> select add #5.2

2 models selected  
Grouped 2 regions  

> show #!2 models

> select clear

> select #5.62

1 model selected  

> hide #!2 models

Drag select of 66837, 70930, 70928, 70911, 70866, 70854, 70826, 70817, 70809,
70719, 70663, 70580, 70472, 70309, 70297, 69873, 69864, 69193, 69181, 69009,
68991, 68802, 68732, 68506, 66383, 67536, 67218, 67115, 66921, 66841, 66733,
69087, 69054, 68855, 68783, 68712, 70899, 70838, 70835, 70832, 70831, 70805,
70801, 70797, 70793, 70771, 70764, 70760, 70717, 70706, 70694, 70652, 70640,
70637, 70562, 70530, 70452, 70349, 70977, 29827 of 31120 triangles  
Grouped 59 regions  
Only showing 60 of 861 regions.  
Showing 60 of 861 region surfaces  

> show #!2 models

> select #5.2

1 model selected  
Ungrouped to 1892 regions, but did not show all surfaces, see Options  

> select #5.1

1 model selected  

> select add #5.3

2 models selected  
Grouped 2 regions  
Only showing 60 of 2751 regions.  
Showing 60 of 2751 region surfaces  

> select #5.2

1 model selected  
Ungrouped to 930 regions, but did not show all surfaces, see Options  
Drag select of 70964, 11652 of 27716 triangles, 70979, 23692 of 34804
triangles, 66696, 1410 of 2676 triangles, 68349, 68350, 68313, 67623, 1554 of
1960 triangles, 68023, 68104, 68068, 1373 of 1672 triangles, 66302, 66289,
66490, 68420, 68346, 780 of 1140 triangles, 66616, 858 of 1436 triangles,
67591, 67270, 66681, 68129, 1188 of 1416 triangles, 66751, 68065, 497 of 1020
triangles, 68456, 67337, 66500, 69901, 69661, 69338, 68907, 68833, 66253,
66163, 67272, 66227, 69787, 69228, 68880, 68525, 66150, 68307, 1164 of 1168
triangles, 66274, 68026, 66544, 67570, 68421, 66760, 66341, 66726, 70186,
69922, 69789, 69681, 69514, 69464, 69275, 68918, 68711, 68636, 66154, 2
coldshock3_12_rec_deconv_scores_threshold_2.5_components_106.mrc  

> select #5.1

1 model selected  
Drag select of 70964, 457 of 27716 triangles, 70979, 5649 of 34804 triangles,
67270, 941 of 1096 triangles, 67337, 958 of 1016 triangles, 69901, 69661, 898
of 956 triangles, 69338, 595 of 956 triangles, 68907, 255 of 956 triangles,
68833, 135 of 956 triangles, 66253, 66163, 67272, 69787, 69228, 725 of 948
triangles, 68880, 379 of 948 triangles, 68525, 15 of 948 triangles, 66150,
66341, 70186, 69922, 69789, 69681, 877 of 884 triangles, 69514, 742 of 884
triangles, 69464, 592 of 884 triangles, 69275, 375 of 884 triangles, 68918,
247 of 884 triangles, 68636, 132 of 884 triangles, 66154  

> select subtract #5.1

27 models selected  
Drag select of 70964, 229 of 27716 triangles, 70979, 4946 of 34804 triangles,
66696, 1715 of 2676 triangles, 68349, 68350, 68313, 1794 of 1796 triangles,
67623, 1679 of 1960 triangles, 68023, 68104, 1124 of 1216 triangles, 68068,
1474 of 1672 triangles, 66302, 66289, 66490, 68420, 118 of 1040 triangles,
68346, 949 of 1140 triangles, 66616, 954 of 1436 triangles, 67591, 66681,
68129, 1281 of 1416 triangles, 66751, 68065, 704 of 1020 triangles, 68456, 391
of 944 triangles, 66500, 66227, 68307, 1148 of 1168 triangles, 66274, 68026,
66544, 67570, 68421, 615 of 916 triangles, 66760, 66726, 29978, 29979  
Grouped 59 regions  
Only showing 60 of 3622 regions.  
Showing 60 of 3622 region surfaces  

> select clear

Drag select of 68711, 70980, 13285 of 50156 triangles, 68015, 67963, 67894,
66510, 66506, 66502, 66499, 68479, 68409, 66345, 67174, 67068, 66917, 66916,
66728, 66628, 66308, 66216, 66213, 66211, 66199, 69888, 69634, 69325, 69318,
69308, 69281, 69263, 69108, 69084, 69027, 68839, 68801, 68788, 68762, 68722,
68678, 68673, 68534, 68465, 68394, 68379, 68176, 68149, 68111, 66559, 899 of
968 triangles, 66472, 68497, 68430, 66393, 67565, 900 of 944 triangles, 67533,
882 of 944 triangles  
Grouped 54 regions  
Drag select of 66876, 810 of 848 triangles, 66830, 66822, 66765, 67505, 716 of
808 triangles, 70981, 4346 of 55424 triangles  
Grouped 6 regions  
Only showing 60 of 3564 regions.  
Showing 60 of 3564 region surfaces  
Drag select of 70982, 7333 of 58188 triangles, 67373, 67307, 66881, 511 of 808
triangles, 66879, 442 of 808 triangles, 66877, 373 of 808 triangles, 66834,
66833, 66832, 66829, 773 of 808 triangles, 66828, 722 of 808 triangles, 66827,
677 of 808 triangles, 66825, 620 of 808 triangles, 66773, 66771, 66770, 66767,
66766, 66143, 501 of 872 triangles, 69960, 475 of 868 triangles, 69902, 463 of
868 triangles, 69788, 412 of 868 triangles, 69662, 191 of 868 triangles,
66269, 482 of 868 triangles, 66257, 533 of 868 triangles, 67863, 72 of 664
triangles  
Grouped 26 regions  
Only showing 60 of 3539 regions.  
Showing 60 of 3539 region surfaces  
Drag select of 66923, 66920, 66918, 66712, 69339, 69068, 69062, 846 of 868
triangles, 68884, 68834, 68526, 66675, 66637, 68145, 68106, 66597, 68056,
68028, 68893, 68809, 773 of 784 triangles, 68580, 773 of 808 triangles, 66503,
69121, 68906, 66604, 66602, 24 of 688 triangles, 66541, 68448, 543 of 704
triangles, 68517, 592 of 696 triangles, 68894, 66210, 69136, 69122, 69290, 5
of 496 triangles, 68850, 197 of 496 triangles, 68703, 319 of 496 triangles,
68696, 81 of 496 triangles, 68162, 68038, 68445, 431 of 496 triangles, 67583,
66740, 66629, 66158, 68816, 66643, 68140, 66865, 67507, 66671, 66631, 69271,
86 of 404 triangles, 68704, 376 of 404 triangles, 68132  

> select add #5.54

54 models selected  

> select add #5.37

55 models selected  

> select add #5.10

56 models selected  

> select add #5.15

57 models selected  
Grouped 57 regions  
Only showing 60 of 3483 regions.  
Showing 60 of 3483 region surfaces  

> select add #5.1

2 models selected  
Grouped 2 regions  

> select clear

> select #5.1

1 model selected  
Drag select of 70964, 5941 of 27716 triangles, 68674, 67901, 66743, 69149,
69138, 69124, 69103, 68908, 68581, 67606, 67504, 66138, 69274, 68895, 68709,
68685, 68521, 68073, 68045, 67906, 66538, 66667, 66200, 66139, 69315, 69252,
69248, 69098, 69076, 69042, 69037, 68853, 68824, 68528, 68485, 68370, 68075,
68040, 68007, 66575, 66523, 68463, 68447, 67607, 67585, 67553, 66948, 69553,
69416, 68103, 68082, 68043, 67817, 67769, 66583, 66466, 66390  

> select subtract #5.62

57 models selected  
Grouped 57 regions  
Only showing 60 of 3426 regions.  
Showing 60 of 3426 region surfaces  

> select add #5.1

2 models selected  
Grouped 2 regions  
Drag select of 70964, 2656 of 27716 triangles, 67635, 67608, 67590, 67581,
67562, 67550, 67531, 67480, 67425, 67370, 67304, 66737, 515 of 516 triangles,
70916, 70703, 70636, 70622, 70612, 70536, 70524, 70510, 70496, 70458, 70445,
70413, 70400, 70378, 70367, 70346, 70337, 70324, 70322, 70315, 70282, 70278,
70277, 70266, 70262, 70163, 70143, 70129, 70118, 70111, 70 of 372 triangles,
70099, 70084, 70048, 70044, 70019, 70012, 69993, 69989, 69988, 69984, 69983,
69939, 69907, 69882  

> select subtract #5.62

57 models selected  
Grouped 57 regions  

> select clear

Only showing 60 of 3369 regions.  
Showing 60 of 3369 region surfaces  

> select #5.1

1 model selected  
Drag select of 70964, 2728 of 27716 triangles, 70168, 5 of 332 triangles,
69859, 175 of 372 triangles, 69836, 69814, 69783, 69776, 69740, 86 of 372
triangles, 69738, 69714, 69698, 69695, 69633, 69626, 69620, 69614, 69592,
69590, 69575, 69572, 105 of 372 triangles, 69568, 69541, 69540, 23 of 332
triangles, 69483, 69437, 69399, 69394, 69393, 69366, 69365, 69300, 272 of 336
triangles, 69291, 69273, 69260, 263 of 336 triangles, 69251, 69246, 69226,
69207, 66128, 69163, 69148, 363 of 460 triangles, 69144, 69117, 69092, 246 of
336 triangles, 69080, 69060, 233 of 336 triangles, 69057, 68982, 68969, 68950,
68935, 68900, 68883, 68863, 68860, 224 of 336 triangles, 68823, 68799, 62 of
372 triangles, 68789, 208 of 336 triangles, 2
coldshock3_12_rec_deconv_scores_threshold_2.5_components_106.mrc  

> select subtract #5.62

60 models selected  
Grouped 58 regions  
Grouped 1 regions  

> select add #5.62

4 models selected  
Ungrouped to 3 regions  

> select clear

> select #5.3

1 model selected  
Ungrouped to 3 regions  

> select #5.5

1 model selected  

> select add #5.6

2 models selected  

> select add #5.1

3 models selected  

> select add #5.4

4 models selected  
Grouped 4 regions  
Ungrouped to 4 regions  

> select clear

> select #5.5

1 model selected  

> select add #5.6

2 models selected  

> select add #5.4

3 models selected  
Grouped 3 regions  

> select clear

> select #5.3

1 model selected  
Ungrouped to 196 regions  

> select #5.1

1 model selected  

> select #5.74

1 model selected  

> select add #5.121

2 models selected  

> select add #5.36

3 models selected  

> select add #5.89

4 models selected  

> select add #5.2

5 models selected  
Grouped 5 regions  

> select subtract #5.2

Nothing selected  

> select #5.2

1 model selected  
Ungrouped to 5 regions  

> select clear

> select #5.121

1 model selected  
Ungrouped to 379 regions, but did not show all surfaces, see Options  

> select add #5.74

4 models selected  

> select add #5.89

5 models selected  

> select add #5.3

6 models selected  
Grouped 6 regions  

> select add #5.36

2 models selected  

> select add #5.86

3 models selected  
Grouped 3 regions  

> select clear

Drag select of 67091, 16 of 688 triangles, 67142, 88 of 1536 triangles, 67216,
37 of 1116 triangles, 67276, 234 of 1404 triangles, 67348, 251 of 1120
triangles, 67415, 301 of 1356 triangles, 67482, 293 of 1128 triangles, 67639,
12 of 236 triangles, 67662, 88 of 1176 triangles, 67663, 62 of 1080 triangles,
67665, 40 of 236 triangles, 67666, 93 of 336 triangles, 67667, 77 of 336
triangles, 67684, 111 of 1224 triangles, 67686, 33 of 236 triangles, 67687, 61
of 236 triangles, 67688, 136 of 336 triangles, 67707, 48 of 236 triangles,
67708, 78 of 236 triangles, 67710, 166 of 336 triangles, 67935, 282 of 1008
triangles, 68192, 117 of 1360 triangles, 68203, 59 of 236 triangles, 68205, 86
of 236 triangles, 68207, 191 of 336 triangles, 68241, 141 of 1284 triangles,
68245, 71 of 236 triangles, 68247, 97 of 236 triangles, 68249, 203 of 336
triangles, 68281, 84 of 236 triangles, 68282, 115 of 236 triangles, 68285, 220
of 336 triangles, 68318, 170 of 1108 triangles, 68323, 95 of 236 triangles,
68325, 122 of 236 triangles, 68326, 235 of 336 triangles, 69883, 194 of 236
triangles, 69887, 120 of 236 triangles, 69897, 168 of 296 triangles, 69903,
167 of 236 triangles, 69912, 186 of 236 triangles, 69916, 154 of 296
triangles, 69919, 137 of 236 triangles, 69920, 190 of 296 triangles, 69923,
169 of 236 triangles, 69925, 181 of 296 triangles, 69927, 156 of 236
triangles, 69931, 158 of 236 triangles, 69936, 147 of 236 triangles, 69940,
143 of 296 triangles, 69961, 131 of 236 triangles, 69962, 247 of 336
triangles, 70050, 132 of 296 triangles, 70052, 106 of 236 triangles, 70638,
133 of 236 triangles, 70995, 178 of 11424 triangles  

> select #5.2

1 model selected  
Ungrouped to 3 regions  

> select #5.74

1 model selected  

> select #5.3

1 model selected  

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
  
You deleted or moved a volume file that is still open in ChimeraX.  
  
/Users/mariehelmke/Desktop/Mount1/hd_wi279-morphological_analysis_P_urativorans/coldshock3_10Å/defocus_6/Deconvolution/MemBrain/Thresholds/Components/coldshock3_12_rec_deconv_scores_threshold_2.5_components_106.mrc  
  
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved  
self._update_position_label_text()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,12
      Model Number: MXCV3D/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 35 Tage, 3 Stunden und 45 Minuten

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.5.0
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    pandas: 2.2.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 18.1.0
    pycollada: 0.8
    pydantic: 2.10.5
    pydantic_core: 2.27.2
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    starfile: 0.5.11
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13