'MRCGrid' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9rc202411272016 (2024-11-27 20:16:15 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  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9rc202411272016 (2024-11-27)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/madhurikanavalli/Downloads/cryosparc_P1_J440_007_volume_map_sharp.mrc

Opened cryosparc_P1_J440_007_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.846, shown at level 0.0642, step 2, values float32  

> open
> /Users/madhurikanavalli/Downloads/cryosparc_P1_J440_007_volume_map_sharp.mrc

Opened cryosparc_P1_J440_007_volume_map_sharp.mrc as #2, grid size
384,384,384, pixel 0.846, shown at level 0.0642, step 2, values float32  

> volume #1 level 0.002372

> volume #1 level 0.1946

> volume #1 level 0.2244

> volume #1 level 0.3869

> volume #2 level 0.1145

> hide #!2 target m

> volume #1 level 0.1397

> volume #1 level 0.09728

> ui tool show "Hide Dust"

> surface dust #1 size 5.07

> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J316_004_volume_map.mrc

Opened cryosparc_P1_J316_004_volume_map.mrc as #3, grid size 450,450,450,
pixel 0.846, shown at level 0.00732, step 2, values float32  

> hide #!1 models

> volume #3 level 0.04843

> volume #3 level 0.02455

> surface dust #1 size 5.07

> volume #3 level 0.03629

> close #3

> close #2

> close #1

> open /Users/madhurikanavalli/Downloads/cryosparc_P1_J316_004_volume_map.mrc

Opened cryosparc_P1_J316_004_volume_map.mrc as #1, grid size 450,450,450,
pixel 0.846, shown at level 0.00732, step 2, values float32  

> volume #1 level 0.0328

> surface dust #1 size 5.07

> open /Users/madhurikanavalli/Desktop/Madhuri/Downloads/Chimera/PDB/5ZF6.pdb

5ZF6.pdb title:  
Crystal structure of the dimeric human pnpase [more info...]  
  
Chain information for 5ZF6.pdb #2  
---  
Chain | Description | UniProt  
A B | polyribonucleotide nucleotidyltransferase 1, mitochondrial | PNPT1_HUMAN 46-669  
  

> select add #2

8555 atoms, 8618 bonds, 12 pseudobonds, 1174 residues, 3 models selected  

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-34.426,0,1,0,35.699,0,0,1,194.85

> transparency 50

> view matrix models #2,1,0,0,-33.436,0,1,0,54.7,0,0,1,172.77

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.51159,0.8,-0.31349,93.261,-0.15358,-0.44411,-0.88271,114.7,-0.84539,-0.40344,0.35007,269.91

> view matrix models
> #2,-0.86292,0.38808,-0.32367,127.77,0.010119,-0.62711,-0.77886,99.767,-0.50524,-0.67537,0.53722,238.56

> ui mousemode right "move picked models"

[Repeated 1 time(s)]

> view matrix models
> #2,-0.86292,0.38808,-0.32367,190.15,0.010119,-0.62711,-0.77886,243.7,-0.50524,-0.67537,0.53722,267.41

> view matrix models
> #2,-0.86292,0.38808,-0.32367,255.98,0.010119,-0.62711,-0.77886,209.55,-0.50524,-0.67537,0.53722,263.21

> view matrix models #1,1,0,0,3.7668,0,1,0,-2.8648,0,0,1,-1.0338

> view matrix models #1,1,0,0,4.7587,0,1,0,-14.271,0,0,1,-4.3209

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 5ZF6.pdb (#2) to map cryosparc_P1_J316_004_volume_map.mrc (#1)
using 8555 atoms  
average map value = 0.03853, steps = 424  
shifted from previous position = 21.5  
rotated from previous position = 48.7 degrees  
atoms outside contour = 4376, contour level = 0.032797  
  
Position of 5ZF6.pdb (#2) relative to cryosparc_P1_J316_004_volume_map.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.53156434 0.78529574 0.31741133 216.60349115  
-0.59268280 -0.07712947 -0.80173446 272.64177933  
-0.60511689 -0.61429768 0.50643056 269.29629968  
Axis 0.11231583 0.55279720 -0.82571206  
Axis point 223.94893953 154.17656876 0.00000000  
Rotation angle (degrees) 123.44468178  
Shift along axis -47.31759047  
  

> select clear

> color #2 #942193ff

> color #2 #ff40ffff

> view matrix models #1,1,0,0,4.5617,0,1,0,-4.7239,0,0,1,-5.1224

> view matrix models #1,1,0,0,5.0977,0,1,0,-12.996,0,0,1,-2.3173

> view matrix models #1,1,0,0,4.6817,0,1,0,-13.458,0,0,1,-2.1004

> select add #2

8555 atoms, 8618 bonds, 12 pseudobonds, 1174 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.51382,0.79057,0.33314,219.29,-0.61233,-0.065983,-0.78784,259.4,-0.60086,-0.6088,0.518,264.16

> view matrix models
> #2,-0.8003,0.53973,-0.26117,266.24,-0.10433,-0.55428,-0.82577,224.31,-0.59045,-0.63361,0.4999,264.21

> view matrix models
> #2,-0.27527,0.81352,0.51226,193.12,-0.65603,0.23055,-0.71866,257.13,-0.70274,-0.53389,0.47023,273.35

> view matrix models
> #2,0.12325,0.97481,-0.18589,181.68,-0.88012,0.020828,-0.4743,270.01,-0.45848,0.22206,0.86051,230.75

> undo

> fitmap #2 inMap #1

Fit molecule 5ZF6.pdb (#2) to map cryosparc_P1_J316_004_volume_map.mrc (#1)
using 8555 atoms  
average map value = 0.03853, steps = 800  
shifted from previous position = 2.66  
rotated from previous position = 19.4 degrees  
atoms outside contour = 4378, contour level = 0.032797  
  
Position of 5ZF6.pdb (#2) relative to cryosparc_P1_J316_004_volume_map.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.53163276 0.78531600 0.31724656 216.60927684  
-0.59276387 -0.07743845 -0.80164474 272.64802852  
-0.60497736 -0.61423290 0.50667577 269.28791065  
Axis 0.11230676 0.55264377 -0.82581599  
Axis point 223.93659470 154.15251920 0.00000000  
Rotation angle (degrees) 123.44922069  
Shift along axis -47.37834105  
  

> view matrix models
> #2,-0.31727,0.78507,0.53198,196.2,-0.73196,0.15395,-0.66373,263.32,-0.60297,-0.59997,0.52579,266.2

> undo

> view matrix models
> #2,-0.53954,0.7733,0.33302,221.56,-0.60364,-0.079536,-0.79328,259.84,-0.58696,-0.62903,0.50971,265.76

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,5.4548,0,1,0,-14.263,0,0,1,-3.3277

> fitmap #2 inMap #1

Fit molecule 5ZF6.pdb (#2) to map cryosparc_P1_J316_004_volume_map.mrc (#1)
using 8555 atoms  
average map value = 0.03853, steps = 104  
shifted from previous position = 1.67  
rotated from previous position = 1.41 degrees  
atoms outside contour = 4373, contour level = 0.032797  
  
Position of 5ZF6.pdb (#2) relative to cryosparc_P1_J316_004_volume_map.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.53159176 0.78530610 0.31733977 216.60415376  
-0.59269523 -0.07723857 -0.80171477 272.64324745  
-0.60508063 -0.61427073 0.50650657 269.29420459  
Axis 0.11232287 0.55274583 -0.82574549  
Axis point 223.94444779 154.16962908 0.00000000  
Rotation angle (degrees) 123.44675936  
Shift along axis -47.33645818  
  

> select clear

> select #2/A:202-306

831 atoms, 845 bonds, 105 residues, 1 model selected  

> select clear

> select #2/B:307-326

165 atoms, 164 bonds, 20 residues, 1 model selected  

> VOLUME GAUSS # STD2

Unknown command: VOLUME GAUSS # STD2  

> VOLUME GAUSS #1 SDEV2

Unknown command: VOLUME GAUSS #1 SDEV2  

> VOLUME GAUSS #1 SDEV 2

Unknown command: VOLUME GAUSS #1 SDEV 2  

> volume gaussian #1 sDev 2

Opened cryosparc_P1_J316_004_volume_map.mrc gaussian as #3, grid size
450,450,450, pixel 0.846, shown at step 1, values float32  

> transparency #3.1 50

> volume gaussian #1 sDev 1

Opened cryosparc_P1_J316_004_volume_map.mrc gaussian as #4, grid size
450,450,450, pixel 0.846, shown at step 1, values float32  

> transparency #3.1#4.1 0

> transparency #3.1#4.1 50

> volume #3 level 0.01531

> close #4

> close #3

> select add #1

165 atoms, 164 bonds, 20 residues, 3 models selected  

> select subtract #1

165 atoms, 164 bonds, 20 residues, 1 model selected  

> show #!1 models

> view matrix models #1,1,0,0,10.473,0,1,0,0.39417,0,0,1,6.3212

> close #2

> close #1

> open
> /Users/madhurikanavalli/Downloads/cryosparc_P17_J177_008_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P17_J177_008_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.84, shown at level 0.0549, step 2, values float32  

> volume #1 level 0.1331

> volume #1 level 0.1917

> surface dust #1 size 5.04

> volume #1 level 0.1111

> volume #1 level 0.08422

> volume gaussian #1 sDev 2

Opened cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian as #2, grid size
400,400,400, pixel 0.84, shown at step 1, values float32  

> volume gaussian #1 sDev 2

Opened cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian as #3, grid size
400,400,400, pixel 0.84, shown at step 1, values float32  

> volume gaussian #1 sDev 2

Opened cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian as #4, grid size
400,400,400, pixel 0.84, shown at step 1, values float32  

> volume gaussian #1 sDev 2

Opened cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian as #5, grid size
400,400,400, pixel 0.84, shown at step 1, values float32  

> close #5

> close #3

> close #4

> color #2 #ff2600ff models

> set bgColor white

> color #2 #ff9300ff models

> ui tool show "Segment Map"

Segmenting cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian, density
threshold 0.057985  
Only showing 60 of 115 regions.  
Showing 60 of 115 region surfaces  
701 watershed regions, grouped to 115 regions  
Showing cryosparc_P17_J177_008_volume_map_sharp gaussian.seg - 115 regions, 60
surfaces  

> view matrix models #3.2,1,0,0,-1.2928,0,1,0,2.5827,0,0,1,15.992

> undo

> select #3.56

1 model selected  

> select add #3.6

2 models selected  

> select add #3.31

3 models selected  

> select add #3.13

4 models selected  

> select add #3.19

5 models selected  

> select add #3.44

6 models selected  

> select add #3.55

7 models selected  

> select add #3.15

8 models selected  

> select add #3.2

9 models selected  

> select add #3.49

10 models selected  

> select add #3.1

11 models selected  

> select add #3.37

12 models selected  

> select add #3.28

13 models selected  

> view matrix models #3.5,1,0,0,-0.0041026,0,1,0,0.011649,0,0,1,0.048435

> view matrix models #3.5,1,0,0,-0.024744,0,1,0,-0.029211,0,0,1,0.31377

> undo

[Repeated 1 time(s)]

> view matrix models #3.5,1,0,0,-0.018869,0,1,0,0.046513,0,0,1,0.19371

> undo

> view matrix models #3.5,1,0,0,-0.012719,0,1,0,-0.014519,0,0,1,0.15728

> undo

[Repeated 2 time(s)]

> select #3.5

1 model selected  

> select #3.46

1 model selected  

> select add #3.5

2 models selected  

> select add #3.42

3 models selected  

> select #2

2 models selected  

> select #2

2 models selected  

> select #2

2 models selected  

> view matrix models #2,1,0,0,0.0011174,0,1,0,-0.049418,0,0,1,0.011975

> view matrix models #3.50,1,0,0,-4.0305,0,1,0,9.4029,0,0,1,1.2906

> undo

> view matrix models #2,1,0,0,18.371,0,1,0,-91.549,0,0,1,12.072

> hide #!2 models

> select #3.25

1 model selected  

> select #3.60

1 model selected  

> select #3.26

1 model selected  
Drag select of 1048, 6225 of 23248 triangles, 1040, 13503 of 20100 triangles,
1052, 17234 of 20344 triangles, 1065, 8311 of 23056 triangles, 1047, 9220 of
17072 triangles, 1046, 3762 of 17504 triangles, 1043, 14001 of 19292
triangles, 1025, 8732 of 15624 triangles, 910, 1033, 6385 of 11540 triangles,
966, 10886 of 13304 triangles, 890, 5304 of 10516 triangles  

> undo

Drag select of 1049, 41 of 20444 triangles, 866, 9870 of 16420 triangles,
1046, 10481 of 17504 triangles, 1032, 9058 of 16780 triangles, 985, 1089 of
16112 triangles, 1044, 3436 of 14748 triangles, 1051, 3296 of 11900 triangles,
1029, 3143 of 11024 triangles  

> select clear

> undo

[Repeated 4 time(s)]

> close #3

> show #!2 models

> ui tool show "Segment Map"

Segmenting cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian, density
threshold 0.057985  
Only showing 60 of 115 regions.  
Showing 60 of 115 region surfaces  
701 watershed regions, grouped to 115 regions  
Showing cryosparc_P17_J177_008_volume_map_sharp gaussian.seg - 115 regions, 60
surfaces  

> hide #!2 models

> show #!2 models

> view matrix models #3.56,1,0,0,8.4954,0,1,0,30.27,0,0,1,-3.2719

> undo

[Repeated 3 time(s)]

> close #3

> show #!2 models

> view matrix models #2,1,0,0,-2.3917,0,1,0,4.2321,0,0,1,16.766

> ui tool show "Segment Map"

Segmenting cryosparc_P17_J177_008_volume_map_sharp.mrc gaussian, density
threshold 0.057985  
Only showing 60 of 115 regions.  
Showing 60 of 115 region surfaces  
701 watershed regions, grouped to 115 regions  
Showing cryosparc_P17_J177_008_volume_map_sharp gaussian.seg - 115 regions, 60
surfaces  

> hide #!2 models

> select #3.36

1 model selected  

> select add #3.17

2 models selected  
Drag select of 1043, 5993 of 25780 triangles, 1062, 14564 of 20100 triangles,
1025, 17863 of 20344 triangles, 1047, 291 of 20444 triangles, 847, 13872 of
17060 triangles, 1028, 10973 of 17072 triangles, 1042, 8752 of 17504
triangles, 1072, 9505 of 19292 triangles, 1041, 10348 of 15624 triangles, 903,
10544 of 12084 triangles, 1051, 3193 of 11540 triangles, 995, 270 of 13304
triangles, 849, 7453 of 10516 triangles  

> select subtract #3.25

14 models selected  

> select add #3.25

15 models selected  

> select subtract #3.54

14 models selected  

> select subtract #3.51

13 models selected  

> select #3.7

1 model selected  

> select #3.25

1 model selected  
Drag select of 1061, 1608 of 15816 triangles, 1067, 7433 of 14748 triangles  
Drag select of 1031, 30416 of 40748 triangles, 1043, 6921 of 25780 triangles,
1063, 6676 of 22488 triangles, 1044, 16183 of 23484 triangles, 1050, 11163 of
20768 triangles, 1062, 17154 of 20100 triangles, 847, 4895 of 17060 triangles,
834, 11468 of 16420 triangles, 1013, 3166 of 17208 triangles, 1049, 5965 of
20088 triangles, 1042, 15433 of 17504 triangles, 1037, 1785 of 17928
triangles, 1072, 766 of 19292 triangles, 970, 13660 of 15136 triangles, 1055,
7673 of 13736 triangles, 1029, 2313 of 13860 triangles, 1048, 11462 of 13516
triangles, 1059, 8012 of 13532 triangles, 1068, 11454 of 12824 triangles, 903,
3373 of 12084 triangles, 1051, 243 of 11540 triangles, 1018, 430 of 10944
triangles, 1026, 4225 of 10892 triangles, 1036, 10786 of 11900 triangles,
1011, 65 of 10256 triangles, 849, 1382 of 10516 triangles  

> select #3.48

1 model selected  

> select #3.43

1 model selected  

> select #3.10

1 model selected  

> select #3.33

1 model selected  

> select #3.47

1 model selected  

> select #3.40

1 model selected  
Drag select of 1064, 1033, 1053, 1047, 1040, 1060, 1045, 985, 1070, 1008, 995,
1066  

> ui tool show Segmentations

> ui view fourup

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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-rc2024.11.27.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.  
  
Exception ignored in: <function Texture.__del__ at 0x102326200>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3165, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  

No segmentations to remove.  

[Repeated 11 time(s)]

> close session

> open
> /Users/madhurikanavalli/Downloads/cryosparc_P17_J177_008_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P17_J177_008_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.84, shown at level 0.0549, step 2, values float32  

> close #1

> open
> /Users/madhurikanavalli/Downloads/cryosparc_P1_J440_007_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P1_J440_007_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.846, shown at level 0.0642, step 2, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1888, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2182, in _drag  
cb(event)  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/histogram.py", line 416, in move_marker_cb  
cb(m)  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1888, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
AttributeError: 'NoneType' object has no attribute 'image_colors'  
  
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 750, in
on_color_changed  
colors = self.view.drawing.parent.image_colors  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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 Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11B0002QZE/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 1 day, 3 hours, 28 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2725H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 100.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    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: 2.7.1
    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-Atomic: 1.58.7
    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: 2.4.7
    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: 1.9rc202411272016
    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: 1.1.11
    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: 3.5.4
    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: 4.55.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    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
    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
    pycollada: 0.8
    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
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    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