'MRCGrid' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.6.6-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  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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/mbaker2/Downloads/cryosparc_P33_J52_009_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P33_J52_009_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 1.08, shown at level 0.0513, step 2, values float32  

> open /Users/mbaker2/Library/CloudStorage/GoogleDrive-
> mariah.baker@gmail.com/.shortcut-targets-by-
> id/1JMKyVTgQqt6XCwoCyiLTpf4311yhUiiE/IP3R-2024/p-Mutants/Image_Processing/phenix/Maps/EGTA/7lhf.cif

7lhf.cif title:  
Structure of full-length IP3R1 channel solubilized in LNMG & lipid in the apo-
state [more info...]  
  
Chain information for 7lhf.cif #2  
---  
Chain | Description | UniProt  
A B C D | Inositol 1,4,5-trisphosphate receptor type 1 | ITPR1_RAT 6-2741  
  
Non-standard residues in 7lhf.cif #2  
---  
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol  
ZN — zinc ion  
  

> close #1

> select add #2

72092 atoms, 73240 bonds, 64 pseudobonds, 9232 residues, 4 models selected  

> show sel cartoons

> hide sel atoms

> ~label (#!2 & sel) atoms

> select clear

[Repeated 1 time(s)]

> select add #2

72092 atoms, 73240 bonds, 64 pseudobonds, 9232 residues, 4 models selected  

> ~label (#!2 & sel) residues

> hide #2.1 models

> hide #!2.2 models

> show #!2.2 models

> select subtract #2.2

72092 atoms, 73240 bonds, 12 pseudobonds, 9232 residues, 2 models selected  

> select subtract #2.1

72092 atoms, 73240 bonds, 9232 residues, 1 model selected  

> select add #2

72092 atoms, 73240 bonds, 64 pseudobonds, 9232 residues, 4 models selected  

> select subtract #2

Nothing selected  

> select add #2.2

52 pseudobonds, 2 models selected  
No visible atoms selected  

> ui tool show "Selection Inspector"

> setattr =sel p halfbond false

Assigning halfbond attribute to 52 items  

> setattr =sel p display false

Assigning display attribute to 52 items  

> setattr =sel p display true

Assigning display attribute to 52 items  

> setattr sel g halfbond false

Assigning halfbond attribute to 1 item  

> setattr sel g display false

Assigning display attribute to 1 item  

> setattr sel g display true

Assigning display attribute to 1 item  

> setattr sel g color #7dbaff

Assigning color attribute to 1 item  

> select clear

[Repeated 2 time(s)]Drag select of 1 pseudobonds  

> select up

52 pseudobonds, 1 model selected  

> ui tool show Toolbar

> ui tool show "Selection Inspector"

> label delete sel

> close

> open /Users/mbaker2/Downloads/cryosparc_P46_J127_008_volume_map_sharp.mrc
> /Users/mbaker2/Downloads/cryosparc_P46_J123_010_volume_map_sharp.mrc

Opened cryosparc_P46_J127_008_volume_map_sharp.mrc as #1.1, grid size
480,480,480, pixel 1.08, shown at level 0.176, step 2, values float32  
Opened cryosparc_P46_J123_010_volume_map_sharp.mrc as #1.2, grid size
480,480,480, pixel 1.08, shown at level 0.183, step 2, values float32  

> volume #1.1 step 1

> volume #1.2 step 1

> ui tool show "Hide Dust"

> surface dust #1.1 size 6.48

> surface dust #1.2 size 6.48

> volume #1.1 level 0.3922

> open /Users/mbaker2/Library/CloudStorage/GoogleDrive-
> mariah.baker@gmail.com/.shortcut-targets-by-
> id/1_VqDHcZ-I0-bu9YKfodXzROVX_Z7vJMF/CellCa_Review2022/ip3r2-af2-model.pdb

Chain information for ip3r2-af2-model.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> hide atoms

> show cartoons

> select clear

> undo

Drag select of 17 residues  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,14.218,0,1,0,30.299,0,0,1,-0.23536

> view matrix models #2,1,0,0,20.069,0,1,0,26.915,0,0,1,-0.76718

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.4116,0.90874,0.069074,-73.554,-0.91116,0.40874,0.052135,366.83,0.019144,-0.084397,0.99625,15.582

> view matrix models
> #2,0.30394,0.95101,-0.056607,-24.998,0.92442,-0.28003,0.25891,42.297,0.23037,-0.13102,-0.96424,494.1

> view matrix models
> #2,0.29316,0.95099,-0.098398,-11.429,0.95592,-0.2898,0.047215,93.036,0.016385,-0.1079,-0.99403,546.89

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.29316,0.95099,-0.098398,-4.3788,0.95592,-0.2898,0.047215,82.836,0.016385,-0.1079,-0.99403,546.08

> view matrix models
> #2,0.29316,0.95099,-0.098398,2.2782,0.95592,-0.2898,0.047215,81.323,0.016385,-0.1079,-0.99403,545.54

> ui tool show "Fit in Map"

> fitmap #2 inMap #1.1

Fit molecule ip3r2-af2-model.pdb (#2) to map
cryosparc_P46_J127_008_volume_map_sharp.mrc (#1.1) using 77896 atoms  
average map value = 0.3167, steps = 236  
shifted from previous position = 35.9  
rotated from previous position = 18.1 degrees  
atoms outside contour = 52616, contour level = 0.39225  
  
Position of ip3r2-af2-model.pdb (#2) relative to
cryosparc_P46_J127_008_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.55978237 0.82863968 -0.00002926 -67.63357311  
0.82863968 -0.55978237 0.00005009 195.88970806  
0.00002512 -0.00005228 -1.00000001 493.49784256  
Axis -0.88311538 -0.46915587 0.00000634  
Axis point 0.00000000 115.91815065 246.74571189  
Rotation angle (degrees) 179.99667918  
Shift along axis -32.17142693  
  

> volume #1.1 level 0.3179

> volume #1.1 color #b2b2b2b9

> ui tool show "Color Actions"

> set bgColor white

> lighting soft

> lighting full

> lighting simple

> view

> volume #1.1 level 0.3285

> volume #1.1 level 0.2594

> volume #1.2 color #ffffb29f

> volume #1.2 color #a5ffb29f

> volume #1.2 color #a595b29f

> volume #1.2 color #a595ff9f

> volume #1.2 color #a595e39f

> volume #1.1 level 0.2541

> volume #1.2 level 0.2629

> volume #1.2 level 0.3277

> volume #1.1 level 0.3869

> open /Users/mbaker2/Downloads/cryosparc_P36_J14_008_volume_map_sharp.mrc

Opened cryosparc_P36_J14_008_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 1.08, shown at level 0.0485, step 2, values float32  

> hide #!1 models

> hide #!1.1 models

> volume #3 step 1

> volume #3 level 0.0638

> volume #3 color #b2ffffb4

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.40154,0.8148,-0.41817,83.2,0.91542,-0.34324,0.21021,69.036,0.027753,-0.46721,-0.88371,566.25

> view matrix models
> #2,0.66671,-0.71129,-0.22263,328.41,0.71186,0.6962,-0.092524,-47.842,0.22081,-0.096796,0.9705,-55.613

> view matrix models
> #2,0.72691,-0.64638,-0.23192,301.42,0.64307,0.7592,-0.10037,-44.408,0.24095,-0.076183,0.96754,-64.427

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.72691,-0.64638,-0.23192,280.29,0.64307,0.7592,-0.10037,-62.378,0.24095,-0.076183,0.96754,-39.037

> view matrix models
> #2,0.72691,-0.64638,-0.23192,278.04,0.64307,0.7592,-0.10037,-65.144,0.24095,-0.076183,0.96754,-38.485

> fitmap #2 inMap #3

Fit molecule ip3r2-af2-model.pdb (#2) to map
cryosparc_P36_J14_008_volume_map_sharp.mrc (#3) using 77896 atoms  
average map value = 0.06474, steps = 196  
shifted from previous position = 10  
rotated from previous position = 15.9 degrees  
atoms outside contour = 40622, contour level = 0.063802  
  
Position of ip3r2-af2-model.pdb (#2) relative to
cryosparc_P36_J14_008_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.82098555 -0.57094898 0.00010835 178.72123797  
0.57094899 0.82098554 -0.00009092 -90.04954819  
-0.00003704 0.00013651 1.00000000 0.00355198  
Axis 0.00019917 0.00012732 0.99999997  
Axis point 232.96270585 239.98210825 0.00000000  
Rotation angle (degrees) 34.81642875  
Shift along axis 0.02768197  
  

> select clear

> volume #3 level 0.07513

> open 7lhf fromDatabase pdb format mmcif

Summary of feedback from opening 7lhf fetched from pdb  
---  
note | Fetching compressed mmCIF 7lhf from http://files.rcsb.org/download/7lhf.cif  
  
7lhf title:  
Structure of full-length IP3R1 channel solubilized in LNMG & lipid in the apo-
state [more info...]  
  
Chain information for 7lhf #4  
---  
Chain | Description | UniProt  
A B C D | Inositol 1,4,5-trisphosphate receptor type 1 | ITPR1_RAT 6-2741  
  
Non-standard residues in 7lhf #4  
---  
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol  
ZN — zinc ion  
  

> select add #4

72092 atoms, 73240 bonds, 64 pseudobonds, 9232 residues, 4 models selected  

> ~label (#!4 & sel) atoms

> ~label (#!4 & sel) residues

[Repeated 1 time(s)]

> ~label (#!4 & sel) atoms

> ui tool show "Color Actions"

> ui tool show "Selection Inspector"

> label delete sel

> select clear

> show cartoons

> hide atoms

> hide #!4 models

> show #!4 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> fitmap #4 inMap #1.2

Fit molecule 7lhf (#4) to map cryosparc_P46_J123_010_volume_map_sharp.mrc
(#1.2) using 72092 atoms  
average map value = 0.1028, steps = 240  
shifted from previous position = 25.4  
rotated from previous position = 10.9 degrees  
atoms outside contour = 65987, contour level = 0.32771  
  
Position of 7lhf (#4) relative to cryosparc_P46_J123_010_volume_map_sharp.mrc
(#1.2) coordinates:  
Matrix rotation and translation  
0.98634443 -0.16455107 0.00690043 59.83014507  
0.16447502 0.98198965 -0.09297466 3.44212111  
0.00852293 0.09283999 0.99564456 -24.52880060  
Axis 0.49173856 -0.00429379 0.87073231  
Axis point 15.89845590 338.22651304 0.00000000  
Rotation angle (degrees) 10.89072132  
Shift along axis 8.04799060  
  

> hide #!2 models

> undo

Drag select of 32 residues  

> view matrix models
> #4,0.98634,-0.16455,0.0069004,40.885,0.16448,0.98199,-0.092975,-8.5508,0.0085229,0.09284,0.99564,-21.905

> fitmap #4 inMap #1.2

Fit molecule 7lhf (#4) to map cryosparc_P46_J123_010_volume_map_sharp.mrc
(#1.2) using 72092 atoms  
average map value = 0.1061, steps = 256  
shifted from previous position = 24.5  
rotated from previous position = 11.3 degrees  
atoms outside contour = 65580, contour level = 0.32771  
  
Position of 7lhf (#4) relative to cryosparc_P46_J123_010_volume_map_sharp.mrc
(#1.2) coordinates:  
Matrix rotation and translation  
0.94954420 -0.31120848 -0.03892416 112.86266747  
0.29657541 0.93133032 -0.21134535 16.26818227  
0.10202372 0.18913780 0.97663609 -60.08579517  
Axis 0.54018115 -0.19011383 0.81979330  
Axis point 19.40362639 344.55900755 0.00000000  
Rotation angle (degrees) 21.75838580  
Shift along axis 8.61554722  
  

> hide #!2 models

> view matrix models
> #4,0.94954,-0.31121,-0.038924,98.805,0.29658,0.93133,-0.21135,9.0869,0.10202,0.18914,0.97664,-61.604

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.80521,-0.59151,0.041837,178.11,0.58723,0.78561,-0.19487,-29.249,0.0824,0.18148,0.97994,-56.026

> view matrix models
> #4,0.83916,-0.54315,0.028124,162.24,0.53947,0.82467,-0.16999,-33.56,0.06914,0.15783,0.98504,-48.642

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.83916,-0.54315,0.028124,159.99,0.53947,0.82467,-0.16999,-34.165,0.06914,0.15783,0.98504,-50.896

> fitmap #4 inMap #1.2

Fit molecule 7lhf (#4) to map cryosparc_P46_J123_010_volume_map_sharp.mrc
(#1.2) using 72092 atoms  
average map value = 0.1031, steps = 148  
shifted from previous position = 5.8  
rotated from previous position = 8.3 degrees  
atoms outside contour = 65733, contour level = 0.32771  
  
Position of 7lhf (#4) relative to cryosparc_P46_J123_010_volume_map_sharp.mrc
(#1.2) coordinates:  
Matrix rotation and translation  
0.80034409 -0.59333364 0.08604959 168.48825585  
0.59827543 0.79970641 -0.05036037 -72.88412726  
-0.03893391 0.09178698 0.99501724 -7.31428025  
Axis 0.11781322 0.10358765 0.98761817  
Axis point 195.41884615 217.20266224 0.00000000  
Rotation angle (degrees) 37.10475467  
Shift along axis 5.07653251  
  

> fitmap #4 inMap #3

Fit molecule 7lhf (#4) to map cryosparc_P36_J14_008_volume_map_sharp.mrc (#3)
using 72092 atoms  
average map value = 0.07417, steps = 144  
shifted from previous position = 9.92  
rotated from previous position = 10.1 degrees  
atoms outside contour = 37170, contour level = 0.075128  
  
Position of 7lhf (#4) relative to cryosparc_P36_J14_008_volume_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.82060312 -0.57149848 0.00002291 178.94285431  
0.57149848 0.82060312 0.00002149 -90.11479479  
-0.00003108 -0.00000454 1.00000000 0.02408688  
Axis -0.00002278 0.00004723 1.00000000  
Axis point 233.00923570 239.96866255 0.00000000  
Rotation angle (degrees) 34.85478556  
Shift along axis 0.01575452  
  

> volume #1.2 level 0.2938

> volume #1.2 level 0.2999

> volume #3 level 0.05531

> volume #3 level 0.06154

> volume #3 level 0.08589

> volume #3 level 0.06437

> surface dust #3 size 10.8

> surface dust #1.2 size 6.14

> surface dust #1.2 size 5.79

[Repeated 1 time(s)]

> volume #3 level 0.1

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open "/Users/mbaker2/Downloads/cryosparc_P19_J157_009_volume_map_sharp
> (1).mrc"

Opened cryosparc_P19_J157_009_volume_map_sharp (1).mrc as #5, grid size
440,440,440, pixel 1.08, shown at level 0.209, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.4397

> fitmap #4 inMap #5

Fit molecule 7lhf (#4) to map cryosparc_P19_J157_009_volume_map_sharp (1).mrc
(#5) using 72092 atoms  
average map value = 0.4237, steps = 208  
shifted from previous position = 3.3  
rotated from previous position = 19.1 degrees  
atoms outside contour = 43114, contour level = 0.4397  
  
Position of 7lhf (#4) relative to cryosparc_P19_J157_009_volume_map_sharp
(1).mrc (#5) coordinates:  
Matrix rotation and translation  
0.96238900 -0.27167518 0.00001985 75.00607245  
0.27167518 0.96238900 0.00012424 -52.93376967  
-0.00005286 -0.00011418 0.99999999 3.35468098  
Axis -0.00043879 0.00013382 0.99999989  
Axis point 228.68339782 244.43350552 0.00000000  
Rotation angle (degrees) 15.76397575  
Shift along axis 3.31468528  
  

> select #5/A:691-1581

Nothing selected  

> select #4/A:691-1581

5196 atoms, 5271 bonds, 4 pseudobonds, 721 residues, 2 models selected  

> molmap sel 20

Opened 7lhf map 20 as #6, grid size 27,40,30, pixel 6.67, shown at level
0.0253, step 1, values float32  

> volume resample #6 onGrid #5

Opened 7lhf map 20 resampled as #7, grid size 440,440,440, pixel 1.08, shown
at step 1, values float32  

> save /Users/mbaker2/Desktop/HD-ARM2_mask.mrc models #7

> show #!6 models

> hide #!6 models

> show #!5 models

> volume #5 color #b2b2ff

> select clear

> volume #5 color #b2b2ff97

> show #!4 atoms

> style #!4 stick

Changed 72092 atom styles  

> volume #5 level 0.373

> hide #!3 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> volume #3 level 0.08362

> volume #3 level 0.06946

> fitmap #3 inMap #5

Fit map cryosparc_P36_J14_008_volume_map_sharp.mrc in map
cryosparc_P19_J157_009_volume_map_sharp (1).mrc using 453874 points  
correlation = 0.9035, correlation about mean = 0.5334, overlap = 2.108e+04  
steps = 224, shift = 3.01, angle = 19.1 degrees  
  
Position of cryosparc_P36_J14_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P19_J157_009_volume_map_sharp (1).mrc (#5) coordinates:  
Matrix rotation and translation  
0.94497312 0.32714800 -0.00000406 -64.65913881  
-0.32714800 0.94497312 0.00000004 90.80713855  
0.00000385 0.00000129 1.00000000 3.01303519  
Axis 0.00000190 -0.00001208 -1.00000000  
Axis point 237.60540901 237.61056019 0.00000000  
Rotation angle (degrees) 19.09576155  
Shift along axis -3.01425526  
  

> show #!5 models

> hide #!5 models

> show #!5 models

> volume #5 level 0.3125

> volume #3 level 0.07468

> surface dust #5 size 6.48

> volume #3 level 0.06555

> open /Users/mbaker2/Downloads/cryosparc_P36_J16_007_volume_map_sharp.mrc

Opened cryosparc_P36_J16_007_volume_map_sharp.mrc as #8, grid size
440,440,440, pixel 1.08, shown at level 0.048, step 2, values float32  

> fitmap #8 inMap #5

Fit map cryosparc_P36_J16_007_volume_map_sharp.mrc in map
cryosparc_P19_J157_009_volume_map_sharp (1).mrc using 106326 points  
correlation = 0.927, correlation about mean = 0.7429, overlap = 3718  
steps = 216, shift = 2.77, angle = 19 degrees  
  
Position of cryosparc_P36_J16_007_volume_map_sharp.mrc (#8) relative to
cryosparc_P19_J157_009_volume_map_sharp (1).mrc (#5) coordinates:  
Matrix rotation and translation  
0.94534968 0.32605826 0.00003278 -64.48667301  
-0.32605826 0.94534967 0.00005671 90.45609678  
-0.00001249 -0.00006429 1.00000000 2.79110991  
Axis -0.00018555 0.00006942 -0.99999998  
Axis point 237.59945656 237.60193856 0.00000000  
Rotation angle (degrees) 19.02970216  
Shift along axis -2.77286475  
  

> volume #8 step 1

> volume #8 level 0.06303

> surface dust #8 size 6.48

> volume #8 level 0.04083

> volume #8 level 0.0487

> show #!6 models

> volume #8 color #b2ffb2bc

> hide #!3 models

> volume #8 color #b2ffb2a8

> show #!4 models

> select clear

> volume #8 level 0.05515

> volume #8 level 0.07663

> hide #!4 atoms

> volume #8 level 0.09669

> volume #5 level 0.3591

> select clear

> ui tool show Orthoplanes

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.  
  




OpenGL version: 4.1 Metal - 83.1
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: iMac
      Model Identifier: iMac21,1
      Model Number: Z12X000RBLL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.6 (22G630)
      Kernel Version: Darwin 22.6.0
      Time since boot: 64 days, 23 hours, 42 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:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    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-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
    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
    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
    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
    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

[Zach Pearson]

Should be fixed in daily builds.