'ArrayGridData' object has no attribute 'dicom_data'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.0-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/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J496_004_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J495_003_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J494_003_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J493_004_volume_map_sharp.mrc"

Opened cryosparc_P16_J496_004_volume_map_sharp.mrc as #1.1, grid size
300,300,300, pixel 0.819, shown at level 0.132, step 2, values float32  
Opened cryosparc_P16_J495_003_volume_map_sharp.mrc as #1.2, grid size
300,300,300, pixel 0.819, shown at level 0.0981, step 2, values float32  
Opened cryosparc_P16_J494_003_volume_map_sharp.mrc as #1.3, grid size
300,300,300, pixel 0.819, shown at level 0.0919, step 2, values float32  
Opened cryosparc_P16_J493_004_volume_map_sharp.mrc as #1.4, grid size
300,300,300, pixel 0.819, shown at level 0.111, step 2, values float32  

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> surface dust #1.3 size 8.19

> surface dust #1.4 size 8.19

> tile

4 models tiled  

> volume #1.4 level 0.09581

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> surface dust #1.3 size 8.19

> surface dust #1.4 size 8.19

> volume #1.4 level 0.2658

> volume #1.4 level 0.2509

> volume #1.3 level 0.2441

> volume #1.3 level 0.1835

> volume #1.2 level 0.1056

> volume #1.1 level 0.114

> volume #1.4 level 0.219

> volume #1.1 level 0.2524

> volume #1.1 level 0.1931

> volume #1.2 level 0.1468

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J467_005_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J468_005_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J470_004_volume_map_sharp.mrc"

Opened cryosparc_P16_J467_005_volume_map_sharp.mrc as #2.1, grid size
300,300,300, pixel 0.819, shown at level 0.208, step 2, values float32  
Opened cryosparc_P16_J468_005_volume_map_sharp.mrc as #2.2, grid size
300,300,300, pixel 0.819, shown at level 0.116, step 2, values float32  
Opened cryosparc_P16_J470_004_volume_map_sharp.mrc as #2.3, grid size
300,300,300, pixel 0.819, shown at level 0.104, step 2, values float32  

> tile

2 models tiled  

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J467_005_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J468_005_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/cryosparc_P16_J470_004_volume_map_sharp.mrc"

Opened cryosparc_P16_J467_005_volume_map_sharp.mrc as #1.1, grid size
300,300,300, pixel 0.819, shown at level 0.208, step 2, values float32  
Opened cryosparc_P16_J468_005_volume_map_sharp.mrc as #1.2, grid size
300,300,300, pixel 0.819, shown at level 0.116, step 2, values float32  
Opened cryosparc_P16_J470_004_volume_map_sharp.mrc as #1.3, grid size
300,300,300, pixel 0.819, shown at level 0.104, step 2, values float32  

> tile

3 models tiled  

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> surface dust #1.3 size 8.19

> volume #1.1 level 0.2454

> volume #1.2 level 0.238

> volume #1.3 level 0.169

> volume #1.2 level 0.1391

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/194_cryosparc_P16_J494_003_volume_map.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/195_cryosparc_P16_J495_003_volume_map.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/196_cryosparc_P16_J496_004_volume_map.mrc"

Opened 194_cryosparc_P16_J494_003_volume_map.mrc as #1.1, grid size
300,300,300, pixel 0.819, shown at level 0.089, step 2, values float32  
Opened 195_cryosparc_P16_J495_003_volume_map.mrc as #1.2, grid size
300,300,300, pixel 0.819, shown at level 0.0929, step 2, values float32  
Opened 196_cryosparc_P16_J496_004_volume_map.mrc as #1.3, grid size
300,300,300, pixel 0.819, shown at level 0.118, step 2, values float32  

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> surface dust #1.3 size 8.19

> volume #1.1 level 0.07807

> volume #1.2 level 0.1037

> volume #1.3 level 0.01822

> volume #1.3 level 0.1248

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/196_cryosparc_P16_J496_004_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/195_cryosparc_P16_J495_003_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/194_cryosparc_P16_J494_003_volume_map_sharp.mrc"

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #1.1, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  
Opened 196_cryosparc_P16_J496_004_volume_map_sharp.mrc as #1.2, grid size
300,300,300, pixel 0.819, shown at level 0.132, step 2, values float32  
Opened 195_cryosparc_P16_J495_003_volume_map_sharp.mrc as #1.3, grid size
300,300,300, pixel 0.819, shown at level 0.0981, step 2, values float32  
Opened 194_cryosparc_P16_J494_003_volume_map_sharp.mrc as #1.4, grid size
300,300,300, pixel 0.819, shown at level 0.0919, step 2, values float32  

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> surface dust #1.3 size 8.19

> surface dust #1.4 size 8.19

> tile

4 models tiled  

> volume #1.1 level 0.1306

> volume #1.1 level 0.1067

> ui mousemode right zoom

> volume #1.1 level 0.09201

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/194_cryosparc_P16_J494_003_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/195_cryosparc_P16_J495_003_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/196_cryosparc_P16_J496_004_volume_map_sharp.mrc"
> "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"

Opened 194_cryosparc_P16_J494_003_volume_map_sharp.mrc as #1.1, grid size
300,300,300, pixel 0.819, shown at level 0.0919, step 2, values float32  
Opened 195_cryosparc_P16_J495_003_volume_map_sharp.mrc as #1.2, grid size
300,300,300, pixel 0.819, shown at level 0.0981, step 2, values float32  
Opened 196_cryosparc_P16_J496_004_volume_map_sharp.mrc as #1.3, grid size
300,300,300, pixel 0.819, shown at level 0.132, step 2, values float32  
Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #1.4, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> surface dust #1.3 size 8.19

> surface dust #1.4 size 8.19

> tile

4 models tiled  

> volume #1.1 level 0.1915

> volume #1.2 level 0.1793

> volume #1.3 level 0.1769

> volume #1.3 level 0.2164

> volume #1.4 level 0.2152

> volume #1.4 level 0.1656

> volume #1.3 level 0.2992

> volume #1.2 level 0.1918

> volume #1.1 level 0.1767

> volume #1.2 level 0.2068

> volume #1.3 level 0.2884

> volume #1.4 level 0.3163

> hide #!1.3 models

> hide #!1.4 models

> volume #1.1 level 0.2225

> volume #1.2 level 0.2168

> volume #1.1 level 0.217

> tile off

> volume #1.1 step 1

> volume #1.2 step 1

> volume #1.1 level 0.1009

> surface dust #1.1 size 8.19

> surface dust #1.2 size 8.19

> volume #1.2 level 0.1115

> volume #1.2 level 0.08362

> volume #1.1 level 0.08194

> volume #1.1 level 0.1036

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/HomoRefine/cryosparc_P16_J493_004_volume_map_sharp.mrc"

Opened cryosparc_P16_J493_004_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.819, shown at level 0.111, step 2, values float32  

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/HomoRefine/cryosparc_P16_J493_004_volume_map_sharp.mrc"

Opened cryosparc_P16_J493_004_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.819, shown at level 0.111, step 2, values float32  

> surface dust #1 size 8.19

> volume #1 step 1

> volume #1 step 4

> volume #1 step 16

> volume #1 level 0.06303

> volume #1 step 4

> volume #1 level 0.1097

> volume #1 level 0.09292

> surface dust #1 size 8.19

> volume #1 step 1

> volume #1 step 2

> volume #1 level 0.1156

> volume #1 level 0.1259

> volume #1 level 0.1342

> volume #1 level 0.1404

> volume #1 level 0.1156

> surface dust #1 size 8.19

[Repeated 1 time(s)]

> volume #1 level 0.1301

> volume #1 level 0.1259

> volume #1 level 0.128

> volume #1 step 4

> volume #1 level 0.1075

> volume #1 style mesh

> volume #1

> volume #1 style surface

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/HomoRefine/cryosparc_P16_J493_004_volume_map_sharp.mrc"

Opened cryosparc_P16_J493_004_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.819, shown at level 0.111, step 2, values float32  

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  

> surface dust #1 size 8.19

> surface dust #2 size 8.19

> volume #2 level 0.1865

> volume #1 level 0.2613

> volume #2 level 0.2079

> volume #1 level 0.2097

> volume #2 level 0.1294

> volume #1 level 0.1747

> volume #2 level 0.07756

> volume #2 level 0.1704

> volume #2 level 0.1026

> hide #!2 models

> show #!2 models

> hide #!1 models

> lighting soft

> set bgColor white

> set bgColor #ffffff00

> lighting full

> lighting soft

> lighting simple

> set bgColor black

> set bgColor transparent

> save /Users/reyesruizcampoy/Desktop/image9.png supersample 3

> surface dust #2 size 8.19

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/reyesruizcampoy/Desktop/movie4.mp4

Movie saved to /Users/reyesruizcampoy/Desktop/movie4.mp4  
  

> volume #2 color #b2b2b2

> volume #2 color #9c9c9c

> set bgColor white

> set bgColor #ffffff00

> volume #2 color #888888

> volume #2 level 0.1151

> volume #2 level 0.09721

> volume #2 level 0.09185

> volume #2 level 0.1204

> volume #2 level 0.1008

> volume #2 level 0.09006

> volume #2 level 0.2901

> cd "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine"

Current working directory is:
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  

> save /Users/reyesruizcampoy/Desktop/image10.png supersample 3

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine" format dicom

Summary of feedback from opening
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  
---  
notes | Pydicom could not read invalid or non-DICOM file 196_cryosparc_P16_J496_004_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
196_cryosparc_P16_J496_004_volume_map.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
197_cryosparc_P16_J497_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map.mrc; skipping.  
3 messages similar to the above omitted  
  

> save /Users/reyesruizcampoy/Desktop/image11.png supersample 3

> save /Users/reyesruizcampoy/Desktop/image12.png supersample 3

> show atoms

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine" format dicom

Summary of feedback from opening
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  
---  
notes | Pydicom could not read invalid or non-DICOM file 196_cryosparc_P16_J496_004_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
196_cryosparc_P16_J496_004_volume_map.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
197_cryosparc_P16_J497_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map.mrc; skipping.  
3 messages similar to the above omitted  
  

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine" format dicom

Summary of feedback from opening
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  
---  
notes | Pydicom could not read invalid or non-DICOM file 196_cryosparc_P16_J496_004_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
196_cryosparc_P16_J496_004_volume_map.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
197_cryosparc_P16_J497_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map.mrc; skipping.  
3 messages similar to the above omitted  
  

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  

> volume #1 color #9c9c9c

> surface dust #1 size 8.19

> volume #1 level 0.07756

> volume gaussian #1 sDev 2

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian as #2, grid
size 300,300,300, pixel 0.819, shown at step 1, values float32  

> volume #2 color #9c9c9c

> volume #2 color #a4a4a4

> volume #2 level 0.06695

> volume #2 level 0.06367

> ui tool show "Segment Map"

Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 29 region surfaces  
67 watershed regions, grouped to 29 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 29 regions,
29 surfaces  

> select #3.16

1 model selected  

> select add #3.14

2 models selected  

> select add #3.26

3 models selected  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 6 region surfaces  
67 watershed regions, grouped to 6 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 6 regions,
6 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 9 region surfaces  
67 watershed regions, grouped to 9 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 9 regions,
9 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 29 region surfaces  
67 watershed regions, grouped to 29 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 29 regions,
29 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 40 region surfaces  
67 watershed regions, grouped to 40 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 40 regions,
40 surfaces  

> select #3.23

1 model selected  

> select add #3.17

2 models selected  

> select add #3.4

3 models selected  

> select add #3.27

4 models selected  

> select add #3.16

5 models selected  

> volume #1 level 0.08546

Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Only showing 10 of 40 regions.  
Showing 10 of 40 region surfaces  
67 watershed regions, grouped to 40 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 40 regions,
10 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Only showing 20 of 40 regions.  
Showing 20 of 40 region surfaces  
67 watershed regions, grouped to 40 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 40 regions,
20 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Only showing 30 of 40 regions.  
Showing 30 of 40 region surfaces  
67 watershed regions, grouped to 40 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 40 regions,
30 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Only showing 30 of 67 regions.  
Showing 30 of 67 region surfaces  
Only showing 30 of 40 regions.  
Showing 30 of 40 region surfaces  
67 watershed regions, grouped to 40 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 40 regions,
30 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Only showing 30 of 67 regions.  
Showing 30 of 67 region surfaces  
Showing 9 region surfaces  
67 watershed regions, grouped to 9 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 9 regions,
9 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 67 region surfaces  
Showing 9 region surfaces  
67 watershed regions, grouped to 9 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 9 regions,
9 surfaces  

> hide #3.67 models

> show #3.67 models

Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 67 region surfaces  
[Repeated 1 time(s)]Showing 40 region surfaces  
67 watershed regions, grouped to 40 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 40 regions,
40 surfaces  
Segmenting 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian, density
threshold 0.063668  
Showing 67 region surfaces  
[Repeated 1 time(s)]Showing 61 region surfaces  
67 watershed regions, grouped to 61 regions  
Showing 197_cryosparc_P16_J497_003_volume_map_sharp gaussian.seg - 61 regions,
61 surfaces  

> select #3.43

1 model selected  

> select add #3.35

2 models selected  

> select add #3.23

3 models selected  

> select add #3.40

4 models selected  

> select add #3.57

5 models selected  

> select add #3.41

6 models selected  

> select subtract #3.57

5 models selected  

> select add #3.15

6 models selected  

> select add #3.62

7 models selected  
Grouped 7 regions  

> select #3.57

1 model selected  

> select add #3.15

2 models selected  
Grouped 2 regions  

> select add #3.60

2 models selected  

> select subtract #3.60

1 model selected  

> select clear

> select #3.15

1 model selected  

> select add #3.60

2 models selected  

> select subtract #3.60

1 model selected  
Grouped 1 regions  

> select #3.60

1 model selected  

> select add #3.15

2 models selected  
Grouped 2 regions  

> select add #3.56

2 models selected  

> select add #3.53

3 models selected  

> select add #3.61

4 models selected  

> select add #3.58

5 models selected  

> select add #3.59

6 models selected  

> select subtract #3.56

5 models selected  

> select subtract #3.53

4 models selected  

> select add #3.53

5 models selected  
Grouped 5 regions  

> select #3.56

1 model selected  

> select add #3.15

2 models selected  
Grouped 2 regions  

> select add #3.67

2 models selected  

> select clear

> select add #3.34

1 model selected  

> select add #3.7

2 models selected  

> select add #3.16

3 models selected  

> select subtract #3.16

2 models selected  

> select #3.54

1 model selected  

> select add #3.55

2 models selected  

> select add #3.21

3 models selected  

> select add #3.33

4 models selected  

> select add #3.27

5 models selected  

> select subtract #3.27

4 models selected  

> select add #3.27

5 models selected  
Grouped 5 regions  

> select add #3.15

2 models selected  
Grouped 2 regions  

> select #3.47

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select #3.15

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select #3.3

1 model selected  
Ungrouped to 2 regions  

> select #3.15

1 model selected  
Ungrouped to 2 regions  

> select #3.3

1 model selected  

> select clear

> select #3.3

1 model selected  
Ungrouped to 0 regions  

> select #3.23

1 model selected  

> select add #3.3

2 models selected  

> select add #3.39

3 models selected  
Grouped 3 regions  

> select #3.21

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select #3.34

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select #3.16

1 model selected  

> select subtract #3.16

Nothing selected  

> select #3.16

1 model selected  

> select add #3.65

2 models selected  

> select add #3.52

3 models selected  
Grouped 3 regions  

> select #3.15

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select add #3.30

2 models selected  
Grouped 2 regions  

> select add #3.6

2 models selected  
Grouped 2 regions  

> select add #3.17

2 models selected  

> select add #3.11

3 models selected  

> select add #3.2

4 models selected  

> select add #3.24

5 models selected  

> select #3.11

1 model selected  

> select add #3.2

2 models selected  

> select add #3.24

3 models selected  

> select add #3.17

4 models selected  
Grouped 4 regions  

> select #3.3

1 model selected  
Grouped 1 regions  

> select #3.2

1 model selected  
Grouped 1 regions  

> select #3.3

1 model selected  

> select add #3.2

2 models selected  
Grouped 2 regions  

> select #3.1

1 model selected  

> select add #3.67

2 models selected  

> select subtract #3.67

1 model selected  
Grouped 1 regions  

> select #3.2

1 model selected  

> select add #3.67

2 models selected  
Grouped 2 regions  

> select #3.1

1 model selected  
Ungrouped to 1 regions  

> select add #3.5

2 models selected  

> select add #3.7

3 models selected  

> select add #3.9

4 models selected  

> select add #3.31

5 models selected  

> select add #3.36

6 models selected  

> select add #3.44

7 models selected  

> select add #3.4

8 models selected  

> select add #3.26

9 models selected  

> select add #3.22

10 models selected  

> select add #3.48

11 models selected  

> select subtract #3.48

10 models selected  

> select subtract #3.22

9 models selected  

> select add #3.20

10 models selected  

> select add #3.19

11 models selected  

> select add #3.2

12 models selected  

> select add #3.37

13 models selected  

> select add #3.28

14 models selected  

> select add #3.18

15 models selected  

> select add #3.10

16 models selected  

> select add #3.45

17 models selected  

> select subtract #3.3

16 models selected  
Grouped 16 regions  

> select #3.46

1 model selected  

> select add #3.29

2 models selected  

> select add #3.22

3 models selected  

> select add #3.48

4 models selected  

> select add #3.8

5 models selected  

> select add #3.1

6 models selected  
Grouped 6 regions  

> select #3.12

1 model selected  

> select add #3.3

2 models selected  
Grouped 2 regions  

> select #3.1

1 model selected  

> select add #3.2

2 models selected  
Grouped 2 regions  

> select #3.25

1 model selected  
Grouped 1 regions  

> select add #3.1

2 models selected  
Grouped 2 regions  

> select #3.14

1 model selected  

> select add #3.32

2 models selected  

> select add #3.1

3 models selected  
Grouped 3 regions  

> select #3.38

1 model selected  

> select add #3.1

2 models selected  
Grouped 2 regions  

> select #3.13

1 model selected  

> select add #3.1

2 models selected  
Grouped 2 regions  

> select clear

> select #3.1

1 model selected  

> select clear

> select #3.1

1 model selected  

> select subtract #3.1

Nothing selected  

> select add #3.1

1 model selected  

> select subtract #3.1

Nothing selected  

> select add #3.1

1 model selected  

> select subtract #3.1

Nothing selected  
Drag select of 104, 39 of 69772 triangles  

> select clear

> select #3.1

1 model selected  

> select #3.1

1 model selected  

> select #3.1

1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 16, 104  
Grouped 2 regions  

> select clear

> select #3.1

1 model selected  
Saving 1 regions to mrc file...  
Opened Mask_197_cryosparc_P16_J497_003_volume_map_sharp_region_105.mrc as #4,
grid size 114,118,138, pixel 0.819, shown at step 1, values float32  
Wrote Mask_197_cryosparc_P16_J497_003_volume_map_sharp_region_105.mrc  

> select clear

> volume #4 level 0.03272

> volume #4 level 0.03832

> volume resample #4 onGrid #1

Opened Mask_197_cryosparc_P16_J497_003_volume_map_sharp_region_105.mrc
resampled as #5, grid size 300,300,300, pixel 0.819, shown at step 1, values
float32  

> volume #5 level 0.01872

> volume #5 level 0

> volume #5 level 0.0399

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine" format dicom

Summary of feedback from opening
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  
---  
notes | Pydicom could not read invalid or non-DICOM file 196_cryosparc_P16_J496_004_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
196_cryosparc_P16_J496_004_volume_map.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
197_cryosparc_P16_J497_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map.mrc; skipping.  
4 messages similar to the above omitted  
  

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine" format dicom

Summary of feedback from opening
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  
---  
notes | Pydicom could not read invalid or non-DICOM file 196_cryosparc_P16_J496_004_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
196_cryosparc_P16_J496_004_volume_map.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
197_cryosparc_P16_J497_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map.mrc; skipping.  
4 messages similar to the above omitted  
  

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine" format dicom

Summary of feedback from opening
/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
Refinements/300px/NURefine  
---  
notes | Pydicom could not read invalid or non-DICOM file 196_cryosparc_P16_J496_004_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
196_cryosparc_P16_J496_004_volume_map.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
197_cryosparc_P16_J497_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map_sharp.mrc; skipping.  
Pydicom could not read invalid or non-DICOM file
195_cryosparc_P16_J495_003_volume_map.mrc; skipping.  
4 messages similar to the above omitted  
  

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  

> surface dust #1 size 8.19

> volume #1 level 0.09721

> volume #1 level 0.1151

> volume #1 level 0.2026

> volume #1 level 0.09899

> volume #1 level 0.2169

> volume #1 level 0.124

> volume #1 level 0.08649

> volume #1 step 4

> volume #1 step 1

> volume #1 step 2

> volume #1 level 0.1115

> volume #1 level 0.1919

> volume gaussian #1 sDev 2

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian as #2, grid
size 300,300,300, pixel 0.819, shown at step 1, values float32  

> volume #2 level 0.1423

> volume #2 level 0.1882

> volume #2 level 0.1434

> surface dust #2 size 8.19

> 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 #2

Opened segmentation 1 of 197_cryosparc_P16_J497_003_volume_map_sharp.mrc
gaussian as #6, grid size 300,300,300, pixel 0.819, shown at level 0.501, step
1, values float64  

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  

> surface dust #1 size 8.19

> volume gaussian #1 sDev 2

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian as #2, grid
size 300,300,300, pixel 0.819, shown at step 1, values float32  
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/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.9.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
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 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.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.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
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 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.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.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
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 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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1735, in <lambda>  
sm.addAction("%d" % step, lambda s=step: self.data_step_cb(s))  
^^^^^^^^^^^^^^^^^^^^  
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 1808, in data_step_cb  
self.plane_viewer.update_and_rerender()  
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 817, in
update_and_rerender  
self.view.drawing.parent.update_drawings()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'update_drawings'  
  
AttributeError: 'NoneType' object has no attribute 'update_drawings'  
  
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 817, in
update_and_rerender  
self.view.drawing.parent.update_drawings()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open "/Users/reyesruizcampoy/Desktop/PhD/AAADATA/CryoEM/eBIC/Local
> Refinements/300px/NURefine/197_cryosparc_P16_J497_003_volume_map_sharp.mrc"

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.819, shown at level 0.0865, step 2, values float32  

> volume #1 level 0.1865

> volume gaussian #1 sDev 2

Opened 197_cryosparc_P16_J497_003_volume_map_sharp.mrc gaussian as #2, grid
size 300,300,300, pixel 0.819, shown at step 1, values float32  
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/map/volume_viewer.py", line 2178, in mouseMoveEvent  
self._drag(event)  
File
"/Applications/ChimeraX-1.9.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1889, in
moved_marker_cb  
self.plane_viewer.on_color_changed()  
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 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.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 Max
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: MacBookPro18,2
      Model Number: Z14V000GEB/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 11881.1.1

Software:

    System Software Overview:

      System Version: macOS 15.0 (24A335)
      Kernel Version: Darwin 24.0.0
      Time since boot: 3 days, 22 hours, 20 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          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
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    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-Clipper: 0.24.0
    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-EMalign: 0.1.3
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LigandRecognizer: 0.2
    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-PhenixUI: 1.3.7
    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
    finufft: 2.3.1
    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
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    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
    more-itertools: 10.3.0
    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
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    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
    platformdirs: 4.2.2
    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
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    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: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2