![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 33 hours ago
Last modified 23 hours ago
#19388 assigned defect
'Segmentation' object has no attribute 'data'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-553.34.1.el8_10.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/seungmi/movies/test3/Refine3D/after_particles_tidy/run_class001.mrc
Opened run_class001.mrc as #1, grid size 288,288,288, pixel 0.85, shown at
level 0.00797, step 2, values float32
> ui tool show "Segment Map"
Segmenting run_class001.mrc, density threshold 0.007969
Only showing 60 of 60 regions.
Showing 60 region surfaces
967 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 60 surfaces
> volume #1 level 0.009068
> select #2.6
1 model selected
> select #2.46
1 model selected
> select add #2.6
2 models selected
> select add #2.11
3 models selected
> select add #2.3
4 models selected
> select add #2.38
5 models selected
> select add #2.4
6 models selected
> select subtract #2.4
5 models selected
> select add #2.4
6 models selected
> select add #2.10
7 models selected
> select add #2.47
8 models selected
> select add #2.2
9 models selected
> ui tool show "Map Eraser"
Segmenting run_class001.mrc, density threshold 0.009068
Only showing 50 of 60 regions.
Showing 50 of 60 region surfaces
948 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 50 surfaces
Segmenting run_class001.mrc, density threshold 0.009068
Only showing 50 of 60 regions.
Showing 50 of 60 region surfaces
948 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 50 surfaces
Segmenting run_class001.mrc, density threshold 0.009068
Only showing 50 of 60 regions.
Showing 50 of 60 region surfaces
948 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 50 surfaces
Segmenting run_class001.mrc, density threshold 0.009068
Only showing 50 of 60 regions.
Showing 50 of 60 region surfaces
948 watershed regions, grouped to 60 regions
> volume #1 level 0.01083
Showing run_class001.seg - 60 regions, 50 surfaces
> volume #1 level 0.01138
> volume #1 level 0.01149
> volume #1 level 0.01215
> volume #1 level 0.01226
> volume #1 level 0.006209
> hide #!2 models
> hide #3 models
> volume #1 level 0.009948
> volume #1 level 0.001
> volume #1 level 0.0001
> volume #1 level 0.01
> show #!2 models
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 50 of 60 regions.
Showing 50 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 50 surfaces
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 25 of 60 regions.
Showing 25 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 25 surfaces
> show #3 models
> volume erase #1 center 122.15,121.72,63.37 radius 61.567
Opened run_class001.mrc copy as #4, grid size 288,288,288, pixel 0.85, shown
at step 1, values float32
> show #!1 models
> hide #!2 models
Can only have one displayed volume when erasing
[Repeated 4 time(s)]
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume erase #1 center 122.15,121.72,63.37 radius 61.567
Opened run_class001.mrc copy as #5, grid size 288,288,288, pixel 0.85, shown
at step 1, values float32
> rename #5 bottom_upper.mrc
> undo
[Repeated 4 time(s)]
> hide #!4 models
> hide #!5 models
> show #!1 models
> hide #!2 models
> volume erase #1 center 121.54,120.12,58.042 radius 61.567
Opened run_class001.mrc copy as #6, grid size 288,288,288, pixel 0.85, shown
at step 1, values float32
> volume erase #6 center 123.24,119.58,58.996 radius 61.567
> rename #6 bottom_upperbody.mrc
> volume subtract #1 #6
Opened volume difference as #7, grid size 288,288,288, pixel 0.85, shown at
step 1, values float32
> rename #7 top_upperbody.mrc
> save
> /home/seungmi/movies/test3/Refine3D/after_particles_tidy/bottom_upperbody.mrc
> models #6
> save
> /home/seungmi/movies/test3/Refine3D/after_particles_tidy/top_upperbody.mrc
> models #7
> hide #!7 models
> undo
[Repeated 1 time(s)]
> show #!6 models
> hide #!2 models
> hide #3 models
> volume #6 level 0.01101
> volume #6 level 0.01146
> volume #6 level 0.01112
> volume #7 level 0.007814
> open /home/seungmi/movies/test3/MaskCreate/bottom_upperbody/mask.mrc
Opened mask.mrc as #8, grid size 288,288,288, pixel 0.85, shown at level
0.819, step 2, values float32
> volume #8 level 0.09767
> volume #8 style mesh
> volume #8 level 0.0111
> open /home/seungmi/movies/test3/MaskCreate/top_upperbody/mask.mrc
Opened mask.mrc as #9, grid size 288,288,288, pixel 0.85, shown at level 1,
step 2, values float32
> volume #9 level 0.00781
> volume #9 style mesh
> volume #9 level 0.0078
> volume #9 level 0.0077
> show #!1 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!2 models
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 30 of 60 regions.
Showing 30 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 30 surfaces
Smoothing and grouping, standard deviation 5 voxels
Only showing 30 of 38 regions.
Showing 30 of 38 region surfaces
Got 38 regions after smoothing 5 voxels.
> select #2.4
1 model selected
Grouped 1 regions
> select add #2.2
2 models selected
Grouped 2 regions
> select add #2.30
2 models selected
> select add #2.13
3 models selected
> select add #2.3
4 models selected
> select add #2.5
5 models selected
> select subtract #2.5
4 models selected
> select add #2.5
5 models selected
> select add #2.12
6 models selected
Grouped 6 regions
Grouped 1 regions
[Repeated 1 time(s)]
> select subtract #2.2
Nothing selected
> select add #2.2
1 model selected
Grouped 1 regions
[Repeated 1 time(s)]
> select #1
2 models selected
> select add #2.1
3 models selected
Grouped 1 regions
[Repeated 3 time(s)]
> select #2.6
1 model selected
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 45 of 60 regions.
Showing 45 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 45 surfaces
> select #1
2 models selected
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 50 of 60 regions.
Showing 50 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 50 surfaces
> select #2.19
1 model selected
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> select add #2.48
1 model selected
> select add #2.38
2 models selected
> select add #2.3
3 models selected
> select add #2.5
4 models selected
> select add #2.11
5 models selected
> select add #2.6
6 models selected
> select subtract #2.11
5 models selected
Grouped 5 regions
> select add #2.1
2 models selected
> select add #2.2
3 models selected
> select add #2.12
4 models selected
> select add #2.11
5 models selected
Grouped 5 regions
> select add #2.47
2 models selected
> select add #2.37
3 models selected
> select add #2.4
4 models selected
> select add #2.31
5 models selected
Grouped 5 regions
> select add #2.15
2 models selected
> select add #2.46
3 models selected
> select subtract #2.15
2 models selected
> select subtract #2.46
1 model selected
> select add #2.7
2 models selected
> select clear
> select add #2.7
1 model selected
> select add #2.46
2 models selected
> select add #2.15
3 models selected
Grouped 3 regions
> select add #2.1
2 models selected
Grouped 2 regions
Grouped 1 regions
> select add #2.14
2 models selected
Grouped 2 regions
> select add #2.18
2 models selected
> select add #2.13
3 models selected
Grouped 3 regions
> select #1
2 models selected
> select #1
2 models selected
> select #2.1
1 model selected
Grouped 1 regions
[Repeated 1 time(s)]
> surface dust #1 size 8.5
> select clear
> select #2.8
1 model selected
> select #2.30
1 model selected
> select #2.24
1 model selected
> select #2.50
1 model selected
> select #2.10
1 model selected
> select #2.25
1 model selected
> select #2.25
1 model selected
> select #2.26
1 model selected
> select add #2.50
2 models selected
> select add #2.10
3 models selected
> select add #2.30
4 models selected
> select add #2.8
5 models selected
> select add #2.51
6 models selected
> select add #2.24
7 models selected
Grouped 7 regions
> select #2.9
1 model selected
> select add #2.29
2 models selected
> select add #2.23
3 models selected
> select add #2.54
4 models selected
Grouped 4 regions
> select add #2.2
2 models selected
Grouped 2 regions
> select add #2.49
2 models selected
> select add #2.16
3 models selected
Grouped 3 regions
> select add #2.43
2 models selected
> select add #2.19
3 models selected
Grouped 3 regions
> select add #2.28
2 models selected
> select add #2.22
3 models selected
Grouped 3 regions
> select add #2.52
2 models selected
Grouped 2 regions
> select add #2.25
2 models selected
Grouped 2 regions
> select add #2.27
2 models selected
> select clear
> select #2.27
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select add #2.44
2 models selected
Grouped 2 regions
> select add #2.45
2 models selected
> select add #2.20
3 models selected
Grouped 3 regions
> select add #2.55
2 models selected
Grouped 2 regions
> select #2.42
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select add #2.41
2 models selected
> select #2.2
1 model selected
> select add #2.41
2 models selected
Grouped 2 regions
> select #2.40
1 model selected
> select add #2.34
2 models selected
> select add #2.39
3 models selected
> select add #2.17
4 models selected
> select add #2.1
5 models selected
> select subtract #2.1
4 models selected
> select add #2.21
5 models selected
> select add #2.1
6 models selected
Grouped 6 regions
> select subtract #2.1
2 models selected
Smoothing and grouping, standard deviation 5 voxels
No new groups smoothing 5 voxels
Showing 11 region surfaces
Got 11 regions after smoothing 6 voxels.
Smoothing and grouping, standard deviation 7 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 7 voxels.
> select add #2.1
3 models selected
> select add #2.4
4 models selected
> select subtract #2.1
3 models selected
> select subtract #2.4
2 models selected
Smoothing and grouping, standard deviation 8 voxels
Showing 7 region surfaces
Got 7 regions after smoothing 8 voxels.
> undo
[Repeated 1 time(s)]
> select add #2.53
4 models selected
> select add #2.1
5 models selected
Grouped 3 regions
> select #2.2
1 model selected
Ungrouped to 2 regions
> select #2.4
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> select #2.3
1 model selected
> hide #2.3 models
> show #2.3 models
> hide #2.5 models
> show #2.5 models
> hide #2.3 models
> show #2.3 models
> hide #2.6 models
> show #2.6 models
> select #2.6
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> hide #2.5 models
> show #2.5 models
> select #2.7
1 model selected
> select add #2.1
2 models selected
Grouped 2 regions
> select add #2.5
2 models selected
> select subtract #2.1
1 model selected
Grouped 1 regions
> select add #2.1
2 models selected
> select subtract #2.2
1 model selected
Grouped 1 regions
[Repeated 1 time(s)]
> hide #2.2 models
> hide #2.1 models
> volume subtract #1 #2.3
volume subtract operation requires exactly two volumes
> select subtract #2.1
Nothing selected
> select add #2
4 models selected
> select add #1
6 models selected
> select subtract #2
2 models selected
> select add #2.3
3 models selected
> volume subtract #1 #2.3
volume subtract operation requires exactly two volumes
> select #1
2 models selected
> select #2.3
1 model selected
> volume subtract #1 #2.3
volume subtract operation requires exactly two volumes
> show #2.2 models
> show #2.1 models
> hide #2.3 models
> select subtract #2.3
Nothing selected
> select subtract #1
Nothing selected
> select add #2
4 models selected
> select add #2.1
4 models selected
> select subtract #2
Nothing selected
> select add #2.2
1 model selected
Grouped 1 regions
[Repeated 4 time(s)]
> select #2.1
1 model selected
> select add #2.2
2 models selected
Grouped 2 regions
> select subtract #2.1
Nothing selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.3 models
> show #2.1 models
> hide #2.3 models
> select #2.1
1 model selected
Deleted 1 regions
> show #2.3 models
> hide #2.3 models
> hide #!2 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> undo
[Repeated 8 time(s)]
> select #2.3
1 model selected
> select #2.3
1 model selected
Opened run_class001_imasked as #10, grid size 288,288,288, pixel 0.85, shown
at step 1, values float32
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #2.3 models
> show #!10 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> show #!10 models
> show #2.3 models
0 or more than 1 volume model selected
> select add #1
2 models selected
Opened run_class001_imasked as #11, grid size 288,288,288, pixel 0.85, shown
at step 1, values float32
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #2.3 models
> show #2.3 models
> select #11
2 models selected
run_class001.seg has 1 regions
> show #!1 models
> hide #!11 models
> select #1
2 models selected
> select #2.3
1 model selected
> select #1
2 models selected
run_class001.seg has 1 regions
[Repeated 5 time(s)]Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> open /home/seungmi/movies/test3/Refine3D/bottom_upperbody/run_class001.mrc
Opened run_class001.mrc as #12, grid size 288,288,288, pixel 0.85, shown at
level 0.00264, step 2, values float32
> hide #!2 models
> hide #!1 models
> select subtract #1
Nothing selected
> open
> /home/seungmi/movies/test3/InitialModel/bottom_upperbody/run_it200_class001.mrc
Opened run_it200_class001.mrc as #13, grid size 288,288,288, pixel 0.85, shown
at level 0.0041, step 2, values float32
> hide #!12 models
> volume #13 level 0.006628
> show #!12 models
> fitmap #12 inMap #13
Fit map run_class001.mrc in map run_it200_class001.mrc using 29835 points
correlation = 0.6516, correlation about mean = 0.1173, overlap = 1.189
steps = 212, shift = 7.64, angle = 32.5 degrees
Position of run_class001.mrc (#12) relative to run_it200_class001.mrc (#13)
coordinates:
Matrix rotation and translation
0.93204929 0.33501780 -0.13801158 -15.37473658
-0.36201417 0.84509562 -0.39339437 112.98994636
-0.01516114 0.41662509 0.90895197 -41.01671828
Axis 0.75303343 -0.11420774 -0.64799478
Axis point 0.00000000 145.56377193 230.50896806
Rotation angle (degrees) 32.53655862
Shift along axis 2.09660253
> ui mousemode right "translate selected models"
> select #12
2 models selected
> view matrix models
> #12,0.93205,0.33502,-0.13801,-16.291,-0.36201,0.8451,-0.39339,131.65,-0.015161,0.41663,0.90895,-61.526
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.18778,-0.75014,-0.63406,320.66,0.83805,0.21432,-0.50174,73.307,0.51226,-0.62559,0.58841,41.956
> fitmap #12 inMap #13
Fit map run_class001.mrc in map run_it200_class001.mrc using 29835 points
correlation = 0.8641, correlation about mean = 0.5247, overlap = 1.936
steps = 120, shift = 13.1, angle = 20.4 degrees
Position of run_class001.mrc (#12) relative to run_it200_class001.mrc (#13)
coordinates:
Matrix rotation and translation
0.02279692 -0.82957637 -0.55792772 305.63037866
0.67892770 0.42249519 -0.60046231 78.93824232
0.73385113 -0.36510389 0.57285397 -9.37450176
Axis 0.11768405 -0.64591601 0.75428308
Axis point 110.28757236 241.63748007 0.00000000
Rotation angle (degrees) 89.48014573
Shift along axis -22.09068057
> tile
2 models tiled
> volume #12 level 0.003777
> volume #13 level 0.006259
> view matrix models
> #12,-0.38838,-0.73531,-0.55541,345,0.84899,-0.051164,-0.52593,102.43,0.3583,-0.6758,0.64414,62.872
> fitmap #12 inMap #13
Fit map run_class001.mrc in map run_it200_class001.mrc using 22848 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of run_class001.mrc (#12) relative to run_it200_class001.mrc (#13)
coordinates:
Matrix rotation and translation
-0.09162176 -0.83429689 -0.54364893 396.62071329
0.69018780 0.34033394 -0.63860287 125.00711173
0.71780656 -0.43372978 0.54463953 137.72577788
Axis 0.10298776 -0.63412173 0.76634401
Axis point 90.49354532 348.70461627 0.00000000
Rotation angle (degrees) 95.93062208
Shift along axis 67.12267907
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.38838,-0.73531,-0.55541,307.6,0.84899,-0.051164,-0.52593,7.0633,0.3583,-0.6758,0.64414,-58.477
> fitmap #12 inMap #13
Fit map run_class001.mrc in map run_it200_class001.mrc using 22848 points
correlation = 0.8837, correlation about mean = 0.397, overlap = 1.873
steps = 76, shift = 3.06, angle = 6.7 degrees
Position of run_class001.mrc (#12) relative to run_it200_class001.mrc (#13)
coordinates:
Matrix rotation and translation
0.02257063 -0.82952338 -0.55801571 305.71697370
0.67869874 0.42254497 -0.60068608 79.06618411
0.73406988 -0.36516670 0.57253358 -9.42293471
Axis 0.11776427 -0.64606795 0.75414042
Axis point 110.29562932 241.73337106 0.00000000
Rotation angle (degrees) 89.49438158
Shift along axis -22.18580601
> view matrix models
> #12,-0.069583,-0.19794,0.97774,-13.433,-0.027811,-0.97935,-0.20024,182.12,0.99719,-0.041126,0.062641,-132.84
> fitmap #12 inMap #13
Fit map run_class001.mrc in map run_it200_class001.mrc using 22848 points
correlation = 0.8837, correlation about mean = 0.3971, overlap = 1.873
steps = 72, shift = 2.15, angle = 0.00446 degrees
Position of run_class001.mrc (#12) relative to run_it200_class001.mrc (#13)
coordinates:
Matrix rotation and translation
0.02252053 -0.82950067 -0.55805149 305.71590277
0.67866799 0.42255788 -0.60071174 79.08555160
0.73409985 -0.36520334 0.57247178 -9.41073659
Axis 0.11775873 -0.64610055 0.75411336
Axis point 110.28547497 241.74491168 -0.00000000
Rotation angle (degrees) 89.49721779
Shift along axis -22.19326326
> show #!1 models
> show #!2 models
> view matrix models
> #12,0.27354,0.71866,-0.6393,75.386,-0.86395,-0.10858,-0.49173,225.76,-0.4228,0.68683,0.59119,-119.52
> select #2.19
1 model selected
> select add #2.47
2 models selected
> select add #2.37
3 models selected
> select add #2.13
4 models selected
> select add #2.6
5 models selected
> select add #2.1
6 models selected
Grouped 6 regions
> select add #2.4
2 models selected
> select add #2.12
3 models selected
> select add #2.2
4 models selected
Grouped 4 regions
> select add #2.18
2 models selected
Grouped 2 regions
> select add #2.9
2 models selected
> select add #2.23
3 models selected
> select add #2.54
4 models selected
> select add #2.29
5 models selected
> select add #2.8
6 models selected
> select add #2.10
7 models selected
> select add #2.30
8 models selected
Grouped 8 regions
> select #2.1
1 model selected
> undo
[Repeated 1 time(s)]Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> undo
[Repeated 5 time(s)]
> hide #!13 models
> show #!13 models
> hide #!2 models
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> close session
> open
> /home/seungmi/movies/test3/InitialModel/bottom_upperbody/run_it200_class001.mrc
> format mrc
Opened run_it200_class001.mrc as #1, grid size 288,288,288, pixel 0.85, shown
at level 0.0041, step 2, values float32
> close session
> open
> /home/seungmi/movies/test3/Refine3D/after_particles_tidy/run_class001.mrc
Opened run_class001.mrc as #1, grid size 288,288,288, pixel 0.85, shown at
level 0.00797, step 2, values float32
> ui tool show "Fit to Segments"
> ui tool show "Segment Map"
Segmenting run_class001.mrc, density threshold 0.007969
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
967 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
Segmenting run_class001.mrc, density threshold 0.007969
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
967 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> ui tool show Orthoplanes
Drag select of 1432, 13 of 6008 triangles, 1 run_class001.mrc
> select add #2.12
4 models selected
> select add #2.2
5 models selected
> select add #2.1
6 models selected
> select add #2.3
7 models selected
> select add #2.37
8 models selected
> select add #2.6
9 models selected
Drag select of 1353, 6 of 4396 triangles
> select add #2.19
11 models selected
> select add #2.15
12 models selected
> select add #2.33
13 models selected
> select add #2.47
14 models selected
Drag select of 1435, 7 of 6320 triangles, 1426, 8 of 5312 triangles, 1424, 6
of 4960 triangles, 1 run_class001.mrc
> select add #2.3
14 models selected
> select add #2.4
15 models selected
> select add #2.14
16 models selected
> select add #2.17
17 models selected
Grouped 17 regions
> select add #2.48
2 models selected
> select add #2.46
3 models selected
> select add #2.38
4 models selected
Grouped 4 regions
> select add #2.16
2 models selected
Grouped 2 regions
> volume #1 level 0.009728
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.001
> volume #1 level 0.01
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> surface dust #1 size 8.5
> select add #2.37
1 model selected
> select add #2.1
2 models selected
> select add #2.6
3 models selected
> select add #2.12
4 models selected
> select add #2.2
5 models selected
> select add #2.4
6 models selected
> select add #2.3
7 models selected
> select add #2.11
8 models selected
> select add #2.48
9 models selected
> select add #2.38
10 models selected
Grouped 10 regions
> select add #2.7
2 models selected
> select add #2.5
3 models selected
> select add #2.46
4 models selected
Segmenting run_class001.mrc, density threshold 0.010000
Only showing 55 of 60 regions.
Showing 55 of 60 region surfaces
931 watershed regions, grouped to 60 regions
Showing run_class001.seg - 60 regions, 55 surfaces
> select add #2.6
1 model selected
> select add #2.1
2 models selected
> select add #2.3
3 models selected
> select add #2.48
4 models selected
> select add #2.5
5 models selected
> select add #2.7
6 models selected
> select add #2.2
7 models selected
> select add #2.31
8 models selected
> select add #2.4
9 models selected
> select add #2.12
10 models selected
Grouped 10 regions
> select add #2.35
4 models selected
> select add #2.37
5 models selected
> select add #2.39
6 models selected
Grouped 4 regions
> select add #2.15
4 models selected
> select add #2.46
5 models selected
Grouped 3 regions
> select add #2.38
4 models selected
> select add #2.14
5 models selected
Grouped 3 regions
> select add #2.13
4 models selected
Grouped 2 regions
> select add #2.22
4 models selected
> select add #2.28
5 models selected
> select add #2.10
6 models selected
> select add #2.52
7 models selected
> select add #2.9
8 models selected
> select add #2.29
9 models selected
> select add #2.49
10 models selected
> select add #2.23
11 models selected
> select add #2.51
12 models selected
> select add #2.8
13 models selected
> select add #2.30
14 models selected
> select add #2.24
15 models selected
Grouped 13 regions
> select add #2.25
4 models selected
> select add #2.50
5 models selected
> select add #2.27
6 models selected
Grouped 4 regions
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> hide #2.11 models
> show #2.11 models
> show #2.1 models
> select subtract #2.1
2 models selected
> select add #2.1
3 models selected
Ungrouped to 4 regions
> select subtract #2.5
5 models selected
> select add #2.5
6 models selected
Ungrouped to 23 regions
> volume sel planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 region 0,0,132,287,287,132
> volume #1 region 0,0,138,287,287,138
> volume sel planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #1 region 0,0,69,287,287,69
> close #1
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1559, in
_surfaceChosen
v = copy_volume_for_auxiliary_display(self.model_menu.value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/segmentation.py", line 115, in
copy_volume_for_auxiliary_display
volume.data, volume.session, style=None, show_dialog=False, open_model=False
^^^^^^^^^^^
AttributeError: 'Segmentation' object has no attribute 'data'
AttributeError: 'Segmentation' object has no attribute 'data'
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/segmentation.py", line 115, in
copy_volume_for_auxiliary_display
volume.data, volume.session, style=None, show_dialog=False, open_model=False
^^^^^^^^^^^
See log for complete Python traceback.
> volume planes z style image imageMode "full region"
No volumes specified
> select add #2
46 models selected
> select subtract #2
Nothing selected
> close session
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1550, in
_surfaceChosen
v.delete()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1912, in delete
Image3d.delete(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 867, in delete
b.remove_image(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1963, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x1509c528d210>
KeyError:
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1963, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> /home/seungmi/movies/test3/Refine3D/after_particles_tidy/run_class001.mrc
Opened run_class001.mrc as #1, grid size 288,288,288, pixel 0.85, shown at
level 0.00797, step 2, values float32
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1550, in
_surfaceChosen
v.delete()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1912, in delete
Image3d.delete(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 867, in delete
b.remove_image(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1963, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x1509c528d210>
KeyError:
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1963, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2524, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 851, in close_request
tool_instance.delete()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplane_tool.py", line 65, in delete
self.viewer.close()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 820, in close
self.view.drawing.delete()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1912, in delete
Image3d.delete(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 867, in delete
b.remove_image(self)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1963, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x1509c528d210>
KeyError:
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1963, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
> volume #1 level 0.001
> close session
> open
> /home/seungmi/movies/test3/Refine3D/after_particles_tidy/run_class001.mrc
Opened run_class001.mrc as #1, grid size 288,288,288, pixel 0.85, shown at
level 0.00797, step 2, values float32
> volume #1 level 0.01
> surface dust #1 size 8.5
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1926, in _update_running_tools
tool_action.setToolTip("%s %s tool" % (("Hide" if tw.shown else "Show"),
tw.title))
^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2343, in shown
return self.__toolkit.shown
^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2718, in shown
return not self.dock_widget.isHidden()
^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2718, in shown
return not self.dock_widget.isHidden()
^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.54.03
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=localhost:12.0
Manufacturer: Intel Corporation
Model: M50CYP2SBSTD
OS: Rocky Linux 8.10
Architecture: 64bit ELF
Virtual Machine: none
CPU: 72 Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz
Cache Size: 55296 KB
Memory:
total used free shared buff/cache available
Mem: 503Gi 32Gi 320Gi 3.6Gi 150Gi 463Gi
Swap: 31Gi 211Mi 31Gi
Graphics:
02:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: ASPEED AST2500
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (1)
comment:1 by , 23 hours ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'Segmentation' object has no attribute 'data' |
Note:
See TracTickets
for help on using tickets.
