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Opened 7 weeks ago
Closed 7 weeks ago
#18672 closed defect (nonchimerax)
Crash in glBufferSubData
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000204ae8c00 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2702 in update_buffer_data
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1903 in update_buffers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1915 in activate_bindings
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 802 in _draw_geometry
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 775 in draw_self
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 768 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1555 in _draw_multiple
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1542 in draw_opaque
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2233 in moved_marker_cb
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/histogram.py", line 416 in move_marker_cb
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2159 in _drag
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2162 in mouseReleaseEvent
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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Address size fault"},"pc":{"value":6925246964},"far":{"value":0}},"frames":[{"imageOffset":4596,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":241},{"imageOffset":80676,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":241},{"imageOffset":40500,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":241},{"imageOffset":5496,"symbol":"mach_msg","symbolLocation":24,"imageIndex":241},{"imageOffset":62126188,"imageIndex":181},{"imageOffset":61883116,"imageIndex":181},{"imageOffset":61885944,"imageIndex":181},{"imageOffset":61884816,"imageIndex":181},{"imageOffset":62101416,"imageIndex":181},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":242},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":242}]},{"id":2429879,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":106854491357184},{"value":0},{"value":106854491357184},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":24879},{"value":0},{"value":1},{"value":24879},{"value":2045},{"value":2577780897},{"value":161},{"value":18446744073709551569},{"value":380928},{"value":0},{"value":33000},{"value":32},{"value":106854491357184},{"value":0},{"value":106854491357184},{"value":13544041824},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6925323044},"cpsr":{"value":4096},"fp":{"value":13544041168},"sp":{"value":13544041088},"esr":{"value":1442840704,"description":" 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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.344, step 1,
values float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc as #7, grid
size 470,522,44, pixel 13.1,13.1,13.1, shown at level 0.158, step 1, values
float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc as #11, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.000346, step 1, values
float32
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc
copy as #3, grid size 495,720,328, pixel 13.1,13.1,13.1, shown at level 0.344,
step 1, values float32
Log from Mon Aug 25 11:03:21 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.344, step 1,
values float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc as #7, grid
size 470,522,44, pixel 13.1,13.1,13.1, shown at level 0.158, step 1, values
float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc as #11, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.000346, step 1, values
float32
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc
copy as #3, grid size 495,720,328, pixel 13.1,13.1,13.1, shown at level 0.344,
step 1, values float32
Log from Mon Aug 25 11:01:06 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.344, step 1,
values float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc as #7, grid
size 470,522,44, pixel 13.1,13.1,13.1, shown at level 0.158, step 1, values
float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc as #11, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.000346, step 1, values
float32
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc
copy as #3, grid size 495,720,328, pixel 13.1,13.1,13.1, shown at level 0.344,
step 1, values float32
Log from Mon Aug 25 10:38:59 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.344, step 1,
values float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc as #7, grid
size 470,522,44, pixel 13.1,13.1,13.1, shown at level 0.158, step 1, values
float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc as #11, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.000346, step 1, values
float32
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc
copy as #3, grid size 495,720,328, pixel 13.1,13.1,13.1, shown at level 0.344,
step 1, values float32
Log from Mon Aug 25 10:32:50 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.344, step 1,
values float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc as #7, grid
size 470,522,44, pixel 13.1,13.1,13.1, shown at level 0.158, step 1, values
float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc as #11, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.000346, step 1, values
float32
Log from Mon Aug 25 09:55:51 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.344, step 1,
values float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc as #7, grid
size 470,522,44, pixel 13.1,13.1,13.1, shown at level 0.158, step 1, values
float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc as #11, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.000346, step 1, values
float32
Log from Sun Aug 24 18:58:48 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_nucleus1.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus1.mrc as #1, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.5, step 4, values float32
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc as #2, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 8.71e-05, step 4, values
float32
> hide #!1 models
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_membrane_smoothed_mask.mrc
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed_mask.mrc as #3, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 5e-05, step 4, values
float32
> volume #3 step 1
> volume #2 step 1
> hide #!3 models
> volume #2 smooth level 2
Expected keyword "smoothLines", "smoothingFactor", or "smoothingIterations"
> volume #2 smoothingFactor 2
> volume #2 smoothingFactor 20
> close #3
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_membrane_smoothed_mask.mrc
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed_mask.mrc as #3, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 1, step 4, values
float32
> volume #3 level 1
> volume #3 step 1
> vop gaussian #3 sdev 3 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed_mask.mrc gaussian as
#4, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values
float32
> volume #4 level 1
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_map.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_map.mrc as #5, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.5, step 4, values
float32
> close #5
> close #4
> close #3
> vop gaussian #2 sdev 3 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc gaussian as #3,
grid size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values float32
> vop gaussian #2 sdev 15 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc gaussian as #4,
grid size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values float32
> close #4
> close #3
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask.mrc as #3, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 1, step 4, values int8
> volume #3 level 0.9889
> volume #3 step 1
> volume dilate #3 voxels -2
Expected a density maps specifier or a keyword
> vop dilate #3 result #4 level 0.05 radius 3
> volume dilate #3 result #4 level 0.05 radius 3
Expected a density maps specifier or a keyword
> vop dilate #2 result #4 level 0.05 radius 3
> volume dilate #2 result #4 level 0.05 radius 3
Expected a density maps specifier or a keyword
> volume dilate t1 #3 result #4 level 0.05 radius 3
Expected a density maps specifier or a keyword
> volume dilate t1 #2 result #4 level 0.05 radius 3
Expected a density maps specifier or a keyword
> vop morphology #3 erode iterations 2
> volume morphology #3 erode iterations 2
Expected a density maps specifier or a keyword
> vop gaussian #3 sdev 3 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask.mrc gaussian as
#4, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values
float32
> volume #4 level 1
> vop gaussian #3 sdev 15 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask.mrc gaussian as
#5, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values
float32
> close #4
> volume #5 level 1
> volume #5 level 0.9815
> scalebar 0.9 #4
Expected a keyword
> close #3
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_1_3_nucleus_smoothed_mesh.mod
Read IMOD model
/Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_1_3_nucleus_smoothed_mesh.mod,
pixel size 1.308, 2 surfaces
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> scalebar 0.9 #3.1
Expected a keyword
> hide #!3 models
> volume #5 level 0.3845
> volume #5 level 0.09612
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask_gaussian.mrc
> models #5
> show #!2 models
> close #2
> close #5
> close #1
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_shell.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell.mrc as #1, grid size
472,535,56, pixel 13.1,13.1,13.1, shown at level 6.36e-06, step 1, values
float32
> volume #1 level 0.001892
> volume #1 level 0.0005
[Repeated 1 time(s)]
> volume #1 level 0.002385
> volume #1 level 1e-06
> vop gaussian #1 sdev 10 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell.mrc gaussian as #2, grid
size 472,535,56, pixel 13.1,13.1,13.1, shown at step 1, values float32
> volume #2 level 7.351e-06
> close #2
> volume #1 sdLevel 2
> volume #1 sdLevel 0.000000001
> volume #1 style image
> volume #1 style surface
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc as
#2, grid size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.125, step 4,
values float32
> surface dust #2 size 131
> volume #2 level 0.3445
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_1_3_nucleus_smoothed_mesh.mod
Read IMOD model
/Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_1_3_nucleus_smoothed_mesh.mod,
pixel size 1.308, 2 surfaces
> volume #2 step 1
> hide #4.1 models
> show #4.1 models
> hide #4.2 models
> color #4.1 #baf5b7ff
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected.mrc
Opened L5_G1_ts_003_corrected.mrc as #5, grid size 511,720,375, pixel
13.1,13.1,13.1, shown at level 0.158, step 4, values float32
> volume #5 step 1
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_mask.mrc as #6, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 1, step 4, values int8
> volume #6 level 0.9723
> volume #6 step 1
> show #4.2 models
> hide #4.2 models
> hide #!4 models
> volume mask #5 #6
Missing required "surfaces" argument
> volume mask #5 surfaces #4.1
Opened L5_G1_ts_003_corrected.mrc masked as #7, grid size 470,522,44, pixel
13.1,13.1,13.1, shown at step 1, values float32
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc
> models #7
> close #5
> close #6
> volume #1 change image level -4.615e-05,0 level 0.004963,0.8 level 0.05005,1
> show #!4 models
> vop gaussian #7 sdev 12 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc gaussian as
#5, grid size 470,522,44, pixel 13.1,13.1,13.1, shown at step 1, values
float32
> vop gaussian #7 sdev 20 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_genome.mrc gaussian as
#6, grid size 470,522,44, pixel 13.1,13.1,13.1, shown at step 1, values
float32
> hide #!4 models
> hide #!5 models
> show #!5 models
> close #6
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_map.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_map.mrc as #6, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.5, step 4, values
float32
> close #6
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_map.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_smoothed_map.mrc as #6, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at level 0.5, step 4, values
float32
> close #6
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_nucleus1.mrc
Opened L5_G1_ts_003_corrected_inv_adj_nucleus1.mrc as #6, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 0.5, step 4, values float32
> close #6
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc as #6, grid size
511,720,375, pixel 13.1,13.1,13.1, shown at level 8.71e-05, step 4, values
float32
> volume #6 step 1
> ui tool show "Map Eraser"
> volume erase #6 center 6106.3,2948,2681.8 radius 1534.3
Opened L5_G1_ts_003_corrected_inv_adj_membrane_smoothed.mrc copy as #9, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values float32
> volume erase #9 center 6269.2,2582.8,2685.6 radius 1530.4
> volume erase #9 center 6281.1,2546.7,2684.2 radius 1530.4
> volume erase #9 center 7017.4,4100.1,2859.2 radius 1530.4
> volume erase #9 center 7399.1,5010.7,2957.1 radius 1530.4
> volume erase #9 center 6790,5840.6,2956.3 radius 781.66
> volume erase #9 center 6703.8,6055.8,2634.8 radius 668.65
> volume erase #9 center 6638.7,6057.5,2765.2 radius 668.65
> volume erase #9 center 6752,6047.2,2542.9 radius 668.65
> volume erase #9 center 6707.9,6039.2,2472.6 radius 668.65
> volume erase #9 center 4735.7,7205.1,2703.1 radius 668.65
> volume erase #9 center 548.48,4984.7,2522 radius 668.65
> volume erase #9 center 143.74,4281.1,2171.4 radius 668.65
> volume erase #9 center 615.69,4117.4,2552.7 radius 207.19
> volume erase #9 center 681.91,4028.6,2568.7 radius 207.19
> volume erase #9 center 750.44,3942,2552.7 radius 207.19
> volume erase #9 center 6019,1141.4,2392.3 radius 207.19
> volume erase #9 center 6078.1,1064.1,2506.2 radius 207.19
> volume erase #7 center 956.54,3948.8,689.91 radius 204.83
> volume erase #7 center 777.06,4363,2410.8 radius 307.25
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc
> models #9
> vop gaussian #9 sdev 15 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc gaussian as #10, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values float32
> vop gaussian #9 sdev 5 valueType float32
Opened L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc gaussian as #11, grid
size 511,720,375, pixel 13.1,13.1,13.1, shown at step 1, values float32
> close #10
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_G1_ts_003_corrected_inv_adj_nucleus_shell2.mrc
> models #11
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/run_data.star
> format star
Summary of feedback from opening
/Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/run_data.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list run_data.star with 1028 particles.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/PAO1_ribosome_13_08_30.mrc
Opened PAO1_ribosome_13_08_30.mrc as #12, grid size 30,30,30, pixel 13.1,
shown at level 0.0172, step 1, values float32
> artiax attach #12 toParticleList #10.2.1
Opened PAO1_ribosome_13_08_30.mrc as #10.2.1.1.1, grid size 30,30,30, pixel
13.1, shown at level 0.0172, step 1, values float32
> volume #10.2.1.1.1 capFaces false
set axis size 196.2
196.2
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']
> artiax particles #10.2.1 originScaleFactor 13.08
> artiax view xy
> artiax particles #10.2.1 radius 0.1
set axis size 16.82167
16.82167
['.arrow', '0', '0', '0', '16.82167', '0', '0', '1.1214446666666666',
'4.485778666666667']
set axis size 16.0616
16.0616
['.arrow', '0', '0', '0', '16.0616', '0', '0', '1.0707733333333331',
'4.2830933333333325']
set axis size 14.54144
14.54144
['.arrow', '0', '0', '0', '14.54144', '0', '0', '0.9694293333333334',
'3.8777173333333335']
set axis size 12.26122
12.26122
['.arrow', '0', '0', '0', '12.26122', '0', '0', '0.8174146666666666',
'3.2696586666666665']
set axis size 9.22091
9.22091
['.arrow', '0', '0', '0', '9.22091', '0', '0', '0.6147273333333333',
'2.458909333333333']
set axis size 6.94068
6.94068
['.arrow', '0', '0', '0', '6.94068', '0', '0', '0.462712', '1.850848']
set axis size 4.66046
4.66046
['.arrow', '0', '0', '0', '4.66046', '0', '0', '0.3106973333333333',
'1.2427893333333333']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
> artiax particles #10.2.1 axesSize 0.1
> artiax particles #10.2.1 surfaceLevel 0.00448
> artiax particles #10.2.1 color 100,100,50,100
> artiax particles #10.2.1 color 88,100,40,100
> artiax particles #10.2.1 color 100,80,60,100
fine
fine
fine
fine
> volume #11 color #b7fbb7
> volume #11 color #c8fbd0
> volume #11 color #c9fbd1
> volume #2 color #70bf79
> volume #7 color #b2b2b2
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.tif
> width 766 height 689 supersample 3
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class name
'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class
return f(class_name)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
->
'M': Unknown class name
'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> close #10
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
> close #5
> close #6
> close #9
> close #1
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
——— End of log from Sun Aug 24 18:58:48 2025 ———
opened ChimeraX session
> volume #2 color #efecb9
> volume #11 color #c1c3f6
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/run_data.star
> format star
Summary of feedback from opening
/Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/run_data.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list run_data.star with 1028 particles.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/PAO1_ribosome_13_08_30.mrc
Opened PAO1_ribosome_13_08_30.mrc as #5, grid size 30,30,30, pixel 13.1, shown
at level 0.0172, step 1, values float32
> artiax attach #5 toParticleList #1.2.1
Opened PAO1_ribosome_13_08_30.mrc as #1.2.1.1.1, grid size 30,30,30, pixel
13.1, shown at level 0.0172, step 1, values float32
> volume #1.2.1.1.1 capFaces false
set axis size 196.2
196.2
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']
> artiax particles #1.2.1 originScaleFactor 13.08
> artiax view xy
> artiax particles #1.2.1 radius 0.1
set axis size 11.50114
11.50114
['.arrow', '0', '0', '0', '11.50114', '0', '0', '0.7667426666666667',
'3.0669706666666667']
set axis size 9.98099
9.98099
['.arrow', '0', '0', '0', '9.98099', '0', '0', '0.6653993333333333',
'2.6615973333333334']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
> artiax particles #1.2.1 axesSize 0.1
> artiax particles #1.2.1 surfaceLevel 0.00409
fine
fine
fine
> artiax particles #1.2.1 color 100,80,60,100
> artiax particles #1.2.1 color 88,100,40,100
> artiax particles #1.2.1 color 0,36,19,100
> artiax particles #1.2.1 color 0,46,86,100
> artiax particles #1.2.1 color 50,50,50,100
> artiax particles #1.2.1 color 26,40,0,100
> artiax particles #1.2.1 color 30,0,36,100
> artiax particles #1.2.1 color 0,36,19,100
> artiax particles #1.2.1 color 0,60,56,100
> artiax particles #1.2.1 color 0,36,19,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 44,75,47,100
> artiax particles #1.2.1 color 56,76,90,100
> artiax particles #1.2.1 color 90,64,60,100
> artiax particles #1.2.1 color 90,69,67,100
> artiax particles #1.2.1 color 90,71,73,100
> artiax particles #1.2.1 color 90,75,78,100
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/ribosome_list.em
> partlist #1.2.1
> artiax particles #1.2.1 color 100,80,60,100
> artiax particles #1.2.1 color 100,66,73,100
> artiax particles #1.2.1 color 87,73,76,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 87,72,75,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 86,72,75,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 86,71,75,100
> artiax particles #1.2.1 color 85,71,75,100
> artiax particles #1.2.1 color 85,71,74,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 84,70,73,100
> artiax particles #1.2.1 color 83,69,72,100
> artiax particles #1.2.1 color 82,69,71,100
> artiax particles #1.2.1 color 82,68,71,100
> artiax particles #1.2.1 color 81,67,71,100
> artiax particles #1.2.1 color 81,67,70,100
> artiax particles #1.2.1 color 80,67,70,100
> artiax particles #1.2.1 color 80,67,69,100
> artiax particles #1.2.1 color 80,66,69,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 79,66,69,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 79,65,68,100
> artiax particles #1.2.1 color 78,65,68,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 78,65,67,100
> artiax particles #1.2.1 color 78,65,68,100
> artiax particles #1.2.1 color 79,66,69,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 80,67,69,100
> artiax particles #1.2.1 color 80,67,70,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 81,67,70,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 81,67,71,100
> artiax particles #1.2.1 color 81,68,71,100
> artiax particles #1.2.1 color 82,68,71,100
> artiax particles #1.2.1 color 82,69,71,100
> artiax particles #1.2.1 color 82,69,72,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 83,69,72,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 83,69,73,100
> artiax particles #1.2.1 color 84,69,73,100
> artiax particles #1.2.1 color 84,70,73,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 85,71,74,100
> artiax particles #1.2.1 color 86,71,75,100
> artiax particles #1.2.1 color 86,72,75,100
> artiax particles #1.2.1 color 87,72,75,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 86,72,75,100
> artiax particles #1.2.1 color 86,70,78,100
> artiax particles #1.2.1 color 86,67,76,100
> artiax particles #1.2.1 color 86,66,68,100
> artiax particles #1.2.1 color 86,66,84,100
> artiax particles #1.2.1 color 86,68,86,100
> artiax particles #1.2.1 color 86,67,81,100
> artiax particles #1.2.1 color 86,66,76,100
> artiax particles #1.2.1 color 84,70,86,100
> artiax particles #1.2.1 color 86,66,86,100
> artiax particles #1.2.1 color 87,66,86,100
> artiax particles #1.2.1 color 89,68,89,100
> artiax particles #1.2.1 color 90,68,89,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 90,69,90,100
> artiax particles #1.2.1 color 91,69,90,100
> artiax particles #1.2.1 color 91,69,91,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 91,70,91,100
> artiax particles #1.2.1 color 92,70,92,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 93,71,93,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 94,71,93,100
> artiax particles #1.2.1 color 94,72,94,100
> artiax particles #1.2.1 color 95,72,94,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 94,72,94,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 94,71,94,100
> artiax particles #1.2.1 color 94,71,93,100
> artiax particles #1.2.1 color 94,71,94,100
> artiax particles #1.2.1 color 94,72,94,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 95,72,94,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 95,72,95,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 95,73,95,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 96,73,95,100
> artiax particles #1.2.1 color 96,73,96,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 96,74,96,100
> artiax particles #1.2.1 color 97,74,96,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 97,74,97,100
> artiax particles #1.2.1 color 98,75,97,100
> artiax particles #1.2.1 color 98,75,98,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 99,75,98,100
> artiax particles #1.2.1 color 98,75,98,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 98,75,97,100
> artiax particles #1.2.1 color 97,74,97,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 97,74,96,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 96,74,96,100
> artiax particles #1.2.1 color 96,73,96,100
[Repeated 5 time(s)]
> artiax particles #1.2.1 color 96,73,95,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 95,73,95,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 97,74,96,100
> artiax particles #1.2.1 color 97,74,97,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 98,74,97,100
> artiax particles #1.2.1 color 98,75,97,100
> artiax particles #1.2.1 color 98,75,98,100
[Repeated 5 time(s)]
> artiax particles #1.2.1 color 99,75,98,100
> artiax particles #1.2.1 color 99,76,99,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 100,76,99,100
> artiax particles #1.2.1 color 100,76,100,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 95,73,95,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 96,74,97,100
> artiax particles #1.2.1 color 97,74,97,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 98,75,98,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 98,75,99,100
> artiax particles #1.2.1 color 99,76,99,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 99,76,100,100
> artiax particles #1.2.1 color 100,76,100,100
[Repeated 4 time(s)]
> artiax particles #1.2.1 color 100,87,98,100
> artiax particles #1.2.1 color 96,83,95,100
> artiax particles #1.2.1 color 95,82,93,100
> artiax particles #1.2.1 color 94,82,93,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 93,81,92,100
> artiax particles #1.2.1 color 93,80,91,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 92,80,91,100
> artiax particles #1.2.1 color 91,79,90,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 91,79,89,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 90,78,89,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 89,78,88,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 89,77,88,100
> artiax particles #1.2.1 color 89,77,87,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 88,77,87,100
> artiax particles #1.2.1 color 88,76,87,100
> artiax particles #1.2.1 color 88,76,86,100
> artiax particles #1.2.1 color 87,76,86,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 87,75,85,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 86,75,85,100
[Repeated 4 time(s)]
> artiax particles #1.2.1 color 86,70,85,100
> artiax particles #1.2.1 color 89,72,87,100
> artiax particles #1.2.1 color 89,73,87,100
> artiax particles #1.2.1 color 89,73,88,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 90,73,88,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 90,73,89,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 90,74,89,100
> artiax particles #1.2.1 color 91,74,89,100
[Repeated 3 time(s)]
> artiax particles #1.2.1 color 91,75,90,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 92,75,90,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 92,75,91,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 93,75,91,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 93,76,91,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 93,76,92,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 94,76,92,100
> artiax particles #1.2.1 color 93,76,92,100
> artiax particles #1.2.1 color 92,75,91,100
> artiax particles #1.2.1 color 92,75,90,100
> artiax particles #1.2.1 color 91,74,89,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 90,73,89,100
> artiax particles #1.2.1 color 89,73,88,100
> artiax particles #1.2.1 color 89,72,87,100
> artiax particles #1.2.1 color 88,72,87,100
> artiax particles #1.2.1 color 88,72,86,100
> artiax particles #1.2.1 color 87,71,86,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 87,71,85,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 86,70,85,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 86,70,84,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 85,70,84,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 85,69,84,100
> artiax particles #1.2.1 color 85,70,84,100
> artiax particles #1.2.1 color 86,70,85,100
> artiax particles #1.2.1 color 87,71,85,100
> artiax particles #1.2.1 color 88,71,86,100
> artiax particles #1.2.1 color 88,72,86,100
> artiax particles #1.2.1 color 88,72,87,100
> artiax particles #1.2.1 color 89,72,87,100
> artiax particles #1.2.1 color 89,73,87,100
> artiax particles #1.2.1 color 89,73,88,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 90,73,88,100
> artiax particles #1.2.1 color 90,73,89,100
> artiax particles #1.2.1 color 90,74,89,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 91,74,89,100
> artiax particles #1.2.1 color 91,75,90,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 92,75,90,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 92,75,91,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 93,75,91,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 93,76,91,100
[Repeated 2 time(s)]
> artiax particles #1.2.1 color 93,76,92,100
> artiax particles #1.2.1 color 94,76,92,100
> artiax particles #1.2.1 color 94,77,93,100
> artiax particles #1.2.1 color 95,77,93,100
[Repeated 1 time(s)]
> artiax particles #1.2.1 color 95,78,93,100
> artiax particles #1.2.1 color 95,78,94,100
[Repeated 1 time(s)]
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/L5_G1_ts_003_corrected.mrc
Opened L5_G1_ts_003_corrected.mrc as #5, grid size 511,720,375, pixel
13.1,13.1,13.1, shown at level 0.158, step 4, values float32
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> volume #5 step 1
> volume #5 color #b2b2b2
> ui tool show "Side View"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> select add #7
3 models selected
> select subtract #7
Nothing selected
> select add #5
3 models selected
> ui mousemode right clip
> ui mousemode right "crop volume"
> volume #2 region 384,0,0,510,719,374
> volume #7 region 0,0,0,469,521,43
> volume #2 region 384,0,0,510,719,327
> volume #2 region 384,0,198,510,719,327
> ui mousemode right "crop volume"
[Repeated 1 time(s)]
> volume #7 region 0,0,1,469,521,43
[Repeated 1 time(s)]
> volume #7 region 0,0,0,469,521,43
[Repeated 3 time(s)]
> volume #7 region 0,0,3,469,521,43
[Repeated 1 time(s)]
> volume #2 region 0,0,198,510,719,327
> volume #7 region 0,0,0,469,521,43
> volume #2 region 16,0,198,510,719,327
> volume #7 region 0,0,0,469,521,43
> volume #7 region 0,0,0,462,521,43
> volume #2 region 16,0,198,510,719,327
[Repeated 1 time(s)]
> volume #2 region 16,0,0,510,719,327
[Repeated 1 time(s)]
> ui mousemode right "crop volume"
> select subtract #5
Nothing selected
> hide #!5 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> close #5
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> close #3
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> show #!4 models
> hide #!4 models
> close #4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented_2.tif
> width 766 height 689 supersample 4
> close #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/ruiliu/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
——— End of log from Mon Aug 25 09:55:51 2025 ———
opened ChimeraX session
> hide #!7 models
> hide #!11 models
> ui tool show "Map Eraser"
> volume erase #2 center 5667.1,7259.8,2312.9 radius 616.49
Opened
L5_G1_ts_003_corrected_inv_MemBrain_seg_v10_alpha.ckpt_segmented_erased.mrc
copy as #3, grid size 495,720,328, pixel 13.1,13.1,13.1, shown at step 1,
values float32
> volume erase #3 center 4424.5,7634.3,2929.2 radius 612.14
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
——— End of log from Mon Aug 25 10:32:50 2025 ———
opened ChimeraX session
> clip off
> ui tool show "Map Eraser"
> volume erase #3 center 3741.5,7517.2,1484.8 radius 536.77
> volume erase #3 center 2880.9,6048.5,2774.4 radius 589.91
> volume erase #3 center 2827.6,5807.5,2843.3 radius 382.65
> surface dust #3 size 131
> volume erase #3 center 1937.6,6100,1933 radius 589.91
> volume erase #3 center 1915.1,6138.2,1944.9 radius 589.91
> volume erase #3 center 764.72,5243.8,2021.2 radius 589.91
> volume erase #3 center 750.61,5219.8,2025.1 radius 589.91
> volume erase #3 center 731.62,5275.5,2030.5 radius 589.91
> volume erase #3 center 748.13,5513.6,1600.7 radius 334.82
> volume erase #3 center 2141.9,4319.3,1645.6 radius 605.86
> clip off
> volume erase #3 center 2092.5,4115.4,1863.6 radius 361.39
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
——— End of log from Mon Aug 25 10:38:59 2025 ———
opened ChimeraX session
> ui tool show "Map Eraser"
> volume erase #3 center -93.462,3195.5,1777.1 radius 616.49
> volume erase #3 center 1542.6,3100.2,2450.8 radius 616.49
> volume erase #3 center 1875.2,1848.5,2192.6 radius 616.49
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
> volume erase #3 center 3322.9,955.82,2921.5 radius 616.49
> volume erase #3 center 3392.8,849.88,2796.6 radius 510.2
> volume erase #3 center 3239.9,699.69,2483.6 radius 292.3
> volume erase #3 center 4715.7,700.22,2932.7 radius 605.86
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
——— End of log from Mon Aug 25 11:01:06 2025 ———
opened ChimeraX session
> clip off
> show #!7 models
> show #!11 models
> ui mousemode right "move picked models"
> ui mousemode right "crop volume"
> volume #11 region 16,0,0,510,719,327
> volume #11 region 16,0,0,510,719,374
[Repeated 3 time(s)]
> volume #3 region 0,0,0,494,719,327
> clip off
> volume #3 region all
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented.cxs
> includeMaps true
——— End of log from Mon Aug 25 11:03:21 2025 ———
opened ChimeraX session
> clip volume off
Expected a keyword
> view
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/ribosome_list.em
> format motl
Summary of feedback from opening
/Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/ribosome_list.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list ribosome_list.em with 845 particles.
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/PAO1_ribosome_13_08_30.mrc
Opened PAO1_ribosome_13_08_30.mrc as #4, grid size 30,30,30, pixel 13.1, shown
at level 0.0172, step 1, values float32
> artiax particles #1.2.1 radius 0.1
set axis size 16.0616
16.0616
['.arrow', '0', '0', '0', '16.0616', '0', '0', '1.0707733333333331',
'4.2830933333333325']
set axis size 15.30152
15.30152
['.arrow', '0', '0', '0', '15.30152', '0', '0', '1.0201013333333333',
'4.080405333333333']
set axis size 14.54144
14.54144
['.arrow', '0', '0', '0', '14.54144', '0', '0', '0.9694293333333334',
'3.8777173333333335']
set axis size 13.78137
13.78137
['.arrow', '0', '0', '0', '13.78137', '0', '0', '0.9187580000000001',
'3.6750320000000003']
set axis size 13.02129
13.02129
['.arrow', '0', '0', '0', '13.02129', '0', '0', '0.868086', '3.472344']
set axis size 12.26122
12.26122
['.arrow', '0', '0', '0', '12.26122', '0', '0', '0.8174146666666666',
'3.2696586666666665']
set axis size 10.74106
10.74106
['.arrow', '0', '0', '0', '10.74106', '0', '0', '0.7160706666666666',
'2.8642826666666665']
set axis size 7.70076
7.70076
['.arrow', '0', '0', '0', '7.70076', '0', '0', '0.513384', '2.053536']
set axis size 3.90038
3.90038
['.arrow', '0', '0', '0', '3.90038', '0', '0', '0.26002533333333333',
'1.0401013333333333']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
> artiax particles #1.2.1 axesSize 0.1
> artiax attach #4 toParticleList #1.2.1
Opened PAO1_ribosome_13_08_30.mrc as #1.2.1.1.1, grid size 30,30,30, pixel
13.1, shown at level 0.0172, step 1, values float32
> volume #1.2.1.1.1 capFaces false
set axis size 196.2
196.2
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']
> artiax particles #1.2.1 originScaleFactor 13.08
> artiax view xy
> artiax particles #1.2.1 surfaceLevel 0.006
> artiax particles #1.2.1 radius 0.1
set axis size 2.38023
2.38023
['.arrow', '0', '0', '0', '2.38023', '0', '0', '0.15868200000000002',
'0.6347280000000001']
set axis size 1.62015
1.62015
['.arrow', '0', '0', '0', '1.62015', '0', '0', '0.10801', '0.43204']
set axis size 7.70076
7.70076
['.arrow', '0', '0', '0', '7.70076', '0', '0', '0.513384', '2.053536']
set axis size 13.78137
13.78137
['.arrow', '0', '0', '0', '13.78137', '0', '0', '0.9187580000000001',
'3.6750320000000003']
set axis size 16.82167
16.82167
['.arrow', '0', '0', '0', '16.82167', '0', '0', '1.1214446666666666',
'4.485778666666667']
set axis size 19.86198
19.86198
['.arrow', '0', '0', '0', '19.86198', '0', '0', '1.3241319999999999',
'5.2965279999999995']
set axis size 23.66236
23.66236
['.arrow', '0', '0', '0', '23.66236', '0', '0', '1.5774906666666666',
'6.309962666666666']
set axis size 25.18251
25.18251
['.arrow', '0', '0', '0', '25.18251', '0', '0', '1.678834', '6.715336']
set axis size 26.70266
26.70266
['.arrow', '0', '0', '0', '26.70266', '0', '0', '1.7801773333333335',
'7.120709333333334']
set axis size 28.98289
28.98289
['.arrow', '0', '0', '0', '28.98289', '0', '0', '1.9321926666666667',
'7.728770666666667']
set axis size 33.54335
33.54335
['.arrow', '0', '0', '0', '33.54335', '0', '0', '2.2362233333333332',
'8.944893333333333']
set axis size 37.34373
37.34373
['.arrow', '0', '0', '0', '37.34373', '0', '0', '2.489582', '9.958328']
set axis size 40.38403
40.38403
['.arrow', '0', '0', '0', '40.38403', '0', '0', '2.6922686666666666',
'10.769074666666667']
set axis size 41.90418
41.90418
['.arrow', '0', '0', '0', '41.90418', '0', '0', '2.793612', '11.174448']
set axis size 42.66426
42.66426
['.arrow', '0', '0', '0', '42.66426', '0', '0', '2.844284', '11.377136']
set axis size 45.70456
45.70456
['.arrow', '0', '0', '0', '45.70456', '0', '0', '3.0469706666666667',
'12.187882666666667']
set axis size 47.22471
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['.arrow', '0', '0', '0', '47.22471', '0', '0', '3.148314', '12.593256']
set axis size 49.50494
49.50494
['.arrow', '0', '0', '0', '49.50494', '0', '0', '3.300329333333333',
'13.201317333333332']
set axis size 50.26502
50.26502
['.arrow', '0', '0', '0', '50.26502', '0', '0', '3.3510013333333335',
'13.404005333333334']
set axis size 51.0251
51.0251
['.arrow', '0', '0', '0', '51.0251', '0', '0', '3.4016733333333335',
'13.606693333333334']
set axis size 53.30532
53.30532
['.arrow', '0', '0', '0', '53.30532', '0', '0', '3.553688', '14.214752']
set axis size 54.0654
54.0654
['.arrow', '0', '0', '0', '54.0654', '0', '0', '3.60436', '14.41744']
set axis size 54.82548
54.82548
['.arrow', '0', '0', '0', '54.82548', '0', '0', '3.655032', '14.620128']
set axis size 55.58555
55.58555
['.arrow', '0', '0', '0', '55.58555', '0', '0', '3.705703333333333',
'14.822813333333333']
set axis size 54.82548
54.82548
['.arrow', '0', '0', '0', '54.82548', '0', '0', '3.655032', '14.620128']
set axis size 54.0654
54.0654
['.arrow', '0', '0', '0', '54.0654', '0', '0', '3.60436', '14.41744']
set axis size 53.30532
53.30532
['.arrow', '0', '0', '0', '53.30532', '0', '0', '3.553688', '14.214752']
set axis size 48.74487
48.74487
['.arrow', '0', '0', '0', '48.74487', '0', '0', '3.2496579999999997',
'12.998631999999999']
set axis size 38.1038
38.1038
['.arrow', '0', '0', '0', '38.1038', '0', '0', '2.5402533333333333',
'10.161013333333333']
set axis size 33.54335
33.54335
['.arrow', '0', '0', '0', '33.54335', '0', '0', '2.2362233333333332',
'8.944893333333333']
set axis size 28.22281
28.22281
['.arrow', '0', '0', '0', '28.22281', '0', '0', '1.8815206666666666',
'7.5260826666666665']
set axis size 25.94259
25.94259
['.arrow', '0', '0', '0', '25.94259', '0', '0', '1.729506', '6.918024']
set axis size 23.66236
23.66236
['.arrow', '0', '0', '0', '23.66236', '0', '0', '1.5774906666666666',
'6.309962666666666']
set axis size 20.62205
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['.arrow', '0', '0', '0', '20.62205', '0', '0', '1.3748033333333334',
'5.4992133333333335']
set axis size 11.50114
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['.arrow', '0', '0', '0', '11.50114', '0', '0', '0.7667426666666667',
'3.0669706666666667']
set axis size 4.66046
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['.arrow', '0', '0', '0', '4.66046', '0', '0', '0.3106973333333333',
'1.2427893333333333']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
> artiax particles #1.2.1 axesSize 0.1
> artiax particles #1.2.1 color 94,64,100,100
> artiax particles #1.2.1 color 95,78,94,100
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented_3.tif
> width 766 height 689 supersample 4
> artiax particles #1.2.1 color 95,78,94,100
> artiax particles #1.2.1 color 94,94,76,100
> artiax particles #1.2.1 color 94,93,83,100
> artiax particles #1.2.1 color 94,94,88,100
> artiax particles #1.2.1 color 93,94,83,100
> volume #11 color #5161f5
> volume #11 color #2247f5
> volume #11 color #2730f5
> volume #11 color #4147f5
> volume #11 color #585af5
> volume #11 color #3753ef
> volume #3 color #f2d1bd
> volume #3 color #f2cfaa
> volume #3 color #f2d8c7
> volume #3 color #f2c8b3
> volume #3 color #f2baaf
> volume #3 color #f2c6a8
> volume #3 color #f2ca98
> volume #3 color #f2c388
> volume #3 color #f2d0ac
> volume #3 color #f2c588
> volume #3 color #f2c79a
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
fine
> volume #7 color #56bebf
> volume #7 color #bfbdbf
> volume #7 color #bfb8b3
> volume #7 color #b2b2b2
> artiax particles #1.2.1 color 93,94,83,100
> artiax particles #1.2.1 color 93,95,79,100
> artiax particles #1.2.1 color 92,95,73,100
> artiax particles #1.2.1 color 93,95,70,100
> artiax particles #1.2.1 color 95,96,71,100
> artiax particles #1.2.1 color 95,97,72,100
> artiax particles #1.2.1 color 96,98,72,100
fine
fine
fine
fine
fine
> volume #3 color #efc9ac
> volume #3 color #efbe80
> volume #3 color #efac61
> volume #3 color #efad77
> volume #3 color #efb288
> volume #3 color #efab6d
> volume #3 color #efb07a
> volume #3 color #efc188
> volume #3 color #efc17d
> volume #3 color #efb374
> volume #3 color #efba80
> volume #3 color #efb07a
> volume #3 color #ef9e5f
fine
fine
fine
fine
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/ribosome_list.em
> partlist #1.2.1
> save
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/L5_1_3_segmented_3.tif
> width 833 height 689 supersample 4
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/PhiKZ_capsid_emd_38845.map
Opened PhiKZ_capsid_emd_38845.map as #4, grid size 1000,1000,1000, pixel 1.6,
shown at step 1, values float32
> volume #4 level -0.002649,0 level 0.01229,0.8 level 0.02372,1
> volume #4 level -0.002649,0 level 0.003922,0.7412 level 0.02372,1
> close #4
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/PhiKZ_capsid_emd_38845.map
Opened PhiKZ_capsid_emd_38845.map as #4, grid size 1000,1000,1000, pixel 1.6,
shown at step 1, values float32
> volume #4 region 0,0,0,999,999,999 step 4
> volume #4 step 1
> vop gaussian #4 sdev 12 valueType float32
Opened PhiKZ_capsid_emd_38845.map gaussian as #5, grid size 1000,1000,1000,
pixel 1.6, shown at step 1, values float32
> volume #4 change image level -0.002649,0 level 0.01229,0.8 level 0.02372,1
> volume #4 level 0.004696
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ruiliu/Desktop/Villa_lab/Data/Titan_processing/042925_PAO1_DarTG_gp104_KO_KZ_40mpi_warp2/segmentation/segmented_maps/PhiKZ_capsid_emd_38845.map
Opened PhiKZ_capsid_emd_38845.map as #1, grid size 1000,1000,1000, pixel 1.6,
shown at step 1, values float32
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1GM000G9LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 6 days, 22 hours, 29 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pyarrow: 17.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
starfile: 0.5.8
superqt: 0.6.7
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in glBufferSubData |
comment:2 by , 7 weeks ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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Adjusting threshold level of a 4 GB map (10003 float32) graphics driver crashed.