id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18672 Crash in glBufferSubData chimerax-bug-report@… Tom Goddard "{{{ 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 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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 47.22471 ['.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 20.62205 ['.arrow', '0', '0', '0', '20.62205', '0', '0', '1.3748033333333334', '5.4992133333333335'] set axis size 11.50114 11.50114 ['.arrow', '0', '0', '0', '11.50114', '0', '0', '0.7667426666666667', '3.0669706666666667'] 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 #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 }}} " defect closed normal Graphics nonchimerax all ChimeraX