id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10239 Crash in GL.glDeleteBuffers() while updating tomogram surfaces chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit 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 0x000000030f0af000 (most recent call first): 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 2643 in release_buffer 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 2634 in delete_buffer 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 1721 in delete 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 1712 in __del__ File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 364 in notify File 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""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 897 in start File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/logger.py"", line 232 in status File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/logger.py"", line 459 in status File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py"", line 111 in message File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py"", line 2092 in update_surface File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py"", line 808 in 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""factorPackIds"" : { ""SIRI_UNDERSTANDING_NL_OVERRIDES"" : ""654e391a4a6560536bdb1c80"" }, ""deploymentId"" : 240000529 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF8989D2A78)"" ] } ===== 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/jenny/Desktop/231128_TemplateComparison.cxs Opened NR_mask_ellipsoid_112px_25x_35y_18z_G2_0,0,0shifts.em as #1, grid size 112,112,112, pixel 1, shown at level 1, step 1, values float32 Opened NRmask_ellipsoid_112px_sx25sy35sz18_dx-2dy-5dz5_G1.em as #2, grid size 112,112,112, pixel 1, shown at level 1, step 1, values float32 Opened NRtmpl_tomsa_r2_b4_NR_center_ref_11.em as #3, grid size 112,112,112, pixel 1, shown at level -0.125, step 1, values float32 Opened EMD14330_NRpublished_CRposition.em as #4, grid size 112,112,112, pixel 1, shown at level -2.45, step 1, values float32 Opened Ver1 as #5, grid size 112,112,112, pixel 1, shown at level -0.145, step 1, values float32 Opened Template as #6, grid size 112,112,112, pixel 1, shown at level -0.73, step 1, values float32 Opened Ver2 as #7, grid size 112,112,112, pixel 1, shown at level -2.36, step 1, values float32 Opened Ver3 as #8, grid size 112,112,112, pixel 1, shown at level -2.45, step 1, values float32 Log from Tue Nov 28 09:43:26 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > artiax start Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em Opened 420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em as #2, grid size 20,65,1, pixel 1, shown at step 1, values float32 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em with 65 particles. > close #2 > hide #!1.2.1 models > show #!1.2.1 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/420_CRpublished_5deg_STD8_dist25_thresh0.0634.em Opened 420_CRpublished_5deg_STD8_dist25_thresh0.0634.em as #2, grid size 20,65,1, pixel 1, shown at step 1, values float32 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/420_CRpublished_5deg_STD8_dist25_thresh0.0634.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/420_CRpublished_5deg_STD8_dist25_thresh0.0634.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 420_CRpublished_5deg_STD8_dist25_thresh0.0634.em with 65 particles. > close #2 > hide #!1.2.1 models > show #!1.2.1 models > view all > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.1 models > show #!1.2.1 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0053.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0053.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 420TEST_CRpublished_5deg_STD8_dist25_thresh0.0053.em with 73 particles. > hide #!1.2.1 models > hide #!1.2.2 models > show #!1.2.2 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.023.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.023.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.023.em with 1324 particles. > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0515.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0515.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0515.em with 656 particles. > hide #!1.2.4 models > hide #!1.2.3 models > hide #!1.2.2 models > show #!1.2.4 models > show #!1.2.3 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0359.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0359.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0359.em with 1742 particles. > hide #!1.2.4 models > hide #!1.2.3 models > hide #!1.2.5 models > hide #!1.2.6 models > show #!1.2.6 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0524.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0524.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0524.em with 641 particles. > view all > hide #!1.2.7 models > hide #!1.2.6 models > show #!1.2.6 models > show #!1.2.5 models > hide #!1.2.6 models > show #!1.2.4 models > hide #!1.2.5 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0417.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0417.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0417.em with 1802 particles. > hide #!1.2.4 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0405.em with 1917 particles. > hide #!1.2.8 models > show #!1.2.8 models > hide #!1.2.8 models > show #!1.2.8 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0405.em with 1917 particles. > hide #!1.2.9 models > hide #!1.2.8 models > hide #!1.2.10 models > show #!1.2.10 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0379.em with 2095 particles. > hide #!1.2.10 models > show #!1.2.10 models > close #1.2 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0379.em with 2095 particles. Opened 251_dose-filt_rec.mrc as #1.1.1, grid size 1024,1024,500, pixel 4, shown at level 39.7, step 1, values float32 > artiax tomo #1.1.1 sliceDirection 0,0,1 > artiax view xy > artiax tomo #1.1.1 pixelSize 1.0 > artiax view xy > artiax tomo #1.1.1 pixelSize 1.0 > artiax view xy > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0697.em with 344 particles. 344 atoms, 344 residues, atom cross_correlation range 0.0697 to 0.135 [Repeated 1 time(s)] > artiax colormap #1.2.2.3 cross_correlation palette redgreen minValue > 0.06972353905439377 maxValue 0.13522033393383026 transparency 0.0 > artiax particles #1.2.2 radius 10.0 set axis size 25.0 25.0 ['.arrow', '0', '0', '0', '25.0', '0', '0', '1.6666666666666667', '6.666666666666667'] set axis size 25.0 25.0 ['.arrow', '0', '0', '0', '25.0', '0', '0', '1.6666666666666667', '6.666666666666667'] > artiax particles #1.2.2 axesSize 25.0 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0697.em with 344 particles. > artiax tomo #1.1.1 slice 344 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0853.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0853.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD10_dist25_thresh0.0853.em with 101 particles. > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > artiax particles #1.2.1 radius 10.0 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD15_dist25_thresh0.1241.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD15_dist25_thresh0.1241.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD15_dist25_thresh0.1241.em with 2 particles. > hide #!1.2.1 models > hide #!1.2.2 models > artiax tomo #1.1.1 slice 261 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD12_dist25_thresh0.1008.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD12_dist25_thresh0.1008.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD12_dist25_thresh0.1008.em with 29 particles. > artiax tomo #1.1.1 slice 177 > show #!1.2.2 models > hide #!1.2.3 models > artiax tomo #1.1.1 slice 154 > show #!1.2.3 models > show #!1.2.1 models > hide #!1.2.1 models > hide #!1.2.3 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > hide #!1.2.2 models > show #!1.2.2 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.093.em with 55 particles. > hide #!1.2.2 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > artiax particles #1.2.5 color 88,100,40,100 > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > hide #!1.2.4 models > show #!1.2.4 models > close #1.1 > close #1.2 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.0992.em with 33 particles. > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.093.em with 55 particles. > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.1 models > show #!1.1.1 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1286.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1286.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.1286.em with 343 particles. > hide #!1.1.3 models > show #!1.1.3 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.1 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1283.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1283.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.1283.em with 346 particles. > hide #!1.1.4 models > hide #!1.1.3 models > show #!1.1.4 models > hide #!1.1.4 models > show #!1.1.4 models > hide #!1.1.4 models > show #!1.1.4 models > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.0992.em with 33 particles. > view all > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0909.em > format motl Summary of feedback from opening /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0909.em --- notes | 15 ['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0'] Opened Particle list 251_NRpublished_5deg_STD10_dist25_thresh0.0909.em with 67 particles. > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.2 models Opened 251_dose-filt_full_rec.mrc as #1.2.1, grid size 1024,500,1024, pixel 4, shown at level 39.7, step 1, values float32 > artiax tomo #1.2.1 sliceDirection 0,0,1 > artiax view xy > close all > set bgColor white > set bgColor #ffffff00 > open > /Volumes/msdata/jesachwe/EM_Projects/Mot2KO_cryo/IntranuclearNPCs/SA_IntranuclearNPC/IntranuclearNPCs_bin4/CompositeMap/oldscripts/wholemount_IR.m Unrecognized file suffix '.m' > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/NR_mask_ellipsoid_112px_25x_35y_18z_G2_0,0,0shifts.em Opened NR_mask_ellipsoid_112px_25x_35y_18z_G2_0,0,0shifts.em as #1, grid size 112,112,112, pixel 1, shown at level 1, step 1, values float32 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/NRmask_ellipsoid_112px_sx25sy35sz18_dx-2dy-5dz5_G1.em Opened NRmask_ellipsoid_112px_sx25sy35sz18_dx-2dy-5dz5_G1.em as #2, grid size 112,112,112, pixel 1, shown at level 1, step 1, values float32 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/NRtmpl_tomsa_r2_b4_NR_center_ref_11.em Opened NRtmpl_tomsa_r2_b4_NR_center_ref_11.em as #3, grid size 112,112,112, pixel 1, shown at level 0.101, step 1, values float32 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/EMD14330_NRpublished_CRposition.em Opened EMD14330_NRpublished_CRposition.em as #4, grid size 112,112,112, pixel 1, shown at level 2.32, step 1, values float32 > view all > volume #4 level -2.451 > volume #3 level -0.1251 > volume all capFaces false Unsupported scale factor (0.000000) detected on Display1 [Repeated 4 time(s)] > vop multiply #3 #1 Opened volume product as #5, grid size 112,112,112, pixel 1, shown at step 1, values float32 > rename #5 version 1 Expected a keyword > rename #5 Ver1 > open > /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_5deg/inputs/EMD14330_NRtemplate.em Opened EMD14330_NRtemplate.em as #6, grid size 112,112,112, pixel 1, shown at level 2.39, step 1, values float32 > vop multiply #6 #1 Opened volume product as #7, grid size 112,112,112, pixel 1, shown at step 1, values float32 > rename #6 Ver1 > vop multiply #4 #2 Opened volume product as #8, grid size 112,112,112, pixel 1, shown at step 1, values float32 > rename #7 Ver3 > rename #6 Ver2 > ui tool show ""Volume Viewer"" > volume #7 level -3.09 > volume all capFaces false > rename #7 Ver2 > rename #8 Ver3 > volume #6 level -0.7298 > rename #6 Template > ui tool show ""Volume Viewer"" > volume #5 color #ffd479 > volume #6 color #7a81ff > volume #7 color #ff85ff > volume #7 color #ff2f92 > tile 3 models tiled > tile off > volume #5 color #ff9300 > graphics silhouettes true > lighting soft > volume #7 level -2.357 > volume #5 level -0.1453 > volume #8 color #00fa92 > volume #8 color #00f900 > volume #8 color #73fcd6 > volume #8 color #7a81ff > volume #8 color #0433ff > ui mousemode right select > select clear > select #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.9506,-0.048013,-0.30669,22.435,0.14231,-0.81065,0.56798,56.984,-0.27589,-0.58356,-0.76377,139.59 > ui mousemode right ""move picked models"" > view matrix models > #8,0.9506,-0.048013,-0.30669,24.969,0.14231,-0.81065,0.56798,63.242,-0.27589,-0.58356,-0.76377,143.74 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.87326,0.049417,0.48474,-19.474,-0.25494,-0.80146,0.54098,85.878,0.41524,-0.596,-0.68729,102.55 > ui mousemode right ""move picked models"" > view matrix models > #8,0.87326,0.049417,0.48474,-20.973,-0.25494,-0.80146,0.54098,87.285,0.41524,-0.596,-0.68729,103.24 > fitmap #8 inMap #7 metric correlation Fit map Ver3 in map Ver2 using 1399302 points correlation = 0.5283, correlation about mean = 0.5294, overlap = 4.362e+04 steps = 116, shift = 2.24, angle = 10 degrees Position of Ver3 (#8) relative to Ver2 (#7) coordinates: Matrix rotation and translation 0.98348560 0.15935560 0.08580126 -10.81601839 0.15850813 -0.98721736 0.01664497 103.20266885 0.08735696 -0.00276989 -0.99617322 106.44537391 Axis -0.99586274 -0.07979802 -0.04347039 Axis point 0.00000000 52.29493812 53.20661068 Rotation angle (degrees) 179.44148558 Shift along axis -2.09132105 > ui mousemode right select > select clear > ui mousemode right select > save /Users/jenny/Desktop/231128_TemplateComparison.cxs ——— End of log from Tue Nov 28 09:43:26 2023 ——— opened ChimeraX session > show #!4 models > hide #!7 models > show #!6 models > show #!7 models > hide #!4 models > hide #!6 models > show #!6 models > hide #!6 models > show #!4 models > hide #!4 models > show #!4 models > show #!6 models > hide #!6 models > show #!6 models > rename #6 EMD14330_NRtemplate.em > save /Users/jenny/Desktop/231128_HumanNR_TemplateComparison.cxs includeMaps > true > close all > artiax start Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho Opened 251_dose-filt_rec.mrc as #1.1.1, grid size 1024,1024,500, pixel 4, shown at level 39.7, step 1, values float32 > artiax tomo #1.1.1 sliceDirection 0,0,1 > artiax view xy Opened 265_dose-filt_rec.mrc as #1.1.2, grid size 1024,1024,500, pixel 4, shown at level 80.4, step 1, values float32 > artiax tomo #1.1.2 sliceDirection 0,0,1 > artiax view xy > hide #!1.1.1 models > hide #!1.1.2 models > show #!1.1.2 models > hide #!1.1.2 models > show #!1.1.1 models > show #!1.1.2 models > hide #!1.1.1 models ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Model Number: MKGP3D/A Chip: Unknown Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 1 day, 2 hours, 12 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 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 DELL U2721DE: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes 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: 2022.9.26 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: 2.0.3 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 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: 0.4.12 superqt: 0.5.3 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 Volume Data fixed Greg Couch chimerax-programmers all ChimeraX