id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16880 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-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 Thread 0x000000031fe4f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031404f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File 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recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000030f013000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run 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 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000030afe3000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00000001fd8d4840 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""d272b91e-f9f0-3854-b5b9-508b21c25dcc"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=14.8G written=3919K(0%) resident=3919K(0%) swapped_out=0K(0%) unallocated=14.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 224K 13 \nColorSync 688K 32 \nCoreAnimation 912K 57 \nCoreGraphics 32K 2 \nCoreGraphics (reserved) 32K 1 reserved VM address space (unallocated)\nCoreUI image data 3056K 24 \nFoundation 48K 2 \nKernel Alloc Once 1456K 5 \nMALLOC 14.0G 227 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 832K 52 \nStack 348.3M 53 \nStack Guard 56.0M 1 \nVM_ALLOCATE 311.8M 625 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 32.8M 1055 \n__DATA_CONST 33.7M 1075 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 636.2M 149 \n__OBJC_RW 2374K 1 \n__TEXT 1.2G 1095 \n__TPRO_CONST 272K 2 \nmapped file 270.0M 53 \nowned unmapped memory 107.9M 1 \npage table in kernel 3919K 1 \nshared memory 3200K 25 \n=========== ======= ======= \nTOTAL 17.2G 6520 \nTOTAL, minus reserved VM space 17.0G 6520 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""logWritingSignature"" : ""95e762d8ecb8b961d72c8c875df3ed3e56c1e3c1"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""654d8c0661e7447155256fcd"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""6798311d431b3972542d1bcf"" }, ""deploymentId"" : 240000274 }, { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : { }, ""deploymentId"" : 240000032 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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/bgreber/Downloads/cryosparc_P20_J90_008_volume_map (1).mrc"" Opened cryosparc_P20_J90_008_volume_map (1).mrc as #1, grid size 128,128,128, pixel 1.4, shown at level 0.103, step 1, values float32 > volume #1 level 0.1853 > volume #1 level 0.2 > open /Users/bgreber/Downloads/run_it013_class002.mrc Opened run_it013_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown at level 0.00464, step 1, values float32 > open /Users/bgreber/Downloads/run_it013_class003.mrc Opened run_it013_class003.mrc as #3, grid size 128,128,128, pixel 1.4, shown at level 0.00552, step 1, values float32 > open /Users/bgreber/Downloads/run_it013_class004.mrc Opened run_it013_class004.mrc as #4, grid size 128,128,128, pixel 1.4, shown at level 0.00431, step 1, values float32 > open /Users/bgreber/Downloads/run_it013_class001.mrc Opened run_it013_class001.mrc as #5, grid size 128,128,128, pixel 1.4, shown at level 0.00415, step 1, values float32 > close #1 > volume #4 level 0.006129 > volume #4 level 0.006828 > volume #5 level 0.006911 > volume #2 level 0.004234 > volume #4 level 0.007 > volume #2 level 0.007 > volume #5 level 0.007 > open /Users/bgreber/Downloads/run_it019_class003.mrc Opened run_it019_class003.mrc as #1, grid size 128,128,128, pixel 1.4, shown at level 0.0053, step 1, values float32 > open /Users/bgreber/Downloads/run_it019_class004.mrc Opened run_it019_class004.mrc as #6, grid size 128,128,128, pixel 1.4, shown at level 0.00443, step 1, values float32 > open /Users/bgreber/Downloads/run_it019_class001.mrc Opened run_it019_class001.mrc as #7, grid size 128,128,128, pixel 1.4, shown at level 0.00422, step 1, values float32 > open /Users/bgreber/Downloads/run_it019_class002.mrc Opened run_it019_class002.mrc as #8, grid size 128,128,128, pixel 1.4, shown at level 0.00453, step 1, values float32 > volume #1 level 0.00509 > volume #6 level 0.007088 > volume #7 level 0.007173 > volume #8 level 0.007069 > open /Users/bgreber/Downloads/run_class001.mrc Opened run_class001.mrc as #9, grid size 128,128,128, pixel 1.4, shown at level 0.00419, step 1, values float32 > volume #9 level 0.009623 > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1 > QXLp modelling/alphafold_fitted-coot-0_real_space_refined_000.pdb"" Chain information for alphafold_fitted-coot-0_real_space_refined_000.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available > show atoms > volume #9 level 0.006144 > transparency 50 target s > volume #9 level 0.006144 > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1 > QXLp modelling/alphafold_fitted-coot-0.pdb"" Summary of feedback from opening /Users/bgreber/Library/CloudStorage/OneDrive- TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1 QXLp modelling/alphafold_fitted-coot-0.pdb --- warnings | Start residue of secondary structure not found: HELIX 18 18 VAL B 172 GLU B 174 1 3 Start residue of secondary structure not found: HELIX 43 43 ALA C 5 CYS C 7 1 3 Start residue of secondary structure not found: HELIX 44 44 SER C 19 CYS C 21 1 3 Start residue of secondary structure not found: SHEET 9 9 9 ILE B 101 ASP B 104 0 Chain information for alphafold_fitted-coot-0.pdb #11 --- Chain | Description A | No description available B | No description available C | No description available > show atoms > close #11 > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/WEE1/2025 CDK2-cyclin A-WEE1 > QXLp modelling/fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif"" Chain information for fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif #11 --- Chain | Description A | . B | . C | . > hide #10 models > show #10 models > hide #11 models > show #11 models > ui tool show Matchmaker > matchmaker #11 to #10 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain A (#10) with fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif, chain A (#11), sequence alignment score = 1493.9 RMSD between 298 pruned atom pairs is 0.455 angstroms; (across all 298 pairs: 0.455) > ui tool show Matchmaker > matchmaker #11 to #10/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain A (#10) with fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif, chain A (#11), sequence alignment score = 1493.9 RMSD between 298 pruned atom pairs is 0.455 angstroms; (across all 298 pairs: 0.455) > matchmaker #11 to #10/B pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10) with fold_wee1qxl_ps1_cdk2_cyclina_model_0.cif, chain B (#11), sequence alignment score = 1343.5 RMSD between 259 pruned atom pairs is 0.383 angstroms; (across all 259 pairs: 0.383) > show atoms > hide #11 models > graphics silhouettes true > set bgColor white > hide #10 cartoons > show #10 cartoons > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/CDK2/2024 CyclinA- > RxLpeptides/Structures/SAMHD1/cyca_cdk2_refined_SAMDH1_pp26-coot-2_real_space_refined_005.pdb"" Chain information for cyca_cdk2_refined_SAMDH1_pp26-coot-2_real_space_refined_005.pdb #12 --- Chain | Description A | No description available B | No description available C | No description available > show #10#!12 atoms > ui tool show Matchmaker > matchmaker #!12 to #10/B pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10) with cyca_cdk2_refined_SAMDH1_pp26-coot-2_real_space_refined_005.pdb, chain A (#12), sequence alignment score = 1265.7 RMSD between 255 pruned atom pairs is 0.506 angstroms; (across all 255 pairs: 0.506) > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/CDK2/2024 CyclinA- > RxLpeptides/Structures/GMNC/CDK2_CyclinA_GMNC_model- > coot-9_real_space_refined_017.pdb"" Chain information for CDK2_CyclinA_GMNC_model- coot-9_real_space_refined_017.pdb #13 --- Chain | Description A | No description available B | No description available C | No description available > show #10#!12-13 atoms > ui tool show Matchmaker > matchmaker #!13 to #10/B pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10) with CDK2_CyclinA_GMNC_model-coot-9_real_space_refined_017.pdb, chain A (#13), sequence alignment score = 1262.1 RMSD between 255 pruned atom pairs is 0.538 angstroms; (across all 255 pairs: 0.538) > hide #!12 models > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/CDK2/2024 CyclinA- > RxLpeptides/Structures/SCAPER/CycA_cdk2_refined_SCAPER_pp42-coot-1_real_space_refined_003.pdb"" Chain information for CycA_cdk2_refined_SCAPER_pp42-coot-1_real_space_refined_003.pdb #14 --- Chain | Description A | No description available B | No description available C | No description available > hide #!13 models > show #10#!14 atoms > matchmaker #!14 to #10/B pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker alphafold_fitted-coot-0_real_space_refined_000.pdb, chain B (#10) with CycA_cdk2_refined_SCAPER_pp42-coot-1_real_space_refined_003.pdb, chain A (#14), sequence alignment score = 1290.9 RMSD between 255 pruned atom pairs is 0.518 angstroms; (across all 255 pairs: 0.518) > transparency 0 target s > open /Users/bgreber/Downloads/postprocess.mrc Opened postprocess.mrc as #15, grid size 128,128,128, pixel 1.4, shown at level 0.00411, step 1, values float32 > volume #15 level 0.007978 > volume #15 level 0.01001 > transparency 50 target s > hide #!14 models > volume #15 level 0.004843 > open /Users/bgreber/Downloads/run17_class001.mrc Opened run17_class001.mrc as #16, grid size 128,128,128, pixel 1.4, shown at level 0.00406, step 1, values float32 > close #15 > volume #16 level 0.007577 > transparency 50 target s > volume #16 level 0.004802 > open /Users/bgreber/Downloads/run30_class001.mrc Opened run30_class001.mrc as #15, grid size 128,128,128, pixel 1.4, shown at level 0.0043, step 1, values float32 > volume #15 level 0.006224 > transparency 50 target s > volume #15 level 0.00601 > volume #15 level 0.005155 > volume #15 level 0.004728 > volume #15 level 0.007506 > volume #15 level 0.006865 > open /Users/bgreber/Downloads/run19_class001.mrc Opened run19_class001.mrc as #17, grid size 128,128,128, pixel 1.4, shown at level 0.00359, step 1, values float32 > volume #17 level 0.006907 > transparency 50 target s > volume #17 level 0.009053 > volume #17 level 0.007883 > volume #9 level 0.008101 > volume #9 level 0.008 > ui mousemode right zoom > volume #9 level 0.005391 > show #!13 models > hide #!13 models > show #!12 models > open /Users/bgreber/Downloads/run35_class001.mrc Opened run35_class001.mrc as #18, grid size 128,128,128, pixel 1.4, shown at level 0.00389, step 1, values float32 > volume #18 level 0.007053 > transparency 50 target s > volume #18 level 0.005865 > show #11 models > hide #11 models > show #11 models > hide #11 models > show #!13 models > show #!14 models > open /Users/bgreber/Downloads/pp32.mrc Opened pp32.mrc as #19, grid size 128,128,128, pixel 1.4, shown at level 0.0161, step 1, values float32 > volume #19 level 0.02401 > hide #!13 models > hide #!14 models > hide #!12 models > transparency 50 target s > volume #19 level 0.01683 > volume #19 level 0.02545 > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/CDK2/2024 > CDK1-cyclinB1-MAD1/Krios/cdk1_pp36.mrc"" Opened cdk1_pp36.mrc as #20, grid size 180,180,180, pixel 1.02, shown at level 0.00452, step 1, values float32 > open ""/Users/bgreber/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Research/Projects/CDK2/2024 > CDK1-cyclinB1-MAD1/Krios/pp36_MAD1.mrc"" Opened pp36_MAD1.mrc as #21, grid size 180,180,180, pixel 1.02, shown at level 0.00452, step 1, values float32 > volume #20 level 0.004516 > close #21 > close #20 > open /Users/bgreber/Downloads/run_it015_class003.mrc Opened run_it015_class003.mrc as #20, grid size 128,128,128, pixel 1.4, shown at level 0.00526, step 1, values float32 > open /Users/bgreber/Downloads/run_it015_class002.mrc Opened run_it015_class002.mrc as #21, grid size 128,128,128, pixel 1.4, shown at level 0.00531, step 1, values float32 > open /Users/bgreber/Downloads/run_it015_class001.mrc Opened run_it015_class001.mrc as #22, grid size 128,128,128, pixel 1.4, shown at level 0.00493, step 1, values float32 > open /Users/bgreber/Downloads/run_it015_class004.mrc Opened run_it015_class004.mrc as #23, grid size 128,128,128, pixel 1.4, shown at level 0.00525, step 1, values float32 > hide #!19 models > hide #!20 models > hide #!21 models > hide #!22 models > hide #!23 models > volume #23 level 0.01206 > volume #23 level 0.01135 > volume #22 level 0.01002 > volume #21 level 0.01678 > volume #20 level 0.007946 > show #11 models > transparency 50 target s > transparency 0 target s > volume #20 level 0.008 > volume #21 level 0.008 > volume #22 level 0.008 > volume #23 level 0.008 > open /Users/bgreber/Downloads/run_it020_class003.mrc Opened run_it020_class003.mrc as #24, grid size 128,128,128, pixel 1.4, shown at level 0.00551, step 1, values float32 > open /Users/bgreber/Downloads/run_it020_class002.mrc Opened run_it020_class002.mrc as #25, grid size 128,128,128, pixel 1.4, shown at level 0.00551, step 1, values float32 > open /Users/bgreber/Downloads/run_it020_class001.mrc Opened run_it020_class001.mrc as #26, grid size 128,128,128, pixel 1.4, shown at level 0.00499, step 1, values float32 > open /Users/bgreber/Downloads/run_it020_class004.mrc Opened run_it020_class004.mrc as #27, grid size 128,128,128, pixel 1.4, shown at level 0.00542, step 1, values float32 > hide #!25 models > hide #!26 models > hide #!27 models > volume #24 level 0.009916 > volume #25 level 0.01243 > volume #25 level 0.008 > volume #26 level 0.008 > volume #26 level 0.01016 > volume #26 level 0.008 > volume #26 level 0.01145 > volume #25 level 0.01446 > volume #24 level 0.01726 > volume #24 level 0.02 > volume #25 level 0.02 > volume #26 level 0.02 > volume #23 level 0.02 > volume #27 level 0.02 > close #20-27 > close #1-8 > open /Users/bgreber/Downloads/cryosparc_P20_peptide_volume_mask.mrc Opened cryosparc_P20_peptide_volume_mask.mrc as #1, grid size 128,128,128, pixel 1.4, shown at level 0.5, step 1, values float32 > volume #1 level 1 > transparency 50 target s > volume #1 level 1 > volume #1 level 0.5878 > volume #1 level 1 > open /Users/bgreber/Downloads/run_it012_class002.mrc Opened run_it012_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown at level 0.00448, step 1, values float32 > open /Users/bgreber/Downloads/run_it012_class001.mrc Opened run_it012_class001.mrc as #3, grid size 128,128,128, pixel 1.4, shown at level 0.00436, step 1, values float32 > hide #!1 models > volume #2 level 0.01228 > volume #3 level 0.01174 > volume #2 level 0.01 > volume #3 level 0.01 > open /Users/bgreber/Downloads/run_it018_class002.mrc Opened run_it018_class002.mrc as #4, grid size 128,128,128, pixel 1.4, shown at level 0.00438, step 1, values float32 > open /Users/bgreber/Downloads/run_it018_class001.mrc Opened run_it018_class001.mrc as #5, grid size 128,128,128, pixel 1.4, shown at level 0.00445, step 1, values float32 > volume #4 level 0.01096 > volume #5 level 0.01182 > close #2-5 > close #15-19 > close #9 > open /Users/bgreber/Downloads/run_it010_class002.mrc Opened run_it010_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown at level 0.00445, step 1, values float32 > open /Users/bgreber/Downloads/run_it010_class001.mrc Opened run_it010_class001.mrc as #3, grid size 128,128,128, pixel 1.4, shown at level 0.00436, step 1, values float32 > volume #3 level 0.01212 > volume #2 level 0.01127 > volume #2 level 0.01 > volume #3 level 0.01 > close #2 > close #3 > open /Users/bgreber/Downloads/run_it010_class002.mrc Opened run_it010_class002.mrc as #2, grid size 128,128,128, pixel 1.4, shown at level 4.93e-08, step 1, values float32 > open /Users/bgreber/Downloads/run_it010_class001.mrc Opened run_it010_class001.mrc as #3, grid size 128,128,128, pixel 1.4, shown at level 6.47e-06, step 1, values float32 > volume #3 level 0.006134 > volume #2 level 0.005943 > volume #2 level 0.01 > volume #3 level 0.01 > transparency 50 target s > open /Users/bgreber/Downloads/run_it015_class001.mrc Opened run_it015_class001.mrc as #4, grid size 128,128,128, pixel 1.4, shown at level 8.88e-07, step 1, values float32 > open /Users/bgreber/Downloads/run_it015_class002.mrc Opened run_it015_class002.mrc as #5, grid size 128,128,128, pixel 1.4, shown at level 8.31e-06, step 1, values float32 > volume #4 level 0.007059 > volume #5 level 0.009763 > volume #4 level 0.01 > volume #5 level 0.01 > volume #5 level 0.007561 > volume #4 level 0.076 > volume #4 level 0.0076 > volume #5 level 0.02 > volume #4 level 0.02 > open /Users/bgreber/Downloads/run_it023_class001.mrc Opened run_it023_class001.mrc as #6, grid size 128,128,128, pixel 1.4, shown at level 1.09e-05, step 1, values float32 > open /Users/bgreber/Downloads/run_it023_class002.mrc Opened run_it023_class002.mrc as #7, grid size 128,128,128, pixel 1.4, shown at level 1.26e-06, step 1, values float32 > volume #6 level 0.003187 > volume #7 level 0.00503 > hide #!4 models > hide #!5 models > volume #7 level 0.02 > volume #6 level 0.02 > volume #6 level 0.01 > volume #7 level 0.01 > transparency 50 target s > volume #7 level 0.007276 > show #!13 models > hide #11 models > hide #10 models > hide #!13 models > show #11 models > transparency 0 target s > volume #7 level 0.001 > volume #7 level 0.01 > volume #7 level 0.007 > volume #6 level 0.007 > transparency 50 target s > open /Users/bgreber/Downloads/run_it025_class001.mrc Opened run_it025_class001.mrc as #8, grid size 128,128,128, pixel 1.4, shown at level 1.07e-05, step 1, values float32 > open /Users/bgreber/Downloads/run_it025_class002.mrc Opened run_it025_class002.mrc as #9, grid size 128,128,128, pixel 1.4, shown at level 1.44e-06, step 1, values float32 > volume #8 level 0.006926 > volume #9 level 0.006582 > volume #8 level 0.007 > volume #9 level 0.007 > volume #8 level 0.02 > volume #9 level 0.02 > volume #8 level 0.009831 > volume #9 level 0.00666 QPainter::begin: Paint device returned engine == 0, type: 3 ===== 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/bgreber/Downloads/run_it025_class002.mrc Opened run_it025_class002.mrc as #1, grid size 128,128,128, pixel 1.4, shown at level 7.54e-06, step 1, values float32 > open /Users/bgreber/Downloads/run_it025_class001.mrc Opened run_it025_class001.mrc as #2, grid size 128,128,128, pixel 1.4, shown at level 2.63e-06, step 1, values float32 OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 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 Air Model Identifier: MacBookAir10,1 Model Number: Z1250001QB/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 6 days, 19 hours, 29 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 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-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 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 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 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 Window Toolkit duplicate all ChimeraX