id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17772 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000038404f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000383043000 (most recent call first): File 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""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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256K 1 \nCG image 736K 35 \nColorSync 656K 33 \nCoreAnimation 1584K 97 \nCoreGraphics 112K 6 \nCoreUI image data 5776K 45 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.8G 111 \nMALLOC guard page 288K 18 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 784K 49 \nStack 207.2M 50 \nStack Guard 56.0M 1 \nVM_ALLOCATE 416.3M 363 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 33.3M 1064 \n__DATA_CONST 34.1M 1080 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 637.0M 154 \n__OBJC_RW 2374K 1 \n__TEXT 1.2G 1101 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 2 \nmapped file 543.7M 78 \nowned unmapped memory 229.1M 1 \npage table in kernel 2361K 1 \nshared memory 3232K 28 \n=========== ======= ======= \nTOTAL 6.4G 6274 \nTOTAL, minus reserved VM space 6.2G 6274 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""003fd9461d5e0e1037f3959c1fe2e5cffad9d35e"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5NJ3 format mmcif fromDatabase pdb 5nj3 title: Structure of an ABC transporter: complete structure [more info...] Chain information for 5nj3 #1 --- Chain | Description | UniProt A B | ATP-binding cassette sub-family G member 2 | ABCG2_HUMAN 2-655 C E | 5D3-Fab heavy chain | D F | 5D3-Fab light chain | Non-standard residues in 5nj3 #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open 1IGY Summary of feedback from opening 1IGY fetched from pdb --- warnings | Atom H1 is not in the residue template for LYS /A:2 Atom H1 is not in the residue template for VAL /B:2 Atom H1 is not in the residue template for LYS /C:2 Atom H1 is not in the residue template for VAL /D:2 1igy title: Structure of immunoglobulin [more info...] Chain information for 1igy #2 --- Chain | Description A C | IGG1 INTACT ANTIBODY MAB61.1.3 B D | IGG1 INTACT ANTIBODY MAB61.1.3 Non-standard residues in 1igy #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) FUL — beta-L-fucopyranose (beta-L-fucose; 6-deoxy-beta-L-galactopyranose; L-fucose; fucose; 6-DEOXY-BETA-L-GALACTOSE) GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine; 2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE) > mmaker #2 to #1 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 5nj3, chain D (#1) with 1igy, chain A (#2), sequence alignment score = 782.4 RMSD between 143 pruned atom pairs is 1.290 angstroms; (across all 206 pairs: 2.366) > select #1 12662 atoms, 12869 bonds, 8 pseudobonds, 1962 residues, 2 models selected > hide sel atoms > show sel cartoons > color sel bychain > undo > select clear > select #1/C,D,E,F 5408 atoms, 5500 bonds, 2 pseudobonds, 836 residues, 2 models selected > color sel bychain > select clear > undo > select clear > hide #!1 models > select #2/B:222 13 atoms, 12 bonds, 1 residue, 1 model selected > select add #2/D:222 26 atoms, 24 bonds, 2 residues, 1 model selected > color red > color sel red > select #2/A:196 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select #2/b,d:222 26 atoms, 24 bonds, 2 residues, 1 model selected > select #2/b,d:222@CA 2 atoms, 2 residues, 1 model selected > distance sel Distance between 1igy #2/B LYS 222 CA and /D LYS 222 CA: 47.716Å > set bgColor white > select #3 1 pseudobond, 2 models selected > color red > color sel red > select clear > save /Users/emilyscheib/Desktop/image1.png supersample 3 > ui mousemode right distance > select #2/D:312 12 atoms, 11 bonds, 1 residue, 1 model selected > ui mousemode right select Drag select of 5 residues > show sel atoms Drag select of 1 residues > show sel atoms > select #2/D:312 12 atoms, 11 bonds, 1 residue, 1 model selected > undo > ui mousemode right rotate > select clear > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > Show interacting residues between two proteins: Unknown command: Show interacting residues between two proteins: > contacts #2/B restrict #2/D distanceOnly 6 reveal true makePseudobonds false > select true 2182 distances > select up 1052 atoms, 1054 bonds, 107 residues, 1 model selected > style sel stick Changed 1052 atom styles > color sel yellow target a > ~select Nothing selected > Show interacting residues between two proteins: Unknown command: Show interacting residues between two proteins: > contacts #2/B restrict #2/B distanceOnly 6 reveal true makePseudobonds false > select true 60522 distances > select up 4119 atoms, 4215 bonds, 434 residues, 1 model selected > style sel stick Changed 4119 atom styles > color sel yellow target a > ~select Nothing selected > undo > select #2 12750 atoms, 13044 bonds, 1 pseudobond, 1312 residues, 2 models selected > hide sel atoms > Select->Residue->CYS” followed by “Actions->Atoms/Bonds->Show Unknown command: Select->Residue->CYS” followed by “Actions->Atoms/Bonds->Show > select ::name=""CYS"" 468 atoms, 419 bonds, 74 residues, 2 models selected > show (#2 & sel) target ab > hide #2 models > show #!1 models > show (#!1 & sel) target ab > show sel & #!1 atoms > hide sel & #!1 atoms > style sel & #!1 stick Changed 214 atom styles > show sel & #!1 atoms > show #2 models > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/B Alignment identifier is 2/B > select #2/B:274 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:274 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:273 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/B:273-275 24 atoms, 23 bonds, 3 residues, 1 model selected > select #2/B:242-243 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/B:242-243 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/B:240 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:240-243 32 atoms, 31 bonds, 4 residues, 1 model selected > show #!1 models > hide #!1 models > show #!1 models > open 1igy Summary of feedback from opening 1igy fetched from pdb --- warnings | Atom H1 is not in the residue template for LYS /A:2 Atom H1 is not in the residue template for VAL /B:2 Atom H1 is not in the residue template for LYS /C:2 Atom H1 is not in the residue template for VAL /D:2 1igy title: Structure of immunoglobulin [more info...] Chain information for 1igy #4 --- Chain | Description A C | IGG1 INTACT ANTIBODY MAB61.1.3 B D | IGG1 INTACT ANTIBODY MAB61.1.3 Non-standard residues in 1igy #4 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) FUL — beta-L-fucopyranose (beta-L-fucose; 6-deoxy-beta-L-galactopyranose; L-fucose; fucose; 6-DEOXY-BETA-L-GALACTOSE) GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine; 2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE) > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #4/B to #1/C pairing ss Parameters --- Chain pairing | ss 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 5nj3, chain C (#1) with 1igy, chain B (#4), sequence alignment score = 587.6 RMSD between 83 pruned atom pairs is 1.147 angstroms; (across all 203 pairs: 4.309) > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #4/B to #1/E pairing ss Parameters --- Chain pairing | ss 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 5nj3, chain E (#1) with 1igy, chain B (#4), sequence alignment score = 587.6 RMSD between 83 pruned atom pairs is 1.147 angstroms; (across all 203 pairs: 4.309) > ui tool show Matchmaker > matchmaker #4 to #1/E 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 5nj3, chain E (#1) with 1igy, chain B (#4), sequence alignment score = 587.6 RMSD between 83 pruned atom pairs is 1.147 angstroms; (across all 203 pairs: 4.309) > ui tool show Matchmaker > matchmaker #4 to #1/D 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 5nj3, chain D (#1) with 1igy, chain A (#4), sequence alignment score = 782.4 RMSD between 143 pruned atom pairs is 1.290 angstroms; (across all 206 pairs: 2.366) > ui tool show Matchmaker > matchmaker #4 to #1/F 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 5nj3, chain F (#1) with 1igy, chain A (#4), sequence alignment score = 782.4 RMSD between 143 pruned atom pairs is 1.290 angstroms; (across all 206 pairs: 2.366) > select #4 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > select ::name=""CYS"" 722 atoms, 655 bonds, 110 residues, 3 models selected > show sel target ab > select #2,4/B:235@CA 2 atoms, 2 residues, 2 models selected > distance sel Distance between 1igy #2/B CYS 235 CA and 1igy #4/B CYS 235 CA: 140.013Å > select #3.1 1 model selected > color red > color sel red > hide #3.1 models > show #3.1 models > hide #!3 models > show #!3 models > select #3 2 pseudobonds, 2 models selected > color sel red > select clear > hide #4 models > show #4 models > hide #3.1 models > show #3.1 models > hide #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > delete #3 > select #3 2 pseudobonds, 2 models selected > delete sel > hide #!3 models > show #!3 models > delete distance Missing or invalid ""atoms"" argument: invalid atoms specifier > ~distance > select #2 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > color light blue > select clear > select #4 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > color sel light green > select clear > show #!1 models > hide #!1 models > select #2 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > color sel light green > select #2 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > select #4 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > color sel light yellow > select clear > select #4 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > color #4 gold > color #4 light goldenrod yellow > color #4 yellow > color #4 dark khaki > color #4 khaki > select clear > select #2,4/B:235@CA 2 atoms, 2 residues, 2 models selected > distance sel Distance between 1igy #2/B CYS 235 CA and 1igy #4/B CYS 235 CA: 140.013Å > color #3 red > select clear > setattr g lineWidth 3 Assigning lineWidth attribute to 2 items Not creating attribute 'lineWidth'; use 'create true' to override > distance radius 1 Missing or invalid ""objects"" argument: invalid objects specifier > psuedobond radius 1 Unknown command: psuedobond radius 1 > psuedobonds radius 1 Unknown command: psuedobonds radius 1 > distance style > distance style 1 Expected a keyword > distance style radius 1 > distance style radius 0.5 > distance style radius 0.3 > distance style number dashes 11 Expected a keyword > distance style number of dashes 11 Expected a keyword > distance style dashes 11 > show #!1 models > hide #!1 models > show #!1 models > select #1/c,d,e,f 5408 atoms, 5500 bonds, 2 pseudobonds, 836 residues, 2 models selected > hide sel > hide sel cartoons > save /Users/emilyscheib/Desktop/image2.png supersample 3 > color #4 blue > color #2 blue > undo > lighting shadows false > lighting shadows true > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting simple > lighting soft > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > ui tool show ""Side View"" > lighting shadows false > lighting shadows true > save /Users/emilyscheib/Desktop/image3.png supersample 3 > ~distance > select #2/B,D:235@CA 2 atoms, 2 residues, 1 model selected > distance sel Distance between 1igy #2/B CYS 235 CA and /D CYS 235 CA: 13.346Å > color #3 red > distance style dashes 3 > distance style dashes 4 > select #2/A:209 12 atoms, 12 bonds, 1 residue, 1 model selected > hide #!1 models > select clear > save /Users/emilyscheib/Desktop/image4.png supersample 3 > show #!1 models > open 1igy Summary of feedback from opening 1igy fetched from pdb --- warnings | Atom H1 is not in the residue template for LYS /A:2 Atom H1 is not in the residue template for VAL /B:2 Atom H1 is not in the residue template for LYS /C:2 Atom H1 is not in the residue template for VAL /D:2 1igy title: Structure of immunoglobulin [more info...] Chain information for 1igy #5 --- Chain | Description A C | IGG1 INTACT ANTIBODY MAB61.1.3 B D | IGG1 INTACT ANTIBODY MAB61.1.3 Non-standard residues in 1igy #5 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) FUL — beta-L-fucopyranose (beta-L-fucose; 6-deoxy-beta-L-galactopyranose; L-fucose; fucose; 6-DEOXY-BETA-L-GALACTOSE) GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine; 2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE) > ui mousemode right ""translate selected models"" > select #5 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > view matrix models #5,1,0,0,52.357,0,1,0,52.526,0,0,1,-20.144 > view matrix models #5,1,0,0,44.115,0,1,0,104.74,0,0,1,-3.4192 > view matrix models #5,1,0,0,62.867,0,1,0,122.21,0,0,1,2.5785 > view matrix models #5,1,0,0,57.618,0,1,0,126.13,0,0,1,-6.5144 > view matrix models #5,1,0,0,60.558,0,1,0,125.8,0,0,1,-2.4258 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.9985,0.0055637,-0.054419,62.997,0.00086824,0.99308,0.11746,120.6,0.054696,-0.11733,0.99159,-3.6713 > view matrix models > #5,0.95248,-0.037001,-0.30235,74.036,0.15357,0.91555,0.37174,107.02,0.26306,-0.40051,0.87772,-3.5163 > view matrix models > #5,0.96027,0.070614,0.26999,49.821,-0.19827,0.85347,0.48195,105.97,-0.1964,-0.51633,0.83356,3.0358 > view matrix models > #5,0.97526,0.21317,-0.058507,65.139,-0.054564,0.48863,0.87078,84.291,0.21421,-0.84605,0.48817,10.475 > view matrix models > #5,0.7861,-0.061723,0.61501,35.792,-0.58372,0.2531,0.7715,93.124,-0.20328,-0.96547,0.16293,28.764 > view matrix models > #5,0.95728,0.14752,0.24871,51.41,-0.28259,0.2948,0.91282,83.645,0.061342,-0.9441,0.32389,18.705 > view matrix models > #5,0.9409,0.059011,0.3335,47.188,-0.32531,0.43137,0.84148,88.384,-0.094206,-0.90024,0.42508,16.525 > view matrix models > #5,0.939,-0.27595,0.20527,50.096,-0.12285,0.28836,0.94961,80.053,-0.32124,-0.9169,0.23687,27.357 > view matrix models > #5,0.98023,-0.19743,0.013367,58.613,0.042821,0.27758,0.95975,77.517,-0.19319,-0.9402,0.28055,23.711 > view matrix models > #5,0.9382,-0.34167,-0.055091,60.943,0.12678,0.1912,0.97333,75.208,-0.32202,-0.92017,0.2227,27.959 > view matrix models > #5,0.94116,-0.25133,-0.22594,69.099,0.27834,0.19724,0.94001,74.877,-0.19169,-0.94759,0.25559,24.722 > view matrix models > #5,0.98637,-0.081992,-0.14268,66.289,0.15665,0.20227,0.96672,75.224,-0.050402,-0.97589,0.21236,24.67 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.98637,-0.081992,-0.14268,120.47,0.15665,0.20227,0.96672,90.171,-0.050402,-0.97589,0.21236,27.373 > view matrix models > #5,0.98637,-0.081992,-0.14268,119.78,0.15665,0.20227,0.96672,89.536,-0.050402,-0.97589,0.21236,18.918 > view matrix models > #5,0.98637,-0.081992,-0.14268,120.12,0.15665,0.20227,0.96672,88.025,-0.050402,-0.97589,0.21236,20.585 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.97744,-0.045369,-0.20627,123.3,0.2056,-0.019106,0.97845,85.127,-0.048333,-0.99879,-0.0093471,30.056 > view matrix models > #5,0.83494,-0.19366,-0.51514,137.31,0.32314,-0.58518,0.74374,89.366,-0.44548,-0.78744,-0.42601,54.771 > undo > view matrix models > #5,0.91718,0.042884,-0.39616,133.04,0.39125,0.091535,0.91572,86.515,0.075533,-0.99488,0.067176,25.246 > view matrix models > #5,0.94773,-0.01183,-0.31885,128.85,0.31885,0.072149,0.94505,85.953,0.011825,-0.99732,0.07215,25.781 > view matrix models > #5,0.96489,-0.045941,-0.25859,125.74,0.26132,0.0694,0.96275,85.855,-0.026284,-0.99653,0.078969,25.951 > view matrix models > #5,0.9385,-0.14429,-0.31368,127.66,0.31829,0.009473,0.94795,85.326,-0.13381,-0.98949,0.054816,28.364 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.9385,-0.14429,-0.31368,132.2,0.31829,0.009473,0.94795,87.559,-0.13381,-0.98949,0.054816,28.836 > view matrix models > #5,0.9385,-0.14429,-0.31368,131.03,0.31829,0.009473,0.94795,86.849,-0.13381,-0.98949,0.054816,14.167 > view matrix models > #5,0.9385,-0.14429,-0.31368,130.06,0.31829,0.009473,0.94795,85.737,-0.13381,-0.98949,0.054816,1.1976 > hide #4 models > hide #5 models > show #5 models > hide #2 models > select #1/c,d,e,f 5408 atoms, 5500 bonds, 2 pseudobonds, 836 residues, 2 models selected > show sel atoms > hide sel atoms > show sel cartoons > select #1/ef Nothing selected > select #1/e,f 2704 atoms, 2750 bonds, 1 pseudobond, 418 residues, 2 models selected > color #1/e,f green > color #1/e,f light green > color #1/c,d khaki > select #5 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.94076,-0.12345,-0.31579,130.29,0.30635,-0.08964,0.94769,85.09,-0.1453,-0.98829,-0.04651,5.771 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #5,0.94076,-0.12345,-0.31579,129.08,0.30635,-0.08964,0.94769,79.201,-0.1453,-0.98829,-0.04651,-6.3177 > show sel surfaces > select #1 12662 atoms, 12869 bonds, 8 pseudobonds, 1962 residues, 2 models selected > show sel surfaces > select #5 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > view matrix models > #5,0.94076,-0.12345,-0.31579,128.51,0.30635,-0.08964,0.94769,84.32,-0.1453,-0.98829,-0.04651,-0.76087 > undo > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.90905,-0.21326,-0.35797,130.66,0.34601,-0.092337,0.93368,79.322,-0.23217,-0.97262,-0.01015,-6.7694 > undo > view matrix models > #5,0.93012,-0.16448,-0.32838,129.47,0.31596,-0.097444,0.94376,79.204,-0.18722,-0.98156,-0.038667,-6.1158 > undo > view matrix models > #5,0.94376,-0.10103,-0.31483,129.17,0.31333,-0.030773,0.94915,79.476,-0.10558,-0.99441,0.0026144,-8.9785 > view matrix models > #5,0.95395,-0.037112,-0.29765,128.82,0.29736,-0.01323,0.95467,79.574,-0.039368,-0.99922,-0.0015851,-9.6367 > undo > view matrix models > #5,0.94361,-0.095585,-0.31695,129.35,0.31348,-0.049745,0.94829,79.236,-0.10641,-0.99418,-0.016977,-8.0522 > view matrix models > #5,0.94291,-0.09193,-0.32012,129.52,0.31359,-0.078714,0.94629,79.097,-0.11219,-0.99265,-0.045391,-6.7282 > view matrix models > #5,0.94338,-0.10848,-0.31347,129.1,0.31389,-0.013567,0.94936,79.438,-0.10724,-0.99401,0.021251,-9.7084 > undo > select clear > select #5 12750 atoms, 13044 bonds, 1312 residues, 1 model selected > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models > #5,0.94291,-0.09193,-0.32012,128.92,0.31359,-0.078714,0.94629,78.838,-0.11219,-0.99265,-0.045391,-8.9704 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.94409,-0.094372,-0.3159,128.71,0.3119,-0.054857,0.94853,78.911,-0.10684,-0.99402,-0.022355,-10.044 > save /Users/emilyscheib/Desktop/boink.pdb > ui tool show ""Show Sequence Viewer"" > sequence chain #1/C Alignment identifier is 1/C ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z124000FLLL/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 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 2 days, 1 hour, 40 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 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 DELL E248WFP: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX