id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18292 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.7.6-x86_64-i386-64bit ChimeraX Version: 1.7.dev202308300120 (2023-08-30 01:20:01 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070000f467000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff8581a7a00 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 1003 in to_h36 File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 1071 in _h_name File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 938 in new_hydrogen File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 899 in add_altloc_hyds File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 898 in _attach_hydrogens File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 214 in add_hydrogens File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 173 in hbond_add_hydrogens File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 66 in cmd_addh File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 84 in assign_charges File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 88 in cmd_coulombic File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 38 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 514 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 571 in run_expanded_command File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 61 in func_plus_tip File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 328 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 409 in run_shortcut File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 391 in try_shortcut File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1365 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 55 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1291 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 386 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 893 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1044 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, 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""6391cacc75b0720ff1f8c695"", ""factorPackIds"" : { ""COREOS_ICD"" : ""63957f508061fa721c8edc4a"" }, ""deploymentId"" : 240000007 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/jbaral/Desktop/Session for structures.cxs"" Opened cryosparc_P1_J136_007_volume_map_sharp.mrc as #1, grid size 420,420,420, pixel 0.833, shown at level 0.0875, step 1, values float32 Opened Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc as #3, grid size 512,512,512, pixel 0.833, shown at level 0.106, step 1, values float32 Log from Mon Jan 27 20:56:18 2025 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jbaral/Library/CloudStorage/OneDrive- > TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission 40bp > supercomplex/Detailed/Maps- > submitted/cryosparc_P1_J136_007_volume_map_sharp.mrc"" Opened cryosparc_P1_J136_007_volume_map_sharp.mrc as #1, grid size 420,420,420, pixel 0.833, shown at level 0.0303, step 2, values float32 > open ""/Users/jbaral/Library/CloudStorage/OneDrive- > TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission 40bp > supercomplex/Detailed/Model/pdb_extract_29665-job-145.cif"" Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive- TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission 40bp supercomplex/Detailed/Model/pdb_extract_29665-job-145.cif --- warnings | Atom H1 is not in the residue template for ASP /A:28 Atom H1 is not in the residue template for ASP /A:56 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for pdb_extract_29665-job-145.cif #2 --- Chain | Description A C E | No description available B D F | No description available G | No description available H | No description available I | No description available J | No description available > volume #1 level 0.1222 > show cartoons > hide atoms > volume #1 step 1 > volume #1 level 0.136 > color bychain > color zone #1 near #2 distance 5 > lighting soft > surface dust #1 size 8.33 > volume #1 level 0.08753 [Repeated 1 time(s)] > volume #1 level 0.091 > volume #1 level 0.09792 > volume #1 level 0.1014 > volume style mesh > open ""/Users/jbaral/Library/CloudStorage/OneDrive- > TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY > supercomplex/Detailed/Maps- > submitted/Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc"" Opened Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc as #3, grid size 512,512,512, pixel 0.833, shown at level 0.0237, step 2, values float32 > open ""/Users/jbaral/Library/CloudStorage/OneDrive- > TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY > supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif"" Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive- TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif --- warning | Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for pdb_extract_8499-J-318.cif #4 --- Chain | Description A I K | No description available B J L | No description available C E G | No description available D F H | No description available > ui tool show matchmaker > matchmaker #4 to #2 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 pdb_extract_29665-job-145.cif, chain C (#2) with pdb_extract_8499-J-318.cif, chain I (#4), sequence alignment score = 1071 RMSD between 189 pruned atom pairs is 1.174 angstroms; (across all 226 pairs: 1.462) > select add #4 24579 atoms, 25014 bonds, 1449 residues, 1 model selected > select subtract #4 Nothing selected > select add #4 24579 atoms, 25014 bonds, 1449 residues, 1 model selected > select add #3 24579 atoms, 25014 bonds, 1449 residues, 3 models selected > close #3 > close #4 > open ""/Users/jbaral/Library/CloudStorage/OneDrive- > TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY > supercomplex/Detailed/Maps- > submitted/Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc"" Opened Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc as #3, grid size 512,512,512, pixel 0.833, shown at level 0.0237, step 2, values float32 > open ""/Users/jbaral/Library/CloudStorage/OneDrive- > TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY > supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif"" Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive- TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif --- warning | Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for pdb_extract_8499-J-318.cif #4 --- Chain | Description A I K | No description available B J L | No description available C E G | No description available D F H | No description available > volume #3 level 0.09441 > surface dust #1 size 8.33 > surface dust #3 size 8.33 > hide #2 models > hide #!1 models > hide #4 cartoons > hide #4 atoms > show #4 cartoons > volume #3 level 0.09441 > surface dust #3 size 8.33 [Repeated 1 time(s)] > volume #3 step 1 > volume #3 level 0.1064 > ui tool show ""Hide Dust"" > surface dust #3 size 8.61 [Repeated 1 time(s)] > surface dust #3 size 42.93 > surface dust #3 size 43.65 > color bychain > color zone #3 near #4 distance 5 [Repeated 1 time(s)] > volume #!3 style mesh > lighting soft [Repeated 1 time(s)] > show #2 models > show #!1 models Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 2 maps. [Repeated 3 time(s)] > select add #2 25454 atoms, 25961 bonds, 1477 residues, 1 model selected > select add #1 25454 atoms, 25961 bonds, 1477 residues, 3 models selected > color zone #1 near sel & #2 distance 5 > select subtract #2 2 models selected > select subtract #1 Nothing selected > select add #3 2 models selected > select add #4 24579 atoms, 25014 bonds, 1449 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.34309,0.28801,0.89406,-104.44,0.093586,0.93661,-0.33763,62.709,-0.93463,0.19951,0.29439,301.28,#4,0.34309,0.28801,0.89406,-104.44,0.093586,0.93661,-0.33763,62.709,-0.93463,0.19951,0.29439,301.28 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.34309,0.28801,0.89406,-104.7,0.093586,0.93661,-0.33763,61.858,-0.93463,0.19951,0.29439,301.48,#4,0.34309,0.28801,0.89406,-104.7,0.093586,0.93661,-0.33763,61.858,-0.93463,0.19951,0.29439,301.48 > view matrix models > #3,0.34309,0.28801,0.89406,-90.629,0.093586,0.93661,-0.33763,112.53,-0.93463,0.19951,0.29439,293.8,#4,0.34309,0.28801,0.89406,-90.629,0.093586,0.93661,-0.33763,112.53,-0.93463,0.19951,0.29439,293.8 > view matrix models > #3,0.34309,0.28801,0.89406,-90.757,0.093586,0.93661,-0.33763,112.56,-0.93463,0.19951,0.29439,293.79,#4,0.34309,0.28801,0.89406,-90.757,0.093586,0.93661,-0.33763,112.56,-0.93463,0.19951,0.29439,293.79 > view matrix models > #3,0.34309,0.28801,0.89406,-115.89,0.093586,0.93661,-0.33763,118.5,-0.93463,0.19951,0.29439,293.42,#4,0.34309,0.28801,0.89406,-115.89,0.093586,0.93661,-0.33763,118.5,-0.93463,0.19951,0.29439,293.42 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.29444,-0.7512,0.59077,178.21,0.29522,0.65944,0.69137,-76.141,-0.90893,-0.029162,0.41593,311.81,#4,0.29444,-0.7512,0.59077,178.21,0.29522,0.65944,0.69137,-76.141,-0.90893,-0.029162,0.41593,311.81 > view matrix models > #3,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97,#4,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97 > set bgColor white > view matrix models > #3,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97,#4,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97 > select clear > select add #3 2 models selected > select add #4 24579 atoms, 25014 bonds, 1449 residues, 3 models selected > view matrix models > #3,-0.085186,-0.50897,0.85656,153.07,0.28686,0.81076,0.51028,-69.539,-0.95418,0.28918,0.076939,323,#4,-0.085186,-0.50897,0.85656,153.07,0.28686,0.81076,0.51028,-69.539,-0.95418,0.28918,0.076939,323 > view matrix models > #3,-0.094515,-0.50117,0.86017,152.66,-0.089877,0.8648,0.494,2.6085,-0.99146,-0.03062,-0.12678,440.87,#4,-0.094515,-0.50117,0.86017,152.66,-0.089877,0.8648,0.494,2.6085,-0.99146,-0.03062,-0.12678,440.87 > view matrix models > #3,-0.016743,-0.91762,0.39711,319.72,-0.062251,0.39735,0.91555,10.064,-0.99792,-0.0093911,-0.063776,424.82,#4,-0.016743,-0.91762,0.39711,319.72,-0.062251,0.39735,0.91555,10.064,-0.99792,-0.0093911,-0.063776,424.82 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.016743,-0.91762,0.39711,280.84,-0.062251,0.39735,0.91555,5.3813,-0.99792,-0.0093911,-0.063776,417.16,#4,-0.016743,-0.91762,0.39711,280.84,-0.062251,0.39735,0.91555,5.3813,-0.99792,-0.0093911,-0.063776,417.16 > view matrix models > #3,-0.016743,-0.91762,0.39711,304.95,-0.062251,0.39735,0.91555,1.6131,-0.99792,-0.0093911,-0.063776,415.39,#4,-0.016743,-0.91762,0.39711,304.95,-0.062251,0.39735,0.91555,1.6131,-0.99792,-0.0093911,-0.063776,415.39 > view matrix models > #3,-0.016743,-0.91762,0.39711,316.57,-0.062251,0.39735,0.91555,29.884,-0.99792,-0.0093911,-0.063776,407.21,#4,-0.016743,-0.91762,0.39711,316.57,-0.062251,0.39735,0.91555,29.884,-0.99792,-0.0093911,-0.063776,407.21 > select clear > volume #1 level 0.07368 > volume #1 level 0.08753 > save ""/Users/jbaral/Desktop/Session for structures.cxs"" includeMaps true ——— End of log from Mon Jan 27 20:56:18 2025 ——— opened ChimeraX session > set bgColor black > volume style mesh > transparency 50 > transparency 0 > hide #2 models > show #2 models > hide #!1 models > hide #2 models > show #2 models > select #2/i.j Expected an objects specifier or a keyword > select #2/i,j 1392 atoms, 1500 bonds, 44 residues, 1 model selected > select #2/i,j 1392 atoms, 1500 bonds, 44 residues, 1 model selected > color sel red > select #2/g,h 2345 atoms, 2528 bonds, 74 residues, 1 model selected > color sel green > hide #!3 models > select #4/c,d 956 atoms, 1029 bonds, 30 residues, 1 model selected > color sel green > select #4/e,f 956 atoms, 1029 bonds, 30 residues, 1 model selected > color sel red > select #4/g,h 956 atoms, 1029 bonds, 30 residues, 1 model selected > color sel red > select protein 43428 atoms, 43860 bonds, 2718 residues, 2 models selected > color sel grey > select #2/a,b 7247 atoms, 7319 bonds, 453 residues, 1 model selected > color sel salmon > color sel magenta > color sel purple > select #4/a,b 7237 atoms, 7309 bonds, 453 residues, 1 model selected > color sel purple > select clear > dssp > select clear > select nucleic0acid Expected an objects specifier or a keyword > select nucleic-acid 6605 atoms, 7115 bonds, 208 residues, 2 models selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 6605 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 6605 atom styles > nucleotides sel tube/slab shape box > select clear Drag select of 1081 residues, 196 shapes > select clear > show #!3 models > hide #!3 models > select add #3 2 models selected > select add #4 24579 atoms, 25014 bonds, 1449 residues, 3 models selected Drag select of 6 residues > select add #3 90 atoms, 6 residues, 3 models selected > select add #4 24579 atoms, 25014 bonds, 1449 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.016743,-0.91762,0.39711,324.7,-0.062251,0.39735,0.91555,57.544,-0.99792,-0.0093911,-0.063776,405.92,#4,-0.016743,-0.91762,0.39711,324.7,-0.062251,0.39735,0.91555,57.544,-0.99792,-0.0093911,-0.063776,405.92 > view matrix models > #3,-0.016743,-0.91762,0.39711,325.43,-0.062251,0.39735,0.91555,58.698,-0.99792,-0.0093911,-0.063776,401.46,#4,-0.016743,-0.91762,0.39711,325.43,-0.062251,0.39735,0.91555,58.698,-0.99792,-0.0093911,-0.063776,401.46 > open ""/Users/jbaral/Desktop/PDB/40bp-mKu complex.pdb"" Chain information for 40bp-mKu complex.pdb #5 --- Chain | Description A | No description available B | No description available G | No description available H | No description available > select clear > select nucleic-acid 7933 atoms, 8546 bonds, 250 residues, 3 models selected > show sel atoms > nucleotides sel tube/slab shape box > select clear > select #2/a,b 7247 atoms, 7319 bonds, 453 residues, 1 model selected > select #2/i,j 1392 atoms, 1500 bonds, 44 residues, 1 model selected > select #2/g,h 2345 atoms, 2528 bonds, 74 residues, 1 model selected > color sel green > select clear > select add #5 8575 atoms, 8750 bonds, 495 residues, 1 model selected > view matrix models #5,1,0,0,14.741,0,1,0,58.275,0,0,1,-1.1596 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.29192,-0.22569,-0.92943,339.33,0.57813,0.81578,-0.016516,-5.5434,0.76194,-0.53251,0.36862,72.92 > view matrix models > #5,-0.27737,0.43285,-0.85773,305.35,0.77536,0.62804,0.066206,-19.725,0.56735,-0.64669,-0.50982,279.18 > view matrix models > #5,0.95312,0.20776,0.22001,-53.083,-0.20878,-0.074828,0.9751,122.79,0.21905,-0.97531,-0.027943,316.57 > view matrix models > #5,0.95128,0.11714,0.28522,-47.445,-0.28047,-0.055535,0.95825,134.61,0.12809,-0.99156,-0.019975,333.96 > view matrix models > #5,0.95141,0.11606,0.28521,-47.27,-0.28052,-0.055265,0.95826,134.57,0.12698,-0.9917,-0.020022,334.18 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.95141,0.11606,0.28521,-45.986,-0.28052,-0.055265,0.95826,136.22,0.12698,-0.9917,-0.020022,290.68 > select #5/a 3619 atoms, 3655 bonds, 226 residues, 1 model selected > color sel purple > select #5/b 3628 atoms, 3664 bonds, 227 residues, 1 model selected > color sel salmon > color sel gold > select #5/g,h 1328 atoms, 1431 bonds, 42 residues, 1 model selected > color sel green > select clear Drag select of 9 residues > select clear > open ""/Users/jbaral/Desktop/PDB/40bp-mKu complex.pdb"" Chain information for 40bp-mKu complex.pdb #6 --- Chain | Description A | No description available B | No description available G | No description available H | No description available > select add #6 8575 atoms, 8750 bonds, 495 residues, 1 model selected > view matrix models #6,1,0,0,-0.010998,0,1,0,-0.051463,0,0,1,-0.070208 > view matrix models #6,1,0,0,15.188,0,1,0,65.243,0,0,1,44.568 > view matrix models #6,1,0,0,16.166,0,1,0,69.688,0,0,1,49.648 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.47844,-0.30628,-0.82298,304.74,0.53705,0.84355,-0.0017164,5.3677,0.69475,-0.44116,0.56807,84.263 > view matrix models > #6,0.46195,0.12087,-0.87863,239.1,0.78181,0.41227,0.46776,-39.275,0.41877,-0.90301,0.095953,298.11 > view matrix models > #6,-0.076661,0.26808,-0.96034,319.77,0.88336,0.46494,0.05927,3.9643,0.46239,-0.84378,-0.27245,343.28 > view matrix models > #6,0.5439,0.29229,-0.7866,177.64,0.81734,0.027813,0.57549,6.2733,0.19008,-0.95593,-0.22377,402.66 > view matrix models > #6,0.051683,0.14819,-0.98761,324.12,0.99627,0.060741,0.06125,57.937,0.069065,-0.98709,-0.14449,415.68 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.051683,0.14819,-0.98761,323.46,0.99627,0.060741,0.06125,56.427,0.069065,-0.98709,-0.14449,417.65 > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 40bp-mKu complex.pdb #6/A TYR 57 O 40bp-mKu complex.pdb #6/A ILE 29 O Using Amber 20 recommended default charges and atom types for standard residues Hydrogen copy of 40bp-mKu complex.pdb #/A TYR 57 HXT bonded to atom that should not have hydrogens (copy of 40bp-mKu complex.pdb #/A TYR 57 OXT) > open ""/Users/jbaral/Desktop/PDB/mKu dimer AF.pdb"" Chain information for mKu dimer AF.pdb #7 --- Chain | Description A B | No description available > open ""/Users/jbaral/Desktop/PDB/mKu dimer AF DNA 21bp.pdb"" Chain information for mKu dimer AF DNA 21bp.pdb #8 --- Chain | Description A B | No description available C | No description available D | No description available > close #6 > close #7 > select add #8 5205 atoms, 5392 bonds, 588 residues, 1 model selected > hide #8 models > show #8 models > hide #8 models > select subtract #8 Nothing selected > ui tool show Matchmaker > matchmaker #8 to #5 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 40bp-mKu complex.pdb, chain B (#5) with mKu dimer AF DNA 21bp.pdb, chain A (#8), sequence alignment score = 990.4 RMSD between 176 pruned atom pairs is 0.986 angstroms; (across all 227 pairs: 1.940) > show #8 models > select add #8 5205 atoms, 5392 bonds, 588 residues, 1 model selected > view matrix models > #8,0.65199,-0.70806,-0.27122,193.37,0.7582,0.61213,0.22458,259.45,0.0070107,-0.35206,0.93595,158.25 > view matrix models > #8,0.65199,-0.70806,-0.27122,189.41,0.7582,0.61213,0.22458,256.42,0.0070107,-0.35206,0.93595,203.58 > view matrix models > #8,0.65199,-0.70806,-0.27122,186.99,0.7582,0.61213,0.22458,251.8,0.0070107,-0.35206,0.93595,223.81 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.90296,0.42647,-0.052831,186.56,-0.37895,0.84818,0.37013,249.58,0.20266,-0.31419,0.92748,224.13 > coulombic sel ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Registration file '/Users/jbaral/Library/Application Support/ChimeraX/registration' has expired UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.7.3 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 529.140.2.0.0 OS Loader Version: 577.140.2~30 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 13.7.6 (22H625) Kernel Version: Darwin 22.6.0 Time since boot: 7 days, 22 hours, 44 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) 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 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.47.1 ChimeraX-AtomicLibrary: 10.0.8 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.4 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: 1.7.dev202308300120 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: 1.1.2 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: 1.1.8 ChimeraX-ListInfo: 1.2 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.9 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: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 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: 2.2.2 ChimeraX-TapeMeasure: 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: 1.31.4 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3 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: 0.1.4 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7.post1 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.7 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.5 numpy: 1.25.1 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: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 }}} " defect closed normal Core duplicate all ChimeraX