id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18439 Crash in python_instances_of_class herrera.alfa@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.7.5-arm64-arm-64bit ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000030e8af000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x000000030d8a3000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x000000030c897000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x000000030b88b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x000000030a87f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x0000000309873000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x0000000308867000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x000000030785b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x000000030684f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x0000000305843000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 Thread 0x0000000304837000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 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 0x00000001fcc9cf80 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 44 in python_instances_of_class File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 149 in combine File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py"", line 522 in bind File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py"", line 376 in cn_peptide_bond File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/cmd.py"", line 205 in cmd_join_peptide File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2904 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 49 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py"", line 774 in _jm_apply_cb File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py"", line 1193 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 280 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 918 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 1069 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, 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, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, 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""26d4d565479e12450ce6804eae3cf4f05e6ab134"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000205 }, { ""rolloutId"" : ""648a2601f74c42732876cb5b"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""6733fcb357a33f0bf26912cf"" }, ""deploymentId"" : 240000272 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Compositor returned null texture > open ""/Users/aho2840/Desktop/Satchell > Lab/MCFHomologs/MCF:Homolog.paper/workingon.closed0716.cxs"" format session opened ChimeraX session > open ""/Users/aho2840/Desktop/Satchell > Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"" opened ChimeraX session > hide #!9 models > hide #53 models > log metadata #104 The model has no metadata > log chains #104 Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104 --- Chain | Description A | No description available > sequence chain #104/A Alignment identifier is 104/A > log metadata #105 The model has no metadata > log chains #105 Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105 --- Chain | Description A | No description available > sequence chain #105/A Alignment identifier is 105/A > select #105/A:1999-2000 28 atoms, 28 bonds, 2 residues, 1 model selected > select #105/A:1800-2000 3081 atoms, 3109 bonds, 201 residues, 1 model selected No visible models! > show #105 models > select #105/A:1999-2000 28 atoms, 28 bonds, 2 residues, 1 model selected > select #105/A:1800-2000 3081 atoms, 3109 bonds, 201 residues, 1 model selected > show sel cartoons > delete atoms sel > delete bonds sel > select #105/A:2093 19 atoms, 18 bonds, 1 residue, 1 model selected > select #105/A:2093-2094 36 atoms, 35 bonds, 2 residues, 1 model selected > select #105/A:2001 10 atoms, 9 bonds, 1 residue, 1 model selected > select #105/A:2001 10 atoms, 9 bonds, 1 residue, 1 model selected > select add #105 21063 atoms, 21226 bonds, 1400 residues, 1 model selected > select subtract #105 Nothing selected > hide #105 models > show #104 models > show #105 models > show #110 models > show #111 models > select #104/A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #104/A:1-123 1934 atoms, 1957 bonds, 123 residues, 1 model selected > select #105/A:2001 10 atoms, 9 bonds, 1 residue, 1 model selected > select #105/A:2001-2146 2178 atoms, 2196 bonds, 146 residues, 1 model selected > select #104/A:1999 18 atoms, 17 bonds, 1 residue, 1 model selected > select #104/A:1936-1999 988 atoms, 996 bonds, 64 residues, 1 model selected > hide #110 models > hide #111 models > hide #105 models > select add #104 30364 atoms, 30638 bonds, 1999 residues, 1 model selected > select subtract #104 Nothing selected > hide #104 models > show #108 models > show #107 models > hide #107 models > hide #108 models > show #104 models > select #104/A:1999 18 atoms, 17 bonds, 1 residue, 1 model selected > select #104/A:1999 18 atoms, 17 bonds, 1 residue, 1 model selected > color sel lime > select add #104 30364 atoms, 30638 bonds, 1999 residues, 1 model selected > select subtract #104 Nothing selected > show #105 models > select #105/A:2089 14 atoms, 13 bonds, 1 residue, 1 model selected > select #105/A:2080-2089 156 atoms, 155 bonds, 10 residues, 1 model selected > select #105/A:2075-2079 59 atoms, 58 bonds, 5 residues, 1 model selected > select #105/A:2020-2079 927 atoms, 933 bonds, 60 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #105,0.070652,0.61953,-0.78179,69.828,-0.84869,0.44916,0.27924,75.159,0.52415,0.64377,0.55752,92.604 > view matrix models > #105,0.070652,0.61953,-0.78179,76.425,-0.84869,0.44916,0.27924,84.784,0.52415,0.64377,0.55752,100.34 > select #105/A:2265-2319 827 atoms, 833 bonds, 55 residues, 1 model selected > select #105/A:2265-2367 1546 atoms, 1554 bonds, 103 residues, 1 model selected > select #105/A:2265 12 atoms, 11 bonds, 1 residue, 1 model selected > select #105/A:2265-2319 827 atoms, 833 bonds, 55 residues, 1 model selected > select #105/A:2001 10 atoms, 9 bonds, 1 residue, 1 model selected > select #105/A:2001 10 atoms, 9 bonds, 1 residue, 1 model selected > color sel red > ui mousemode right ""rotate selected models"" > view matrix models > #105,-0.26571,0.91879,-0.29193,74.464,0.36029,-0.18624,-0.91406,93.006,-0.8942,-0.34806,-0.28154,86.054 > view matrix models > #105,-0.13796,0.94724,-0.28933,75.613,0.57439,-0.16147,-0.8025,95.483,-0.80687,-0.2769,-0.52181,85.593 > view matrix models > #105,-0.17164,0.94046,-0.29339,75.293,0.52077,-0.16619,-0.83737,94.827,-0.83627,-0.29651,-0.46124,85.644 > view matrix models > #105,-0.18698,0.9372,-0.29444,75.151,0.49567,-0.16877,-0.85196,94.529,-0.84815,-0.30525,-0.43298,85.684 > view matrix models > #105,-0.24492,0.92393,-0.29389,74.639,0.39713,-0.18093,-0.89975,93.407,-0.88448,-0.33708,-0.3226,85.929 > view matrix models > #105,-0.18093,0.9385,-0.29409,75.207,0.50562,-0.16772,-0.8463,94.647,-0.84357,-0.30182,-0.44418,85.667 > view matrix models > #105,-0.22163,0.92945,-0.29498,74.84,0.43746,-0.17558,-0.88193,93.857,-0.8715,-0.3245,-0.36768,85.812 > ui mousemode right ""translate selected models"" > view matrix models > #105,-0.22163,0.92945,-0.29498,62.302,0.43746,-0.17558,-0.88193,86.244,-0.8715,-0.3245,-0.36768,47.764 > select add #105 21063 atoms, 21226 bonds, 1400 residues, 1 model selected > select subtract #105 Nothing selected > ui mousemode right select Drag select of 2 residues > ui tool show ""Build Structure"" > build join peptide sel length 1.33 omega 180 phi -120 move small > select add #104 51426 atoms, 51864 bonds, 3399 residues, 1 model selected > select subtract #104 Nothing selected > select add #104 51426 atoms, 51864 bonds, 3399 residues, 1 model selected > select subtract #104 Nothing selected > log metadata #104 The model has no metadata > log chains #104 Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104 --- Chain | Description A | No description available > sequence chain #104/A Alignment identifier is 104/A > select clear > delete atoms #104 > delete bonds #104 > undo > close session > open ""/Users/aho2840/Desktop/Satchell > Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"" opened ChimeraX session > hide #!9 models > hide #53 models > show #105 models > hide #105 models > show #105 models > log metadata #105 The model has no metadata > log chains #105 Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105 --- Chain | Description A | No description available > sequence chain #105/A Alignment identifier is 105/A > select #105/A:2000 14 atoms, 14 bonds, 1 residue, 1 model selected > select #105/A:1800-2000 3081 atoms, 3109 bonds, 201 residues, 1 model selected > show #104 models > log metadata #104 The model has no metadata > log chains #104 Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104 --- Chain | Description A | No description available > sequence chain #104/A Alignment identifier is 104/A > select #105/A:1899 17 atoms, 16 bonds, 1 residue, 1 model selected > select #105/A:1800-1899 1560 atoms, 1573 bonds, 100 residues, 1 model selected > delete atoms sel > delete bonds sel > rename #105 GMGC10.011_528_202.ranked_0.1900.3500.pdb > select clear > delete atoms #104-105 > delete bonds #104-105 > close session > open ""/Users/aho2840/Desktop/Satchell > Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"" opened ChimeraX session > hide #!9 models > hide #53 models > show #105 models > log metadata #105 The model has no metadata > log chains #105 Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105 --- Chain | Description A | No description available > sequence chain #105/A Alignment identifier is 105/A > log metadata #104 The model has no metadata > log chains #104 Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104 --- Chain | Description A | No description available > sequence chain #104/A Alignment identifier is 104/A > select #105/A:1899 17 atoms, 16 bonds, 1 residue, 1 model selected > select #105/A:1800-1899 1560 atoms, 1573 bonds, 100 residues, 1 model selected > delete atoms sel > delete bonds sel > select #105/A:2037 22 atoms, 21 bonds, 1 residue, 1 model selected > select #105/A:2037-2039 55 atoms, 55 bonds, 3 residues, 1 model selected > select add #105 22584 atoms, 22762 bonds, 1501 residues, 1 model selected > select subtract #105 Nothing selected > hide #105 models > show #104 models > select clear > ui mousemode right ""translate selected models"" > select #104/A:1999 18 atoms, 17 bonds, 1 residue, 1 model selected > select #104/A:1999 18 atoms, 17 bonds, 1 residue, 1 model selected > color sel lime > ui mousemode right ""rotate selected models"" > view matrix models > #104,0.29294,-0.94332,-0.15599,32.47,0.67976,0.090735,0.7278,21.614,-0.6724,-0.31924,0.66781,-17.296 > view matrix models > #104,0.70895,-0.70178,-0.06998,26.296,-0.17643,-0.27255,0.94583,23.607,-0.68283,-0.6582,-0.31704,9.5095 > select add #104 30364 atoms, 30638 bonds, 1999 residues, 1 model selected > select subtract #104 Nothing selected > show #105 models > ui mousemode right ""translate selected models"" > select #105/A:1983-2037 893 atoms, 903 bonds, 55 residues, 1 model selected > select #105/A:1972-1983 175 atoms, 176 bonds, 12 residues, 1 model selected > view matrix models > #105,0.070652,0.61953,-0.78179,-50.196,-0.84869,0.44916,0.27924,33.335,0.52415,0.64377,0.55752,46.74 > view matrix models > #105,0.070652,0.61953,-0.78179,-78.989,-0.84869,0.44916,0.27924,9.2126,0.52415,0.64377,0.55752,56.82 > select #105/A:1900 16 atoms, 15 bonds, 1 residue, 1 model selected > select #105/A:1900 16 atoms, 15 bonds, 1 residue, 1 model selected > color sel red > view matrix models > #105,0.070652,0.61953,-0.78179,-83.665,-0.84869,0.44916,0.27924,30.632,0.52415,0.64377,0.55752,25.148 > select #105/A:1900 16 atoms, 15 bonds, 1 residue, 1 model selected > select #105/A:1900-2445 8224 atoms, 8285 bonds, 546 residues, 1 model selected > show sel cartoons > select add #105 22584 atoms, 22762 bonds, 1501 residues, 1 model selected > select subtract #105 Nothing selected > select #105/A:2094-2095 36 atoms, 35 bonds, 2 residues, 1 model selected > select #105/A:2029-2095 1009 atoms, 1013 bonds, 67 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #105,0.92879,-0.037345,0.36873,-68.4,-0.065942,-0.99569,0.065259,41.702,0.3647,-0.084927,-0.92724,19.441 > ui mousemode right ""translate selected models"" > view matrix models > #105,0.92879,-0.037345,0.36873,-74.092,-0.065942,-0.99569,0.065259,27.971,0.3647,-0.084927,-0.92724,58.477 > view matrix models > #105,0.92879,-0.037345,0.36873,-72.83,-0.065942,-0.99569,0.065259,27.978,0.3647,-0.084927,-0.92724,58.484 > ui mousemode right select Drag select of 2 residues > ui tool show ""Build Structure"" > build join peptide sel length 1.33 omega 180 phi -120 move small ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z160000B1LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.5 (23H527) Kernel Version: Darwin 23.6.0 Time since boot: 28 days, 15 hours, 20 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.1.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 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: 2.12.1 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: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202403210048 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 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: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 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: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 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: 1.0 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: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 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: 1.37.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 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: 2.0.0 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: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Structure Editing duplicate all ChimeraX