id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16227 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.7-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001fe2d4f40 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/matrix.py"", line 467 in length File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/matrix.py"", line 440 in normalize_vector File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/common_geom.py"", line 19 in test_phi File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/acceptor_geom.py"", line 80 in test_phi_psi File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/acceptor_geom.py"", line 48 in acc_syn_anti File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py"", line 614 in find_hbonds File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/cmd.py"", line 94 in cmd_hbonds File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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, 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""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Unable to find icon for toolbar provider 'Dump Bead Data' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Genome Distance' in bundle 'ChimeraX-GenomeTools' 1 messages similar to the above omitted UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/dwheeler/Downloads/relaxed_model_1_multimer_v3_pred_0-2.pdb > format pdb Chain information for relaxed_model_1_multimer_v3_pred_0-2.pdb #1 --- Chain | Description A | No description available B | No description available C D | No description available E F | No description available > close session > open > /Users/dwheeler/Downloads/fold_phpnuc_2024_10_31_14_11/fold_phpnuc_2024_10_31_14_11_model_4.cif Chain information for fold_phpnuc_2024_10_31_14_11_model_4.cif #1 --- Chain | Description A B | . C D | . E F | . G H | . I J | . > hide atoms > show cartoons > open > /Users/dwheeler/Downloads/fold_php_nuc_moc3_2024_10_31_14_32/fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif Chain information for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif #2 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . > hide atoms > show cartoons > name end /B:100-114 > color end red > ui tool show Matchmaker > matchmaker #2/I#2/J to #1/I#1/J pairing ss Reference chain (fold_phpnuc_2024_10_31_14_11_model_4.cif (#1) chain I) not compatible with BLOSUM-62 similarity matrix > matchmaker #2/A#2/B to #1/A#1/B 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 fold_phpnuc_2024_10_31_14_11_model_4.cif, chain A (#1) with fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif, chain A (#2), sequence alignment score = 176.2 Matchmaker fold_phpnuc_2024_10_31_14_11_model_4.cif, chain B (#1) with fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif, chain B (#2), sequence alignment score = 176.2 RMSD between 54 pruned atom pairs is 0.964 angstroms; (across all 202 pairs: 10.594) > hide #2 models > show #2 models > hide #1 models > hide #2 models > show #1 models > hide #1 models > show #2 models > name php3 #1/B |#2/B > hide ~ php3 arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~php3 arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #1 models > hide arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1 models > hide #2 models > show php3 arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show php3 cartoons > show #1 models > show #2 models > hide ~php3 cartoons > hide #1 models > show all > hide #2 atoms > show #2 cartoons > view #2 > hide #2 models > show #1 models > hide #1 atoms > show #1 cartoons > color #1 bychain > color #1 bypolymer > coulombic #1 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_A SES surface #1.1: minimum, -18.52, mean -1.45, maximum 13.65 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_B SES surface #1.2: minimum, -17.57, mean -1.45, maximum 10.66 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_C SES surface #1.3: minimum, -27.23, mean -0.78, maximum 15.27 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_D SES surface #1.4: minimum, -22.94, mean -0.79, maximum 15.72 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_E SES surface #1.5: minimum, -8.30, mean 4.17, maximum 16.00 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_F SES surface #1.6: minimum, -8.28, mean 4.19, maximum 15.78 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_G SES surface #1.7: minimum, -12.88, mean 2.54, maximum 13.94 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_H SES surface #1.8: minimum, -12.93, mean 2.56, maximum 13.73 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_I SES surface #1.9: minimum, -32.07, mean -14.98, maximum -4.06 Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_J SES surface #1.10: minimum, -34.01, mean -14.99, maximum -3.96 To also show corresponding color key, enter the above coulombic command and add key true > hide @ca & @@bfactor surface style dot > surface style mesh > hide /J | /I arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide /J | /I surfaces > show #2 models > hide #!1 models > coulombic #2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_A SES surface #2.1: minimum, -13.44, mean 2.92, maximum 14.80 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_B SES surface #2.2: minimum, -10.85, mean 2.94, maximum 16.29 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_C SES surface #2.3: minimum, -16.77, mean 3.02, maximum 17.32 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_D SES surface #2.4: minimum, -16.87, mean 3.01, maximum 17.14 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_E SES surface #2.5: minimum, -8.24, mean 4.21, maximum 16.09 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_F SES surface #2.6: minimum, -8.15, mean 4.21, maximum 16.48 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_G SES surface #2.7: minimum, -16.46, mean 2.76, maximum 13.76 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_H SES surface #2.8: minimum, -21.34, mean 2.73, maximum 13.49 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_I SES surface #2.9: minimum, -12.11, mean -0.01, maximum 16.56 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_J SES surface #2.10: minimum, -12.96, mean -0.06, maximum 15.27 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_K SES surface #2.11: minimum, -27.89, mean -15.25, maximum -4.13 Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_L SES surface #2.12: minimum, -29.44, mean -15.25, maximum -4.10 To also show corresponding color key, enter the above coulombic command and add key true > hide @ca & @@bfactor surface style #2 mesh > hide /J | /I surfaces > hide /K | /L surfaces > show/J | /I s Unknown command: show/J | /I s > show #2/J | #2/I surfaces > close session > open > /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif #1 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . > hide surfaces > hide cartoons > show cartoons > hide atoms > open > /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_3.cif > /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_2.cif > /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_1.cif > /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_0.cif Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_3.cif #2 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_2.cif #3 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_1.cif #4 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_0.cif #5 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . > hide #1 models > hide #3 models > hide #4 models > hide #5 models > show #2 cartoons > hide #2 atoms > show #3 models > hide #2 models > show #3 cartoons > hide #3 atoms > show #4 models > hide #3 models > show #4 cartoons > hide #4 atoms > hide #4 models > show #5 models > show #5 cartoons > hide #5 atoms > hide #5 models > show #1 models > hide arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide all arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1 models > show #1/C | #1/I > show #1/C | #1/I cartoons > show #1 models > name X #1/C | #1/I > hide #1/ arcs > hide #1/ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1/ c > hide #1/ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1/ arcs > hide #1/* arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1/A arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1/B arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #1 target m > show X cartoons > view X No displayed objects specified. > view X c Expected keyword ""clip"" or ""cofr"" > show #1/C | #1/I cartoons > show #1 models > hide ~( #1/C | #1/I) arcs Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~( #1/C | #1/I) cartoons > show #1/C | #1/I surfaces > show #!1 cartoons > hide #!1 cartoons > select #1/C | #1/I 7248 atoms, 7425 bonds, 923 residues, 1 model selected > show sel cartoons > hide sel atoms > hide sel surfaces > ~select Nothing selected > ui tool show Matchmaker > split #1/C #1/I Split fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif (#1) into 12 models Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif A #1.1 --- Chain | Description A | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif B #1.2 --- Chain | Description B | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif C #1.3 --- Chain | Description C | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif D #1.4 --- Chain | Description D | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif E #1.5 --- Chain | Description E | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif F #1.6 --- Chain | Description F | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif G #1.7 --- Chain | Description G | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif H #1.8 --- Chain | Description H | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif I #1.9 --- Chain | Description I | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif J #1.10 --- Chain | Description J | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif K #1.11 --- Chain | Description K | No description available Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif L #1.12 --- Chain | Description L | No description available > ui tool show Matchmaker > matchmaker #1.9/I to #1.3/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 fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif C, chain C (#1.3) with fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif I, chain I (#1.9), sequence alignment score = 254.4 RMSD between 10 pruned atom pairs is 1.377 angstroms; (across all 382 pairs: 35.313) No model chosen to save relative to > save /Users/dwheeler/HistoneFold/php3.pdb models #1.3 relModel #1 > save /Users/dwheeler/HistoneFold/moc3.pdb models #1.9 relModel #1 > close session > open /Users/dwheeler/HistoneFold/moc3.pdb > /Users/dwheeler/HistoneFold/php3.pdb Chain information for moc3.pdb #1 --- Chain | Description I | No description available Chain information for php3.pdb #2 --- Chain | Description C | No description available > ui mousemode right ""rotate selected models"" > select add #1 3979 atoms, 4078 bonds, 508 residues, 1 model selected > view matrix models > #1,0.13985,-0.92395,0.35604,43.851,0.29152,0.38206,0.87695,52.684,-0.94629,-0.018847,0.32278,-24.131 > view matrix models > #1,0.70382,0.1283,0.69869,24.144,0.58392,-0.66463,-0.46616,31.186,0.40456,0.73607,-0.5427,-83.841 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.70382,0.1283,0.69869,25.322,0.58392,-0.66463,-0.46616,-2.7728,0.40456,0.73607,-0.5427,-84.034 > view matrix models > #1,0.70382,0.1283,0.69869,39.245,0.58392,-0.66463,-0.46616,-3.662,0.40456,0.73607,-0.5427,-79.015 > view matrix models > #1,0.70382,0.1283,0.69869,66.172,0.58392,-0.66463,-0.46616,36.109,0.40456,0.73607,-0.5427,-95.642 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.95808,-0.1982,0.2069,60.134,-0.050642,-0.59362,-0.80315,21.983,0.282,-0.77996,0.5587,-5.9639 > view matrix models > #1,-0.87077,0.27489,-0.40766,21.407,0.35379,-0.22546,-0.90774,5.8507,-0.34144,-0.93467,0.099069,-18.059 > view matrix models > #1,0.58085,0.75728,0.29856,31.548,0.80387,-0.59135,-0.064025,49.236,0.12807,0.2772,-0.95224,-97.208 > view matrix models > #1,0.83357,0.45652,0.31103,40.686,0.54809,-0.75373,-0.3626,42.963,0.068899,0.47273,-0.87851,-100.14 > view matrix models > #1,0.69687,0.42718,0.5761,52.27,0.53452,-0.84492,-0.020061,59.226,0.47819,0.32192,-0.81713,-93.965 > view matrix models > #1,-0.027276,-0.22564,0.97383,89.23,-0.49022,-0.84599,-0.20975,53.868,0.87117,-0.48311,-0.087539,-41.58 > view matrix models > #1,-0.31034,-0.76726,0.56124,90.078,-0.94979,0.22544,-0.21699,21.889,0.039968,-0.6004,-0.7987,-64.279 > view matrix models > #1,-0.73319,-0.50487,-0.45556,42.988,-0.56802,0.82301,0.0020898,11.537,0.37388,0.2603,-0.8902,-94.751 > view matrix models > #1,-0.3413,0.33608,-0.87782,0.0045776,-0.45646,0.75712,0.46735,31.6,0.82168,0.5602,-0.105,-73.929 > view matrix models > #1,-0.33347,0.32636,-0.88447,0.023446,-0.46869,0.75663,0.4559,31.189,0.818,0.56658,-0.099354,-73.894 > view matrix models > #1,-0.70688,-0.59615,-0.38068,48.656,-0.64919,0.33311,0.68381,53.402,-0.28085,0.7305,-0.62248,-97.228 > view matrix models > #1,-0.96012,-0.091031,-0.26437,38.358,-0.27594,0.461,0.84341,55.027,0.045098,0.88272,-0.46774,-96.438 > view matrix models > #1,-0.70215,0.37485,-0.60537,10.256,-0.28625,0.62987,0.72203,45.138,0.65195,0.68026,-0.33496,-86.279 > view matrix models > #1,-0.29396,0.10539,-0.94999,4.0965,-0.82864,0.46727,0.30825,34.921,0.47639,0.87781,-0.050028,-80.744 > select subtract #1 Nothing selected > select add #2 3269 atoms, 3347 bonds, 415 residues, 1 model selected > view matrix models > #2,0.95759,-0.00091914,-0.28813,-8.1163,0.054012,0.98284,0.17637,5.1774,0.28302,-0.18446,0.94121,0.51819 > view matrix models > #2,0.90767,-0.04481,-0.41728,-11.727,0.11586,0.9824,0.14653,4.6604,0.40337,-0.18135,0.89689,-0.1263 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,0.90767,-0.04481,-0.41728,13.617,0.11586,0.9824,0.14653,21.486,0.40337,-0.18135,0.89689,-35.523 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.075416,-0.97513,-0.2084,19.117,-0.60952,0.12032,-0.78359,-4.0578,0.78917,0.18612,-0.58529,-75.861 > view matrix models > #2,-0.93282,-0.35841,0.037275,18.432,-0.062934,0.06019,-0.9962,-6.9915,0.3548,-0.93162,-0.078702,-59.48 > view matrix models > #2,-0.14692,0.58192,-0.79986,-4.5904,-0.067812,-0.81266,-0.57878,8.0263,-0.98682,-0.030794,0.15886,-63.175 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.14692,0.58192,-0.79986,11.702,-0.067812,-0.81266,-0.57878,26.584,-0.98682,-0.030794,0.15886,-47.126 > view matrix models > #2,-0.14692,0.58192,-0.79986,6.392,-0.067812,-0.81266,-0.57878,26.371,-0.98682,-0.030794,0.15886,-36.505 > view matrix models > #2,-0.14692,0.58192,-0.79986,4.9394,-0.067812,-0.81266,-0.57878,28.537,-0.98682,-0.030794,0.15886,-36.826 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.33348,0.75098,-0.56993,9.6544,-0.094421,-0.6281,-0.77239,22.333,-0.93802,-0.20376,0.28036,-32.543 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.33348,0.75098,-0.56993,15.52,-0.094421,-0.6281,-0.77239,14.302,-0.93802,-0.20376,0.28036,-27.177 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.65405,-0.21568,-0.72505,20.026,0.1543,-0.9003,0.407,49.021,-0.74054,-0.37808,-0.55557,-48.461 > view matrix models > #2,0.51036,-0.20644,0.83481,62.132,-0.85995,-0.11685,0.49683,43.343,-0.0050187,-0.97146,-0.23716,-33.706 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.51036,-0.20644,0.83481,51.226,-0.85995,-0.11685,0.49683,48.217,-0.0050187,-0.97146,-0.23716,-47.535 > view matrix models > #2,0.51036,-0.20644,0.83481,45.356,-0.85995,-0.11685,0.49683,57.171,-0.0050187,-0.97146,-0.23716,-43.33 > view matrix models > #2,0.51036,-0.20644,0.83481,45.741,-0.85995,-0.11685,0.49683,80,-0.0050187,-0.97146,-0.23716,-81.988 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.38546,-0.11094,0.91603,46.973,-0.90575,-0.23502,0.35267,76.302,0.17617,-0.96564,-0.19108,-79.865 > view matrix models > #2,0.33217,-0.081273,0.93971,47.242,-0.91209,-0.28151,0.29806,74.962,0.24032,-0.95611,-0.16764,-78.948 > view matrix models > #2,-0.75921,0.63559,-0.14011,9.3358,0.061788,-0.14392,-0.98766,43.823,-0.64791,-0.75849,0.069996,-77.552 > view matrix models > #2,0.1864,0.26047,-0.94732,-6.6967,0.57678,-0.80958,-0.10911,73.187,-0.79535,-0.52606,-0.30114,-89.416 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.1864,0.26047,-0.94732,17.912,0.57678,-0.80958,-0.10911,26.511,-0.79535,-0.52606,-0.30114,-60.044 > view matrix models > #2,0.1864,0.26047,-0.94732,23.31,0.57678,-0.80958,-0.10911,27.888,-0.79535,-0.52606,-0.30114,-58.782 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99302,0.02984,0.11413,57.334,-0.065443,-0.66558,0.74345,47.589,0.098145,-0.74573,-0.65898,-63.363 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.99302,0.02984,0.11413,33.505,-0.065443,-0.66558,0.74345,60.109,0.098145,-0.74573,-0.65898,-82.662 > view matrix models > #2,0.99302,0.02984,0.11413,33.222,-0.065443,-0.66558,0.74345,66.901,0.098145,-0.74573,-0.65898,-89.124 > view matrix models > #2,0.99302,0.02984,0.11413,40.052,-0.065443,-0.66558,0.74345,69.944,0.098145,-0.74573,-0.65898,-86.123 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.98601,0.060639,-0.15528,22.896,0.023287,-0.87226,-0.48849,37.386,-0.16507,-0.48528,0.85864,-46.788 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.98601,0.060639,-0.15528,40.461,0.023287,-0.87226,-0.48849,17.575,-0.16507,-0.48528,0.85864,-21.844 > view matrix models > #2,-0.98601,0.060639,-0.15528,45.767,0.023287,-0.87226,-0.48849,23.89,-0.16507,-0.48528,0.85864,-32.016 > view matrix models > #2,-0.98601,0.060639,-0.15528,52.851,0.023287,-0.87226,-0.48849,20.401,-0.16507,-0.48528,0.85864,-26.655 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.64524,0.73287,0.21579,61.947,-0.75875,-0.64772,-0.06898,27.198,0.089219,-0.20824,0.974,-23.384 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.64524,0.73287,0.21579,80.044,-0.75875,-0.64772,-0.06898,48.609,0.089219,-0.20824,0.974,-22.318 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.67821,-0.0941,-0.72882,63.928,0.39114,-0.79339,0.46642,69.506,-0.62213,-0.6014,-0.50128,-64.689 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.67821,-0.0941,-0.72882,60.458,0.39114,-0.79339,0.46642,51.812,-0.62213,-0.6014,-0.50128,-49.519 > view matrix models > #2,0.67821,-0.0941,-0.72882,32.765,0.39114,-0.79339,0.46642,33.052,-0.62213,-0.6014,-0.50128,-37.372 > view matrix models > #2,0.67821,-0.0941,-0.72882,41.104,0.39114,-0.79339,0.46642,41.945,-0.62213,-0.6014,-0.50128,-63.429 > view matrix models > #2,0.67821,-0.0941,-0.72882,14.66,0.39114,-0.79339,0.46642,38.742,-0.62213,-0.6014,-0.50128,-62.891 > view matrix models > #2,0.67821,-0.0941,-0.72882,16.857,0.39114,-0.79339,0.46642,47.285,-0.62213,-0.6014,-0.50128,-68.603 > view matrix models > #2,0.67821,-0.0941,-0.72882,12.866,0.39114,-0.79339,0.46642,49.243,-0.62213,-0.6014,-0.50128,-69.754 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.89835,-0.014926,-0.43904,21.572,0.24386,-0.81435,0.52666,50.267,-0.36539,-0.58018,-0.72793,-74.817 > view matrix models > #2,0.84878,0.12961,-0.51261,18.718,0.3155,-0.90214,0.2943,44.593,-0.4243,-0.41152,-0.80661,-77.956 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.84878,0.12961,-0.51261,24.953,0.3155,-0.90214,0.2943,43.157,-0.4243,-0.41152,-0.80661,-74.725 > close session > open > /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif > format mmcif Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif #1 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . > show cartoons > hide atoms > show atoms > style stick Changed 26058 atom styles > hide cartoons > select zone /J:54 10 Selected 258 atoms > hide ~sel > view sel > style sel stick Changed 258 atom styles > color sel byhetero > select zone /J:54 15 Selected 608 atoms > show sel > hbonds sel reveal true ===== Log before crash end ===== Log: Startup Messages --- warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle 'ChimeraX-GenomeTools' Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX- GenomeTools' Unable to find icon for toolbar provider 'Genome Distance' in bundle 'ChimeraX-GenomeTools' 1 messages similar to the above omitted Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 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 Pro OpenGL vendor: Apple 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: Mac14,9 Model Number: Z17G002HSLL/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.1.1 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7 (23H124) Kernel Version: Darwin 23.6.0 Time since boot: 14 days, 3 hours, 1 minute Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 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: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 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: 1.7.1 ChimeraX-CoreFormats: 1.2 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: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-GenomeTools: 0.9 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: 1.2.2 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 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: 1.5.14 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: 1.13.1 ChimeraX-PDB: 2.7.3 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 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: 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 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-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: 1.33.3 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: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 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.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX