id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15771 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6.7-x86_64-i386-64bit 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 Thread 0x00007000055c5000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff8505da7c0 (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/OpenGL/arrays/lists.py"", line 157 in asArray File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2828 in set_matrix File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 817 in set_projection_matrix File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 725 in _use_shader File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 801 in _opengl_shader File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 698 in shader File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 818 in _draw_geometry File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 791 in draw_self File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567 in _draw_multiple File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1560 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1289 in draw_transparent File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1559 in draw_transparent File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 265 in _draw_scene File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_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, 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, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/Combine 3 > components/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_001.pdb"" Chain information for combine_3comp_W19-coot-8_real_space_refined_093_001.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available H | No description available L | No description available > lighting simple > hide atoms > show cartoons > select /H 2030 atoms, 2085 bonds, 1 pseudobond, 251 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /L 846 atoms, 867 bonds, 1 pseudobond, 107 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > open ""/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/Combine 3 > components/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_001.pdb"" Chain information for combine_3comp_W19-coot-8_real_space_refined_093_001.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available H | No description available L | No description available > close #2 > open /Users/boskostojanovski/Desktop/ALL-coot-5.pdb Chain information for ALL-coot-5.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select #2/A 10700 atoms, 10992 bonds, 1 pseudobond, 1318 residues, 2 models selected > select #2/C 1863 atoms, 1905 bonds, 235 residues, 1 model selected > select #2/B 1089 atoms, 1114 bonds, 139 residues, 1 model selected > select #2/D 4496 atoms, 4615 bonds, 1 pseudobond, 565 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select add #2 13652 atoms, 14012 bonds, 1 pseudobond, 1692 residues, 2 models selected > select subtract #2 Nothing selected > select add #1 13272 atoms, 13621 bonds, 3 pseudobonds, 1650 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.82041,0.57151,0.017232,-69.406,0.46299,-0.64634,-0.60654,298.32,-0.33551,0.50559,-0.79487,258.38 > view matrix models > #1,0.57932,0.58435,0.56826,-120.8,0.81261,-0.46848,-0.34668,169.65,0.063638,0.66261,-0.74625,159.08 > view matrix models > #1,0.85104,-0.5248,0.017847,109.53,-0.41693,-0.69599,-0.58461,446.69,0.31922,0.49008,-0.81112,156.77 Drag select of 49 residues > select add #1 13272 atoms, 13621 bonds, 3 pseudobonds, 1650 residues, 2 models selected > view matrix models > #1,0.85104,-0.5248,0.017847,199.95,-0.41693,-0.69599,-0.58461,507.11,0.31922,0.49008,-0.81112,194.53 > view matrix models > #1,0.85104,-0.5248,0.017847,191.36,-0.41693,-0.69599,-0.58461,532.56,0.31922,0.49008,-0.81112,196.96 > view matrix models > #1,0.85186,-0.52343,0.019012,183.59,-0.41516,-0.6969,-0.58479,527.41,0.31934,0.49026,-0.81096,194.65 > view matrix models > #1,0.85186,-0.52343,0.019012,181.13,-0.41516,-0.6969,-0.58479,526.85,0.31934,0.49026,-0.81096,192.89 > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker combine_3comp_W19-coot-8_real_space_refined_093_001.pdb, chain B (#1) with ALL-coot-5.pdb, chain A (#2), sequence alignment score = 5977.5 RMSD between 570 pruned atom pairs is 1.364 angstroms; (across all 1313 pairs: 2.888) > select subtract #1 Nothing selected > close #2 > close #1 > open > /Users/boskostojanovski/Desktop/Phenix/RealSpaceRefine_70/_Users_boskostojanovski_Combine_3comp_W15-Phenix_061_coot-01-coot-5.pdb Chain information for _Users_boskostojanovski_Combine_3comp_W15-Phenix_061_coot-01-coot-5.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available H | No description available L | No description available > lighting simple > hide atoms > show cartoons > open > /Users/boskostojanovski/Desktop/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_002.pdb Chain information for combine_3comp_W19-coot-8_real_space_refined_093_002.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available H | No description available L | No description available > hide atoms > show cartoons > select #1/H#2/H 4060 atoms, 4170 bonds, 2 pseudobonds, 502 residues, 4 models selected > delete atoms (#!1-2 & sel) > delete bonds (#!1-2 & sel) > select #1/L#2/L 1692 atoms, 1734 bonds, 2 pseudobonds, 214 residues, 4 models selected > delete atoms (#!1-2 & sel) > delete bonds (#!1-2 & sel) > show atoms > style stick Changed 26552 atom styles > color byhetero > color #1 #00fdffff > color byhetero > hide #!1 models > open ""/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/starting map > and pdbs/comp_1350+1351_DEEP_W19.mrc"" Opened comp_1350+1351_DEEP_W19.mrc as #3, grid size 400,400,400, pixel 0.842, shown at level -0.000457, step 2, values float32 > volume #3 step 1 > volume #3 color #b2b2b299 > volume #3 level 0.1691 > volume #3 level 0.203 > hide #!3 models > show #!3 models > volume #3 level 0.1 > volume #3 level 0.2187 > volume #3 level 0.1 > hide #!2 atoms > hide #!3 models > show #!2 atoms > select #2/C 1863 atoms, 1904 bonds, 1 pseudobond, 235 residues, 2 models selected > color (#!2 & sel) cornflower blue > select clear > select #2/C 1863 atoms, 1904 bonds, 1 pseudobond, 235 residues, 2 models selected > color (#!2 & sel) dim gray > color (#!2 & sel) light sea green > color (#!2 & sel) byhetero > view matrix models > #2,0.97758,0.17103,0.12282,-44.76,-0.1681,0.98519,-0.033903,35.494,-0.1268,0.012496,0.99185,20.002 > view matrix models > #2,0.97586,0.17745,0.12731,-46.276,-0.1743,0.98405,-0.035587,36.971,-0.1316,0.012538,0.99122,20.882 > select clear > select #1/A#2/A 1364 atoms, 1396 bonds, 182 residues, 2 models selected > hide (#!2 & sel) target a > cartoon hide (#!2 & sel) > view matrix models > #1,0.80061,0.18606,-0.56957,93.121,-0.10933,0.97997,0.16644,-5.4978,0.58913,-0.070985,0.80492,-53.287,#2,0.82381,0.31802,-0.46926,51.057,-0.2994,0.94703,0.11619,39.267,0.48136,0.04478,0.87538,-66.366 > view matrix models > #1,0.99832,-0.057243,0.0090093,8.3722,0.057848,0.97537,-0.21286,28.79,0.0033973,0.21302,0.97704,-32.275,#2,0.98301,0.12093,0.13807,-39.754,-0.08554,0.96741,-0.23833,57.729,-0.16239,0.22248,0.96132,-4.1548 > view matrix models > #1,0.99822,-0.033727,0.049148,-1.9589,0.044083,0.97269,-0.22787,33.896,-0.040121,0.22963,0.97245,-27.177,#2,0.97354,0.14456,0.177,-48.373,-0.096531,0.96214,-0.25487,63.059,-0.20715,0.23104,0.95064,3.475 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99822,-0.033727,0.049148,-2.5065,0.044083,0.97269,-0.22787,34.907,-0.040121,0.22963,0.97245,-28.718,#2,0.97354,0.14456,0.177,-48.921,-0.096531,0.96214,-0.25487,64.07,-0.20715,0.23104,0.95064,1.9346 > view matrix models > #1,0.99822,-0.033727,0.049148,-4.6563,0.044083,0.97269,-0.22787,36.683,-0.040121,0.22963,0.97245,-32.962,#2,0.97354,0.14456,0.177,-51.071,-0.096531,0.96214,-0.25487,65.846,-0.20715,0.23104,0.95064,-2.3092 > view matrix models > #1,0.99822,-0.033727,0.049148,-7.0285,0.044083,0.97269,-0.22787,38.42,-0.040121,0.22963,0.97245,-35.776,#2,0.97354,0.14456,0.177,-53.443,-0.096531,0.96214,-0.25487,67.582,-0.20715,0.23104,0.95064,-5.1237 > view matrix models > #1,0.99822,-0.033727,0.049148,-3.3795,0.044083,0.97269,-0.22787,37.208,-0.040121,0.22963,0.97245,-33.256,#2,0.97354,0.14456,0.177,-49.794,-0.096531,0.96214,-0.25487,66.371,-0.20715,0.23104,0.95064,-2.603 > view matrix models > #1,0.99822,-0.033727,0.049148,-3.1897,0.044083,0.97269,-0.22787,37.509,-0.040121,0.22963,0.97245,-32.712,#2,0.97354,0.14456,0.177,-49.604,-0.096531,0.96214,-0.25487,66.672,-0.20715,0.23104,0.95064,-2.0598 > view matrix models > #1,0.99822,-0.033727,0.049148,-5.4855,0.044083,0.97269,-0.22787,37.973,-0.040121,0.22963,0.97245,-21.903,#2,0.97354,0.14456,0.177,-51.9,-0.096531,0.96214,-0.25487,67.136,-0.20715,0.23104,0.95064,8.7496 > view matrix models > #1,0.99822,-0.033727,0.049148,-7.1223,0.044083,0.97269,-0.22787,38.247,-0.040121,0.22963,0.97245,-13.924,#2,0.97354,0.14456,0.177,-53.537,-0.096531,0.96214,-0.25487,67.41,-0.20715,0.23104,0.95064,16.729 > view matrix models > #1,0.99822,-0.033727,0.049148,-3.4819,0.044083,0.97269,-0.22787,42.357,-0.040121,0.22963,0.97245,-8.5176,#2,0.97354,0.14456,0.177,-49.896,-0.096531,0.96214,-0.25487,71.52,-0.20715,0.23104,0.95064,22.135 > view matrix models > #1,0.99822,-0.033727,0.049148,0.74602,0.044083,0.97269,-0.22787,47.599,-0.040121,0.22963,0.97245,-4.9909,#2,0.97354,0.14456,0.177,-45.669,-0.096531,0.96214,-0.25487,76.762,-0.20715,0.23104,0.95064,25.662 > view matrix models > #1,0.99822,-0.033727,0.049148,3.608,0.044083,0.97269,-0.22787,50.919,-0.040121,0.22963,0.97245,-4.1406,#2,0.97354,0.14456,0.177,-42.807,-0.096531,0.96214,-0.25487,80.082,-0.20715,0.23104,0.95064,26.512 > view matrix models > #1,0.99822,-0.033727,0.049148,4.9944,0.044083,0.97269,-0.22787,52.422,-0.040121,0.22963,0.97245,-3.6535,#2,0.97354,0.14456,0.177,-41.42,-0.096531,0.96214,-0.25487,81.585,-0.20715,0.23104,0.95064,26.999 > view matrix models > #1,0.99822,-0.033727,0.049148,5.3424,0.044083,0.97269,-0.22787,53.718,-0.040121,0.22963,0.97245,-3.5568,#2,0.97354,0.14456,0.177,-41.072,-0.096531,0.96214,-0.25487,82.881,-0.20715,0.23104,0.95064,27.096 > view matrix models > #1,0.99822,-0.033727,0.049148,6.9491,0.044083,0.97269,-0.22787,53.339,-0.040121,0.22963,0.97245,-2.9063,#2,0.97354,0.14456,0.177,-39.465,-0.096531,0.96214,-0.25487,82.502,-0.20715,0.23104,0.95064,27.746 > view matrix models > #1,0.99822,-0.033727,0.049148,6.1419,0.044083,0.97269,-0.22787,54.528,-0.040121,0.22963,0.97245,-4.0811,#2,0.97354,0.14456,0.177,-40.273,-0.096531,0.96214,-0.25487,83.691,-0.20715,0.23104,0.95064,26.571 > view matrix models > #1,0.99822,-0.033727,0.049148,4.0916,0.044083,0.97269,-0.22787,56.557,-0.040121,0.22963,0.97245,-5.991,#2,0.97354,0.14456,0.177,-42.323,-0.096531,0.96214,-0.25487,85.719,-0.20715,0.23104,0.95064,24.661 > view matrix models > #1,0.99822,-0.033727,0.049148,5.9956,0.044083,0.97269,-0.22787,54.443,-0.040121,0.22963,0.97245,-8.1451,#2,0.97354,0.14456,0.177,-40.419,-0.096531,0.96214,-0.25487,83.606,-0.20715,0.23104,0.95064,22.507 > view matrix models > #1,0.99822,-0.033727,0.049148,6.9912,0.044083,0.97269,-0.22787,53.413,-0.040121,0.22963,0.97245,-9.7917,#2,0.97354,0.14456,0.177,-39.423,-0.096531,0.96214,-0.25487,82.576,-0.20715,0.23104,0.95064,20.861 > view matrix models > #1,0.99822,-0.033727,0.049148,11.179,0.044083,0.97269,-0.22787,54.604,-0.040121,0.22963,0.97245,-14.27,#2,0.97354,0.14456,0.177,-35.235,-0.096531,0.96214,-0.25487,83.767,-0.20715,0.23104,0.95064,16.383 > view matrix models > #1,0.99822,-0.033727,0.049148,12.637,0.044083,0.97269,-0.22787,52.593,-0.040121,0.22963,0.97245,-12.062,#2,0.97354,0.14456,0.177,-33.778,-0.096531,0.96214,-0.25487,81.756,-0.20715,0.23104,0.95064,18.59 > view matrix models > #1,0.99822,-0.033727,0.049148,9.9151,0.044083,0.97269,-0.22787,49.097,-0.040121,0.22963,0.97245,-14.274,#2,0.97354,0.14456,0.177,-36.499,-0.096531,0.96214,-0.25487,78.26,-0.20715,0.23104,0.95064,16.379 > view matrix models > #1,0.99822,-0.033727,0.049148,6.7218,0.044083,0.97269,-0.22787,45.214,-0.040121,0.22963,0.97245,-16.455,#2,0.97354,0.14456,0.177,-39.693,-0.096531,0.96214,-0.25487,74.377,-0.20715,0.23104,0.95064,14.198 > view matrix models > #1,0.99822,-0.033727,0.049148,2.925,0.044083,0.97269,-0.22787,40.931,-0.040121,0.22963,0.97245,-18.418,#2,0.97354,0.14456,0.177,-43.49,-0.096531,0.96214,-0.25487,70.094,-0.20715,0.23104,0.95064,12.234 > view matrix models > #1,0.99822,-0.033727,0.049148,1.8442,0.044083,0.97269,-0.22787,49.379,-0.040121,0.22963,0.97245,-19.511,#2,0.97354,0.14456,0.177,-44.57,-0.096531,0.96214,-0.25487,78.542,-0.20715,0.23104,0.95064,11.142 > view matrix models > #1,0.99822,-0.033727,0.049148,3.0466,0.044083,0.97269,-0.22787,51.821,-0.040121,0.22963,0.97245,-17.527,#2,0.97354,0.14456,0.177,-43.368,-0.096531,0.96214,-0.25487,80.983,-0.20715,0.23104,0.95064,13.126 > view matrix models > #1,0.99822,-0.033727,0.049148,2.9203,0.044083,0.97269,-0.22787,54.108,-0.040121,0.22963,0.97245,-16.716,#2,0.97354,0.14456,0.177,-43.494,-0.096531,0.96214,-0.25487,83.271,-0.20715,0.23104,0.95064,13.936 > view matrix models > #1,0.99822,-0.033727,0.049148,3.4591,0.044083,0.97269,-0.22787,54.231,-0.040121,0.22963,0.97245,-17.89,#2,0.97354,0.14456,0.177,-42.955,-0.096531,0.96214,-0.25487,83.394,-0.20715,0.23104,0.95064,12.762 > view matrix models > #1,0.99822,-0.033727,0.049148,3.6158,0.044083,0.97269,-0.22787,54.244,-0.040121,0.22963,0.97245,-18.432,#2,0.97354,0.14456,0.177,-42.799,-0.096531,0.96214,-0.25487,83.407,-0.20715,0.23104,0.95064,12.22 > view matrix models > #1,0.99822,-0.033727,0.049148,4.5996,0.044083,0.97269,-0.22787,55.332,-0.040121,0.22963,0.97245,-18.34,#2,0.97354,0.14456,0.177,-41.815,-0.096531,0.96214,-0.25487,84.495,-0.20715,0.23104,0.95064,12.312 > view matrix models > #1,0.99822,-0.033727,0.049148,3.6812,0.044083,0.97269,-0.22787,55.631,-0.040121,0.22963,0.97245,-15.685,#2,0.97354,0.14456,0.177,-42.733,-0.096531,0.96214,-0.25487,84.794,-0.20715,0.23104,0.95064,14.967 > view matrix models > #1,0.99822,-0.033727,0.049148,4.872,0.044083,0.97269,-0.22787,56.429,-0.040121,0.22963,0.97245,-17.644,#2,0.97354,0.14456,0.177,-41.543,-0.096531,0.96214,-0.25487,85.592,-0.20715,0.23104,0.95064,13.009 > view matrix models > #1,0.99822,-0.033727,0.049148,4.8129,0.044083,0.97269,-0.22787,55.758,-0.040121,0.22963,0.97245,-19.492,#2,0.97354,0.14456,0.177,-41.602,-0.096531,0.96214,-0.25487,84.921,-0.20715,0.23104,0.95064,11.161 > hide #!2 models > select add #2 13954 atoms, 14319 bonds, 3 pseudobonds, 1741 residues, 3 models selected > select add #1 26552 atoms, 27251 bonds, 5 pseudobonds, 3301 residues, 4 models selected > select subtract #1 13272 atoms, 13621 bonds, 3 pseudobonds, 1650 residues, 2 models selected > select subtract #2 Nothing selected > open 7tpp 7tpp title: Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution [more info...] Chain information for 7tpp #4 --- Chain | Description | UniProt A | Factor X light chain | FA10_HUMAN 1-139 B | Activated factor Xa heavy chain | FA10_HUMAN 195-448 C | Coagulation factor Va | FA5_HUMAN 1-709 D | Coagulation factor Va | FA5_HUMAN 1546-2196 E | Prothrombin | THRB_HUMAN 1-579 > show #!4 cartoons > hide #!4 atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #4/B Alignment identifier is 4/B > select #4/B:356 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/B:356 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > ui tool show ""Show Sequence Viewer"" > sequence chain #4/E Alignment identifier is 4/E > select #4/E:316 12 atoms, 12 bonds, 1 residue, 1 model selected > select #4/E:316-317 20 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 20 atom styles > view matrix models #4,1,0,0,-4.2459,0,1,0,3.48,0,0,1,7.2033 > view matrix models #4,1,0,0,-4.5692,0,1,0,5.8107,0,0,1,10.848 > view matrix models #4,1,0,0,-2.4935,0,1,0,-2.0883,0,0,1,14.015 > view matrix models #4,1,0,0,0.8336,0,1,0,-20.727,0,0,1,12.47 > view matrix models #4,1,0,0,1.3737,0,1,0,-26.846,0,0,1,12.043 > select #4/E:320 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/E:318-320 23 atoms, 22 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 23 atom styles > select #4/B:373 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:373 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > close #4 > show #!2 models > view orient > hide #!2 atoms > show #!2 atoms > hide #!2 atoms > show #!3 models > show #!1 models > hide #!1 models > close #3 > show #!1 models > close #2 > close #1 > open > /Users/boskostojanovski/Desktop/Phenix/RealSpaceRefine_93/combine_3comp_W19-coot-8_real_space_refined_093_004.pdb Chain information for combine_3comp_W19-coot-8_real_space_refined_093_004.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available H | No description available L | No description available > lighting simple > show cartoons > hide atoms > open ""/Users/boskostojanovski/Desktop/DES_PTse_COOT/0.DEEP_W19/starting map > and pdbs/comp_1350+1351_DEEP_W19.mrc"" Opened comp_1350+1351_DEEP_W19.mrc as #2, grid size 400,400,400, pixel 0.842, shown at level -0.000457, step 2, values float32 > volume #2 step 1 > volume #2 color #b2b2b299 > volume #2 level 0.1 > show atoms > style stick Changed 16148 atom styles > color #1 #00fdffff > color #1 #fffc79ff ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet 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 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine OpenGL vendor: ATI Technologies 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: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.5 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 16 GB System Firmware Version: 529.120.1.0.0 OS Loader Version: 577.140.2~22 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 13.6.7 (22G720) Kernel Version: Darwin 22.6.0 Time since boot: 14 days, 6 hours, 1 minute Graphics/Displays: Radeon Pro 575: Chipset Model: Radeon Pro 575 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c4 ROM Revision: 113-D000AA-931 VBIOS Version: 113-D0001A1P-025 EFI Driver Version: 01.00.931 Metal Support: Metal 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG UltraFine: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 201NTRLKF070 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort 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-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 Tom Goddard all ChimeraX