id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14450 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000204993240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 1382 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 1382 in get_tangents File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 1189 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 156 in _make_ribbon_graphics File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py"", line 600 in compute_ribbons File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 667 in _create_ribbon_graphics File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 357 in update_graphics_if_needed File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1891 in _update_graphics_if_needed File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 294 in check_for_drawing_change File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 76 in draw_new_frame File ""/Applications/ChimeraX-1.7.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.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.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.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.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.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write, lxml.builder (total: 56) 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210.777 132.849 165.787 Atom #1/A:588@CD 210.645 131.762 164.738 Atom #1/A:588@OE1 209.786 130.873 164.907 Atom #1/A:588@OE2 211.398 131.797 163.741 Atom #1/A:589@N 211.980 134.911 168.399 Atom #1/A:589@CA 213.267 135.089 169.059 Atom #1/A:589@C 213.385 136.388 169.839 Atom #1/A:589@O 214.228 136.463 170.739 Atom #1/A:589@CB 214.409 135.020 168.035 Atom #1/A:589@CG 214.266 133.880 167.046 Atom #1/A:589@CD 215.249 134.008 165.901 Atom #1/A:589@CE 216.642 133.578 166.315 Atom #1/A:589@NZ 217.507 133.341 165.130 Atom #1/A:590@N 212.586 137.406 169.529 Atom #1/A:590@CA 212.458 138.678 170.230 Atom #1/A:590@C 213.646 139.611 169.963 Atom #1/A:590@O 213.553 140.798 170.273 Atom #1/A:590@CB 212.283 138.494 171.753 Atom #1/A:590@CG 212.160 139.765 172.584 Atom #1/A:590@CD 212.041 139.480 174.074 Atom #1/A:590@OE1 210.905 139.322 174.564 Atom #1/A:590@OE2 213.085 139.410 174.753 Atom #1/A:591@N 214.721 139.142 169.332 Atom #1/A:591@CA 215.885 139.977 169.066 Atom #1/A:591@C 216.756 139.298 168.019 Atom #1/A:591@O 216.958 138.084 168.068 Atom #1/A:591@CB 216.708 140.235 170.336 Atom #1/A:591@CG2 217.954 141.038 170.008 Atom #1/A:591@OG1 215.923 140.962 171.288 Atom #1/A:592@N 217.270 140.091 167.082 Atom #1/A:592@CA 218.189 139.622 166.052 Atom #1/A:592@C 219.352 140.601 165.980 Atom #1/A:592@O 219.140 141.818 165.962 Atom #1/A:592@CB 217.502 139.498 164.678 Atom #1/A:592@CG1 216.135 138.830 164.816 Atom #1/A:592@CG2 218.370 138.705 163.723 Atom #1/A:592@CD1 215.212 139.090 163.646 Atom #1/A:593@N 220.576 140.077 165.931 Atom #1/A:593@CA 221.744 140.949 165.967 Atom #1/A:593@C 222.821 140.525 164.973 Atom #1/A:593@O 222.570 139.698 164.091 Atom #1/A:593@CB 222.306 141.021 167.388 Atom #1/A:593@CG 222.830 139.718 167.936 Atom #1/A:593@CD 223.258 139.844 169.382 Atom #1/A:593@OE1 223.107 140.946 169.949 Atom #1/A:593@OE2 223.742 138.845 169.954 Atom #1/A:594@N 224.028 141.065 165.143 Atom #1/A:594@CA 224.986 141.307 164.074 Atom #1/A:594@C 225.190 140.298 162.960 Atom #1/A:594@O 224.837 140.584 161.812 Atom #1/A:595@N 225.748 139.124 163.259 Atom #1/A:595@CA 226.068 138.199 162.175 Atom #1/A:595@C 224.848 137.404 161.731 Atom #1/A:595@O 224.684 137.132 160.537 Atom #1/A:595@CB 227.205 137.265 162.588 Atom #1/A:595@CG 228.550 137.966 162.611 Atom #1/A:595@OD1 228.730 138.929 161.834 Atom #1/A:595@OD2 229.425 137.555 163.401 Atom #1/A:596@N 223.977 137.033 162.669 Atom #1/A:596@CA 222.734 136.372 162.292 Atom #1/A:596@C 221.825 137.301 161.495 Atom #1/A:596@O 221.026 136.831 160.677 Atom #1/A:596@CB 222.017 135.861 163.539 Atom #1/A:596@CG 220.660 135.254 163.266 Atom #1/A:596@CD 220.387 134.040 164.126 Atom #1/A:596@OE1 219.499 133.243 163.759 Atom #1/A:596@OE2 221.057 133.880 165.168 Atom #1/A:597@N 221.932 138.613 161.715 Atom #1/A:597@CA 221.096 139.564 160.991 Atom #1/A:597@C 221.629 139.850 159.592 Atom #1/A:597@O 220.842 140.120 158.680 Atom #1/A:597@CB 220.974 140.869 161.782 Atom #1/A:597@CG 220.131 141.971 161.139 Atom #1/A:597@CD1 218.734 141.465 160.822 Atom #1/A:597@CD2 220.070 143.198 162.030 Atom #1/A:598@N 222.951 139.801 159.403 Atom #1/A:598@CA 223.518 140.019 158.076 Atom #1/A:598@C 223.081 138.932 157.103 Atom #1/A:598@O 222.745 139.218 155.948 Atom #1/A:598@CB 225.042 140.077 158.159 Atom #1/A:598@CG 225.609 141.483 158.206 Atom #1/A:598@CD 227.121 141.458 158.323 Atom #1/A:598@NE 227.556 141.274 159.703 Atom #1/A:598@CZ 227.875 142.269 160.523 Atom #1/A:598@NH1 227.808 143.524 160.099 Atom #1/A:598@NH2 228.261 142.014 161.765 Atom #1/A:599@N 223.081 137.677 157.554 Atom #1/A:599@CA 222.692 136.575 156.681 Atom #1/A:599@C 221.227 136.677 156.276 Atom #1/A:599@O 220.879 136.441 155.113 Atom #1/A:599@CB 222.970 135.243 157.374 Atom #1/A:599@CG 222.601 134.022 156.552 Atom #1/A:599@CD 222.880 132.742 157.319 Atom #1/A:599@NE 222.249 132.743 158.635 Atom #1/A:599@CZ 220.944 132.599 158.838 Atom #1/A:599@NH1 220.123 132.444 157.808 Atom #1/A:599@NH2 220.456 132.612 160.071 Atom #1/A:600@N 220.352 137.026 157.221 Atom #1/A:600@CA 218.926 137.115 156.920 Atom #1/A:600@C 218.653 138.240 155.930 Atom #1/A:600@O 217.864 138.080 154.991 Atom #1/A:600@CB 218.117 137.292 158.218 Atom #1/A:600@CG1 218.121 135.997 159.029 Atom #1/A:600@CG2 216.694 137.727 157.907 Atom #1/A:600@CD1 217.568 136.153 160.426 Atom #1/A:601@N 219.299 139.392 156.117 Atom #1/A:601@CA 219.095 140.518 155.215 Atom #1/A:601@C 219.702 140.289 153.837 Atom #1/A:601@O 219.390 141.045 152.911 Atom #1/A:601@CB 219.673 141.797 155.826 Atom #1/A:601@CG 218.843 142.469 156.922 Atom #1/A:601@CD1 219.516 143.742 157.404 Atom #1/A:601@CD2 217.436 142.760 156.433 Atom #1/A:602@N 220.556 139.279 153.678 Atom #1/A:602@CA 221.105 138.943 152.371 Atom #1/A:602@C 220.240 137.931 151.631 Atom #1/A:602@O 220.109 138.010 150.406 Atom #1/A:602@CB 222.530 138.403 152.516 Atom #1/A:602@OG 223.399 139.393 153.034 Atom #1/A:603@N 219.651 136.975 152.353 Atom #1/A:603@CA 218.702 136.059 151.728 Atom #1/A:603@C 217.511 136.816 151.154 Atom #1/A:603@O 217.035 136.498 150.058 Atom #1/A:603@CB 218.240 135.012 152.738 Atom #1/A:603@CG 219.370 134.363 153.516 Atom #1/A:603@CD 218.924 133.844 154.870 Atom #1/A:603@OE1 217.730 133.998 155.203 Atom #1/A:603@OE2 219.768 133.284 155.602 Atom #1/A:604@N 217.017 137.810 151.879 Atom #1/A:604@CA 216.028 138.736 151.354 Atom #1/A:604@C 216.731 139.887 150.642 Atom #1/A:604@O 217.938 140.092 150.784 Atom #1/A:604@CB 215.137 139.269 152.477 Atom #1/A:604@CG 213.870 138.462 152.714 Atom #1/A:604@CD 214.131 137.147 153.420 Atom #1/A:604@OE1 215.016 137.107 154.300 Atom #1/A:604@OE2 213.450 136.152 153.096 Atom #1/A:605@N 215.959 140.637 149.863 Atom #1/A:605@CA 216.491 141.790 149.139 Atom #1/A:605@C 217.571 141.384 148.141 Atom #1/A:605@O 217.751 140.202 147.848 Atom #1/A:605@CB 217.052 142.827 150.117 Atom #1/A:605@CG 216.019 143.418 151.030 Atom #1/A:605@CD1 215.036 144.254 150.535 Atom #1/A:605@CD2 216.028 143.131 152.383 Atom #1/A:605@CE1 214.087 144.795 151.372 Atom #1/A:605@CE2 215.082 143.669 153.223 Atom #1/A:605@CZ 214.111 144.503 152.718 Atom #1/A:800@MG 215.753 154.838 193.412 Atom #1/A:800@ZN 209.382 154.659 164.824 Atom #1/A:801@PA 216.413 150.494 192.485 Atom #1/A:801@PB 215.484 152.570 190.821 Atom #1/A:801@PG 213.280 154.344 191.040 Atom #1/A:801@C5' 214.629 148.660 193.123 Atom #1/A:801@O5' 215.921 148.976 192.619 Atom #1/A:801@C4' 214.494 147.161 193.368 Atom #1/A:801@O4' 214.448 146.457 192.129 Atom #1/A:801@C3' 215.630 146.577 194.195 Atom #1/A:801@O3' 215.139 146.174 195.476 Atom #1/A:801@C2' 216.147 145.394 193.403 Atom #1/A:801@O2' 215.973 144.192 194.151 Atom #1/A:801@C1' 215.337 145.341 192.115 Atom #1/A:801@N1 219.167 143.201 189.203 Atom #1/A:801@O1A 217.868 150.442 192.111 Atom #1/A:801@O1B 215.863 152.672 189.373 Atom #1/A:801@O1G 213.314 154.901 189.643 Atom #1/A:801@C2 218.612 142.760 190.345 Atom #1/A:801@O2A 216.001 151.261 193.715 Atom #1/A:801@O2B 216.231 153.382 191.845 Atom #1/A:801@O2G 211.893 154.080 191.559 Atom #1/A:801@N3 217.630 143.410 190.993 Atom #1/A:801@O3A 215.561 151.018 191.224 Atom #1/A:801@O3B 213.906 152.864 190.927 Atom #1/A:801@O3G 214.172 155.063 192.020 Atom #1/A:801@C4 217.128 144.572 190.518 Atom #1/A:801@C5 217.687 145.113 189.279 Atom #1/A:801@C6 218.761 144.348 188.624 Atom #1/A:801@N6 219.300 144.811 187.481 Atom #1/A:801@N7 217.040 146.250 189.023 Atom #1/A:801@C8 216.142 146.436 190.010 Atom #1/A:801@N9 216.198 145.440 190.910 Atom #1/A:801@HN61 220.033 144.301 187.025 Atom #1/A:801@HN62 218.964 145.671 187.087 Atom #1/A:801@HO2' 216.594 144.190 194.888 Atom #1/A:801@HO3' 215.879 146.088 196.092 Atom #1/A:801@H2 218.974 141.838 190.768 Atom #1/A:801@H8 215.478 147.284 190.060 Atom #1/A:801@H1' 214.770 144.405 192.092 Atom #1/A:801@H2' 217.209 145.545 193.182 Atom #1/A:801@H3' 216.441 147.301 194.322 Atom #1/A:801@H4' 213.559 146.989 193.910 Atom #1/A:801@H5'1 214.457 149.203 194.050 Atom #1/A:801@H5'2 213.876 148.978 192.406 > getcrd #3 screen No atoms specified > getcrd #3 scene No atoms specified > ui tool show ""Volume Viewer"" > show #!3 models > close #2 > view orient > sym #1 c1*h,9.1,157.5,5 coordinateSystem #3 addMmcifAssembly true Made 5 copies for FtsH_fresh_group1_segi.cif symmetry c1*h,9.1,157.5,5 > hide #!3 models > show #!3 models > view > hide #!2 models > show #!1 models > view orient > move [223.5,223.5,0] models #1 Missing or invalid ""axis"" argument: Expected 3 floats or ""x"", or ""y"", or ""z"" or two atoms > move x 223.5 1 y 223.5 1 models #1 Expected a keyword > move x 223.5 1, y 223.5 1 models #1 Expected an integer >= 1 or a keyword > move x 223.5 1 models #1 > view > move x 223.5 1 models #1 > view > move x 223.5 1 models #1 > view > move x -223.5 1 models #1 > move y 223.5 1 models #1 > move y -223.5 1 models #1 > view orient > select add #1 3176 atoms, 3218 bonds, 406 residues, 1 model selected > close #3 > close #1 > close #2 > open /Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif Summary of feedback from opening /Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif --- warnings | Unknown polymer entity '1' near line 37 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for FtsH_fresh_group1_segi.cif #1 --- Chain | Description A | No description available > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA > W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc"" format mrc Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32 > volume #2 step 1 > volume #2 level 1.5 > view orient > view #2 clip false > move y 20 1 coordinateSystem #2 models #1 > hide #!2 models > move y -20 1 coordinateSystem #2 models #1 > show #!2 models > hide #!2 models > move y -20 1 models #1 > show #!2 models > hide #!2 models > open /Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif Summary of feedback from opening /Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif --- warnings | Unknown polymer entity '1' near line 37 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for FtsH_fresh_group1_segi.cif #3 --- Chain | Description A | No description available > move y -20 1 models #1 > show #!2 models > hide #!2 models > move y 20 1 models #1 > move y 20 1 coordinateSystem #2 models #3 > show #!2 models > hide #!2 models > move y -20 1 coordinateSystem #2 models #3 > move y -20 1 models #1 > sym #1 h,9.1,157.5,5 coordinateSystem #2 Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5 > sym #3 h,9.1,157.5,5 Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5 > view > hide #!4 models > show #!4 models > view position #2 Missing required ""same_as_models"" argument > view matrix models #2 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view matrix models #1 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view matrix models Missing ""models"" keyword's argument > view matrix models #2 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view matrix view matrix camera 1,0,0,3.2827,0,1,0,-31.654,0,0,1,1457 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.2,-0.92388,-0.38268,0,0,0.38268,-0.92388,0,0,0,0,1,9.1,#4.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.3,0.70711,0.70711,0,0,-0.70711,0.70711,0,0,0,0,1,18.2,#4.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.4,-0.38268,-0.92388,0,0,0.92388,-0.38268,0,0,0,0,1,27.3,#4.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.5,-4.4409e-16,1,0,0,-1,-4.4409e-16,0,0,0,0,1,36.4,#4.5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,-0.92388,-0.38268,0,0,0.38268,-0.92388,0,0,0,0,1,9.1,#5.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.3,0.70711,0.70711,0,0,-0.70711,0.70711,0,0,0,0,1,18.2,#5.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.4,-0.38268,-0.92388,0,0,0.92388,-0.38268,0,0,0,0,1,27.3,#5.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.5,-4.4409e-16,1,0,0,-1,-4.4409e-16,0,0,0,0,1,36.4,#5.5.1,1,0,0,0,0,1,0,0,0,0,1,0 > close #4 > close #5 > view matrix view matrix camera 1,0,0,3.2827,0,1,0,-31.654,0,0,1,1457 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0 > hide #2.1 models > show #!2 models > show #!3 models > sym #3 h,9.1,157.5,5 Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5 > combine #4 Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.2 to 'B' Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.3 to 'C' Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.4 to 'D' Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.5 to 'E' > save ""/Users/yiyingli/Desktop/try pdb.pdb"" > sym #3 h,9.1,157.5,5 addMmcifAssembly true Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M2 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: Mac Model Identifier: Mac14,2 Model Number: FLY13LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 3 days, 8 hours, 53 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: Yes Connection Type: Internal DELL U2414H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 50.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 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: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 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 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 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: 1.5.13 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: 1.0.3 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: 1.12.3 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: 1.33.2 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: 0.2.0 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: 4.47.0 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: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 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: 10.0.1 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 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: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect accepted normal Core Tom Goddard all ChimeraX