id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18068 Crash in glBufferSubData chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x00000001f9e64840 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2744 in update_buffer_data File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1912 in update_buffers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1924 in activate_bindings File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 814 in _draw_geometry File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 787 in draw_self File ""/Applications/ChimeraX-1.8.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-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1554 in draw_opaque File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1579 in draw_depth File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1647 in use_multishadow_map File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 633 in _compute_shadowmaps File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 227 in _draw_scene File ""/Applications/ChimeraX-1.8.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-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 169 in update_graphics_now File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py"", line 2245 in moved_marker_cb File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/histogram.py"", line 416 in move_marker_cb File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py"", line 2171 in _drag File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py"", line 2167 in mouseMoveEvent File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 57) 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""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250527-MpPSI-core-1est-2nd-coot-8.cif Summary of feedback from opening /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- building/250527-MpPSI-core-1est-2nd-coot-8.cif --- warnings | Unknown polymer entity '1' on line 516 Unknown polymer entity '2' on line 1887 Unknown polymer entity '3' on line 3028 Unknown polymer entity '4' on line 4332 Unknown polymer entity '5' on line 5607 22 messages similar to the above omitted Unable to fetch template for 'CLA': will connect using distance criteria Unable to fetch template for 'A86': will connect using distance criteria Unable to fetch template for 'DD6': will connect using distance criteria Unable to fetch template for 'KC1': will connect using distance criteria Unable to fetch template for 'LHG': will connect using distance criteria Unknown polymer entity '33' on line 39720 Unknown polymer entity '34' on line 39728 Unknown polymer entity '35' on line 39735 Unknown polymer entity '36' on line 39740 Unknown polymer entity '37' on line 39751 5 messages similar to the above omitted Unable to fetch template for 'BCR': will connect using distance criteria Unable to fetch template for 'PQN': will connect using distance criteria Unable to fetch template for 'SF4': will connect using distance criteria Unable to fetch template for 'LMG': will connect using distance criteria Unable to fetch template for 'DGD': will connect using distance criteria Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 250527-MpPSI-core-1est-2nd-coot-8.cif #1 --- Chain | Description 1 | No description available 10 | No description available 11 | No description available 13 | No description available 15 | No description available 16 | No description available 17 | No description available 18 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available I | No description available J | No description available L | No description available M | No description available R | No description available a | No description available 16912 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide atoms > show cartoons > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/250211-Core-2p47-cryosparc_P3_J1253_005_volume_map_sharp.mrc Opened 250211-Core-2p47-cryosparc_P3_J1253_005_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.22, shown at level 0.71, step 2, values float32 > volume #2 step 1 > volume #2 level 0.8 > ui tool show ""Hide Dust"" > surface dust #2 size 7.3 > lighting soft > volume #2 level 1 > volume #2 level 1.2 > volume #2 level 1 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP1-LR-0p5-Recenter- > cryosparc_P3_J2526_003_volume_map_sharp.mrc Opened FCP1-LR-0p5-Recenter-cryosparc_P3_J2526_003_volume_map_sharp.mrc as #3, grid size 512,512,512, pixel 1.22, shown at level 0.285, step 2, values float32 > volume #3 level 0.5 > volume #3 step 1 > surface dust #3 size 7.3 > volume #3 level 0.8 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP2-LR-maskbased-AF1228943-FCP17-1-Recenter- > cryosparc_P3_J2827_004_volume_map_sharp.mrc Opened FCP2-LR-maskbased-AF1228943-FCP17-1-Recenter- cryosparc_P3_J2827_004_volume_map_sharp.mrc as #4, grid size 512,512,512, pixel 1.22, shown at level 0.131, step 2, values float32 > volume #4 level 0.5 > volume #4 step 1 > surface dust #4 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP3-LR-133k-cryosparc_P3_J2531_003_volume_map_sharp.mrc Opened FCP3-LR-133k-cryosparc_P3_J2531_003_volume_map_sharp.mrc as #5, grid size 512,512,512, pixel 1.22, shown at level 0.264, step 2, values float32 > volume #5 level 0.5 > surface dust #5 size 7.3 > volume #5 step 1 > volume #5 level 0.8 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP4-ligands-LR-1-Recenter- > cryosparc_P3_J2848_004_volume_map_sharp.mrc Opened FCP4-ligands-LR-1-Recenter-cryosparc_P3_J2848_004_volume_map_sharp.mrc as #6, grid size 512,512,512, pixel 1.22, shown at level 0.148, step 2, values float32 > volume #6 level 0.8 > volume #6 step 1 > surface dust #6 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP4-LR-104k-cryosparc_P3_J2538_003_volume_map_sharp.mrc Opened FCP4-LR-104k-cryosparc_P3_J2538_003_volume_map_sharp.mrc as #7, grid size 512,512,512, pixel 1.22, shown at level 0.153, step 2, values float32 > volume #7 level 0.8 > volume #7 step 1 > surface dust #7 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP5-ligands-LR-recenter- > cryosparc_P3_J2851_004_volume_map_sharp.mrc Opened FCP5-ligands-LR-recenter-cryosparc_P3_J2851_004_volume_map_sharp.mrc as #8, grid size 512,512,512, pixel 1.22, shown at level 0.232, step 2, values float32 > volume #8 level 0.8 > volume #8 step 1 > surface dust #8 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP5-LR-121k-cryosparc_P3_J2532_003_volume_map_sharp.mrc Opened FCP5-LR-121k-cryosparc_P3_J2532_003_volume_map_sharp.mrc as #9, grid size 512,512,512, pixel 1.22, shown at level 0.226, step 2, values float32 > surface dust #9 size 7.3 > volume #9 level 0.8 > volume #9 step 1 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP6-LR-133k-cryosparc_P3_J2533_003_volume_map_sharp.mrc Opened FCP6-LR-133k-cryosparc_P3_J2533_003_volume_map_sharp.mrc as #10, grid size 512,512,512, pixel 1.22, shown at level 0.264, step 2, values float32 > volume #10 level 0.8 > volume #10 step 1 > surface dust #10 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP7-LR-133k-cryosparc_P3_J2534_003_volume_map_sharp.mrc Opened FCP7-LR-133k-cryosparc_P3_J2534_003_volume_map_sharp.mrc as #11, grid size 512,512,512, pixel 1.22, shown at level 0.232, step 2, values float32 > volume #11 level 0.8 > volume #11 step 1 > surface dust #11 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP8-LR-133k-cryosparc_P3_J2535_003_volume_map_sharp.mrc Opened FCP8-LR-133k-cryosparc_P3_J2535_003_volume_map_sharp.mrc as #12, grid size 512,512,512, pixel 1.22, shown at level 0.285, step 2, values float32 > volume #12 level 0.8 > volume #12 step 1 > surface dust #12 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP9-LR-93k-cryosparc_P3_J2539_005_volume_map_sharp.mrc Opened FCP9-LR-93k-cryosparc_P3_J2539_005_volume_map_sharp.mrc as #13, grid size 512,512,512, pixel 1.22, shown at level 0.137, step 2, values float32 > volume #13 level 8 > volume #13 level 0.8 > volume #13 step 1 > surface dust #13 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP10-LR-133k-cryosparc_P3_J2536_005_volume_map_sharp.mrc Opened FCP10-LR-133k-cryosparc_P3_J2536_005_volume_map_sharp.mrc as #14, grid size 512,512,512, pixel 1.22, shown at level 0.259, step 2, values float32 > volume #14 level 0.8 > volume #14 step 1 > surface dust #13 size 7.3 > surface dust #14 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP11-LR-119k-cryosparc_P3_J2537_004_volume_map_sharp.mrc Opened FCP11-LR-119k-cryosparc_P3_J2537_004_volume_map_sharp.mrc as #15, grid size 512,512,512, pixel 1.22, shown at level 0.288, step 2, values float32 > volume #15 level 0.8 > volume #15 step 1 > surface dust #15 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP13-LR-104k-cryosparc_P3_J2541_003_volume_map_sharp.mrc Opened FCP13-LR-104k-cryosparc_P3_J2541_003_volume_map_sharp.mrc as #16, grid size 512,512,512, pixel 1.22, shown at level 0.139, step 2, values float32 > volume #16 level 0.8 > volume #16 step 1 > surface dust #16 size 7.3 > volume #16 level 0.5 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP15-LR-1-Recenter- > cryosparc_P3_J2842_005_volume_map_sharp.mrc Opened FCP15-LR-1-Recenter-cryosparc_P3_J2842_005_volume_map_sharp.mrc as #17, grid size 512,512,512, pixel 1.22, shown at level 0.124, step 2, values float32 > volume #17 level 0.5 > volume #17 step 1 > surface dust #16 size 7.3 > surface dust #17 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP16-LR-1-recenter- > cryosparc_P3_J2843_009_volume_map_sharp.mrc Opened FCP16-LR-1-recenter-cryosparc_P3_J2843_009_volume_map_sharp.mrc as #18, grid size 512,512,512, pixel 1.22, shown at level 0.109, step 2, values float32 > volume #18 level 0.5 > volume #18 step 1 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite- > map/FCP17-LR-92-cryosparc_P3_J2544_003_volume_map_sharp.mrc Opened FCP17-LR-92-cryosparc_P3_J2544_003_volume_map_sharp.mrc as #19, grid size 512,512,512, pixel 1.22, shown at level 0.137, step 2, values float32 > volume #19 level 0.5 > volume #19 step 1 > surface dust #19 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCP19-0p5-28kpart- > cryosparc_P3_J2945_003_volume_map_sharp.mrc Opened FCP19-0p5-28kpart-cryosparc_P3_J2945_003_volume_map_sharp.mrc as #20, grid size 512,512,512, pixel 1.22, shown at level 0.145, step 2, values float32 > volume #20 level 0.5 > volume #20 step 1 > surface dust #20 size 7.3 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/250623-Composite-map/FCPA- > LR-1-maskJ2877-inputs-J2214-cryosparc_P3_J2877_004_volume_map_sharp.mrc Opened FCPA- LR-1-maskJ2877-inputs-J2214-cryosparc_P3_J2877_004_volume_map_sharp.mrc as #21, grid size 512,512,512, pixel 1.22, shown at level 0.132, step 2, values float32 > volume #21 level 0.5 > volume #21 step 1 > surface dust #21 size 7.3 > volume #13 level 0.5 > set bgColor white > save /Users/pablo/trasnfer/Composite-maps/250624-composite-maps.cxs > includeMaps true > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > show #!18 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!1 models > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/FCP15/250612/250602-FCP15-based-F-AF9630469-coot-2.pdb Summary of feedback from opening /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- building/FCP15/250612/250602-FCP15-based-F-AF9630469-coot-2.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ALA 1 50 GLU 1 66 1 17 Start residue of secondary structure not found: HELIX 2 2 TYR 1 70 LYS 1 72 1 3 Start residue of secondary structure not found: HELIX 3 3 LYS 1 80 ALA 1 104 1 25 Start residue of secondary structure not found: HELIX 4 4 PRO 1 117 TRP 1 120 1 4 Start residue of secondary structure not found: HELIX 5 5 ASN 1 134 VAL 1 151 1 18 261 messages similar to the above omitted Chain information for 250602-FCP15-based-F-AF9630469-coot-2.pdb #22 --- Chain | Description 15 | No description available > show #!17 models > color #17 #ffb2b27b models > ui tool show ""Fit in Map"" > surface dust #21 size 7.29 > surface dust #21 size 7.28 > surface dust #21 size 7.27 > surface dust #21 size 7.26 > surface dust #21 size 7.25 > surface dust #21 size 7.24 > surface dust #21 size 7.23 > surface dust #21 size 7.22 > fitmap #22 inMap #17 Fit molecule 250602-FCP15-based-F-AF9630469-coot-2.pdb (#22) to map FCP15-LR-1-Recenter-cryosparc_P3_J2842_005_volume_map_sharp.mrc (#17) using 1758 atoms average map value = 0.6035, steps = 60 shifted from previous position = 0.428 rotated from previous position = 0.215 degrees atoms outside contour = 751, contour level = 0.5 Position of 250602-FCP15-based-F-AF9630469-coot-2.pdb (#22) relative to FCP15-LR-1-Recenter-cryosparc_P3_J2842_005_volume_map_sharp.mrc (#17) coordinates: Matrix rotation and translation 0.99999582 -0.00126563 -0.00259811 1.70691212 0.00127184 0.99999633 0.00239103 -1.59112855 0.00259508 -0.00239433 0.99999377 -0.01894299 Axis -0.63772112 -0.69207086 0.33815633 Axis point 9.69370590 0.00000000 658.49614550 Rotation angle (degrees) 0.21496972 Shift along axis 0.00623411 > fitmap #22 inMap #17 Fit molecule 250602-FCP15-based-F-AF9630469-coot-2.pdb (#22) to map FCP15-LR-1-Recenter-cryosparc_P3_J2842_005_volume_map_sharp.mrc (#17) using 1758 atoms average map value = 0.6035, steps = 40 shifted from previous position = 0.0112 rotated from previous position = 0.0236 degrees atoms outside contour = 751, contour level = 0.5 Position of 250602-FCP15-based-F-AF9630469-coot-2.pdb (#22) relative to FCP15-LR-1-Recenter-cryosparc_P3_J2842_005_volume_map_sharp.mrc (#17) coordinates: Matrix rotation and translation 0.99999497 -0.00123376 -0.00292307 1.83172354 0.00124148 0.99999574 0.00264352 -1.67930488 0.00291980 -0.00264713 0.99999223 -0.06838869 Axis -0.64037716 -0.70721722 0.29960124 Axis point 24.48540888 0.00000000 625.31943527 Rotation angle (degrees) 0.23668317 Shift along axis -0.00584991 > save /Users/pablo/pdbs/250624-FCP15-based-AF9630469.pdb models #22 > hide #!17 models > show #!18 models > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/FCP16/250612/250610-Mp-FCPI-17_in-position-for-Mp-FCP16.pdb Chain information for 250610-Mp-FCPI-17_in-position-for-Mp-FCP16.pdb #23 --- Chain | Description A | No description available > fitmap #23 inMap #18 Fit molecule 250610-Mp-FCPI-17_in-position-for-Mp-FCP16.pdb (#23) to map FCP16-LR-1-recenter-cryosparc_P3_J2843_009_volume_map_sharp.mrc (#18) using 2000 atoms average map value = 0.491, steps = 44 shifted from previous position = 0.959 rotated from previous position = 1.24 degrees atoms outside contour = 1055, contour level = 0.5 Position of 250610-Mp-FCPI-17_in-position-for-Mp-FCP16.pdb (#23) relative to FCP16-LR-1-recenter-cryosparc_P3_J2843_009_volume_map_sharp.mrc (#18) coordinates: Matrix rotation and translation 0.99998111 0.00027450 -0.00614042 1.67503206 -0.00040217 0.99978356 -0.02080061 8.63634574 0.00613338 0.02080269 0.99976479 -7.79438977 Axis 0.95901420 -0.28292839 -0.01559803 Axis point 0.00000000 379.75823126 401.51293143 Rotation angle (degrees) 1.24288056 Shift along axis -0.71551076 > save /Users/pablo/pdbs/250624-FCP16-based-FCP17.pdb models #23 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/FCP19-ex18/250612/250610-Mp-FCPI-17_in-position-for-Mp- > FCP19-coot-2.pdb Chain information for 250610-Mp-FCPI-17_in-position-for-Mp-FCP19-coot-2.pdb #24 --- Chain | Description A | No description available > hide #!18 models > show #!20 models > fitmap #24 inMap #20 Fit molecule 250610-Mp-FCPI-17_in-position-for-Mp-FCP19-coot-2.pdb (#24) to map FCP19-0p5-28kpart-cryosparc_P3_J2945_003_volume_map_sharp.mrc (#20) using 2000 atoms average map value = 0.6033, steps = 52 shifted from previous position = 1.2 rotated from previous position = 0.802 degrees atoms outside contour = 890, contour level = 0.5 Position of 250610-Mp-FCPI-17_in-position-for-Mp-FCP19-coot-2.pdb (#24) relative to FCP19-0p5-28kpart-cryosparc_P3_J2945_003_volume_map_sharp.mrc (#20) coordinates: Matrix rotation and translation 0.99991113 0.01045080 0.00827719 -5.71115849 -0.01041538 0.99993647 -0.00431090 4.67103162 -0.00832172 0.00422431 0.99995645 0.94387786 Axis 0.30487338 0.59290496 -0.74532941 Axis point 426.57163559 559.58305389 0.00000000 Rotation angle (degrees) 0.80205001 Shift along axis 0.32479767 > save /Users/pablo/pdbs/250624-FCP19-based-FCP17.pdb models #24 > open /Users/pablo/Library/CloudStorage/Dropbox/Postdoc/250527-Model- > building/FCP2/250611-AF-9397072-FCP2-ligands-from-diatom.pdb 250611-AF-9397072-FCP2-ligands-from-diatom.pdb title: Organization and energy transfer In A huge diatom ψ-FCPI supercomplex [more info...] Chain information for 250611-AF-9397072-FCP2-ligands-from-diatom.pdb #25 --- Chain | Description A | FCPI-7 Non-standard residues in 250611-AF-9397072-FCP2-ligands-from-diatom.pdb #25 --- A86 — (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-β,β-caroten-3'- yl acetate (fucoxanthin) CLA — chlorophyll A KC1 — chlorophyll C1 LMT — dodecyl-β-D-maltoside > show #!4 models > fitmap #25 inMap #4 Fit molecule 250611-AF-9397072-FCP2-ligands-from-diatom.pdb (#25) to map FCP2-LR-maskbased-AF1228943-FCP17-1-Recenter- cryosparc_P3_J2827_004_volume_map_sharp.mrc (#4) using 2029 atoms average map value = 0.3823, steps = 68 shifted from previous position = 0.67 rotated from previous position = 1.95 degrees atoms outside contour = 1254, contour level = 0.5 Position of 250611-AF-9397072-FCP2-ligands-from-diatom.pdb (#25) relative to FCP2-LR-maskbased-AF1228943-FCP17-1-Recenter- cryosparc_P3_J2827_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.99942297 -0.02302076 0.02497534 -1.33729253 0.02304416 0.99973424 -0.00064965 -7.17948989 -0.02495375 0.00122482 0.99968786 7.10820467 Axis 0.02758244 0.73469594 0.67783559 Axis point 297.50974485 0.00000000 59.87321539 Rotation angle (degrees) 1.94725224 Shift along axis -0.49343378 > save /Users/pablo/pdbs/250624-FCP12-based-9397072.pdb models #25 > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > show #!13 models > show #!14 models > show #!15 models > show #!16 models > show #!17 models > volume #13 level -3.027 > lighting soft > set bgColor black > volume #14 level 1e-05 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac21,1 Model Number: Z12R000LULL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 1 day, 4 hours, 45 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL S2425HS: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 100.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Graphics nonchimerax all ChimeraX