id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17370 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000033f367000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033e35b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000338313000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000337307000 (most 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recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003332d7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003322cb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003312bf000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ee4cc240 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio (total: 62) 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UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > save > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs opened ChimeraX session > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J745_006_volume_map.mrc Opened cryosparc_P130_J745_006_volume_map.mrc as #1, grid size 480,480,480, pixel 0.647, shown at level 0.0077, step 2, values float32 > set bgColor white > volume #1 step 1 > volume #1 level 0.0122 > volume #1 level 0.01027 > close > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J727_008_volume_map.mrc Opened cryosparc_P130_J727_008_volume_map.mrc as #1, grid size 480,480,480, pixel 0.647, shown at level 0.019, step 2, values float32 > volume #1 step 1 > volume #1 level 0.02695 > volume #1 level 0.0329 > volume #1 level 0.04017 > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera3.cxs restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Opened MBD-CRBN_fitToJ547.pdb map 15 thresholded as #21, grid size 480,480,480, pixel 0.647, shown at level 0.005, step 2, values float32 Opened cryosparc_P130_J616_006_volume_map.mrc as #2, grid size 480,480,480, pixel 0.647, shown at level 0.0118, step 1, values float32 Opened cryosparc_P130_J618_007_volume_map.mrc as #8, grid size 480,480,480, pixel 0.647, shown at level 0.0133, step 1, values float32 Opened cryosparc_P130_J618_007_volume_mask_refine.mrc as #9, grid size 480,480,480, pixel 0.647, shown at level 1, step 2, values float32 Opened cryosparc_P130_J617_003_volume_map.mrc as #7.1, grid size 480,480,480, pixel 0.647, shown at level 0.0126, step 1, values float32 Opened cryosparc_P130_J617_003_volume_mask_refine.mrc as #7.2, grid size 480,480,480, pixel 0.647, shown at level 0.99, step 1, values float32 Opened MBD-CRBN_fitToJ547.pdb map 20 as #5, grid size 480,480,480, pixel 0.647, shown at level 0.001, step 1, values float32 Opened FocusMask_J617_1pt8_0pt001.mrc as #10, grid size 480,480,480, pixel 0.647, shown at level 0.001, step 1, values float32 Opened FocusMask_J617_1pt8_0pt001-Binary.mrc as #11, grid size 480,480,480, pixel 0.647, shown at level 0.001, step 1, values float32 Opened SubtractionMask_to_J617Binary.mrc as #12, grid size 480,480,480, pixel 0.647, shown at level 0.9, step 1, values float32 Opened volume difference as #14, grid size 480,480,480, pixel 0.647, shown at level 0.99, step 1, values float32 Opened volume difference as #15, grid size 480,480,480, pixel 0.647, shown at level 0.99, step 1, values float32 Could not restore coloring on surface because surface does not exist. restore_snapshot for ""VolumeColor"" returned None opened ChimeraX session > show #!2 models > hide #!2 models > close #2 > hide #!3 models > show #!3 models > hide #!7 models > hide #!7.1 models > hide #!11 models > show #!11 models > hide #!11 models > hide #!12 models > select subtract #3 Nothing selected > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J727_008_volume_map.mrc Opened cryosparc_P130_J727_008_volume_map.mrc as #1, grid size 480,480,480, pixel 0.647, shown at level 0.019, step 2, values float32 > volume #1 step 1 > transparency #1.1 50 > volume #1 level 0.03535 > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J728_006_volume_map.mrc Opened cryosparc_P130_J728_006_volume_map.mrc as #2, grid size 480,480,480, pixel 0.647, shown at level 0.0205, step 2, values float32 > transparency #1.1#2.1 0 > transparency #1.1#2.1 50 > volume #2 step 1 > volume #2 level 0.05348 > volume #1 level 0.02855 > volume #1 level 0.05169 > open > /Users/zmotiwal@amgen.com/Downloads/cryosparc_P130_J762_013_volume_map.mrc Opened cryosparc_P130_J762_013_volume_map.mrc as #6, grid size 480,480,480, pixel 0.647, shown at level 0.0147, step 2, values float32 > transparency #1.1#2.1#6.1 0 > transparency #1.1#2.1#6.1 50 > volume #6 step 1 > volume #6 level 0.02334 > volume #6 level 0.03321 > volume #6 level 0.04555 > open > ""/Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J440_mask > (1).mrc"" Opened cryosparc_P130_J440_mask (1).mrc as #16, grid size 512,512,512, pixel 0.647, shown at level 1, step 2, values float32 > hide #!16 models > show #!16 models > volume #16 step 1 > volume #16 level 1 > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > fitmap #3 inMap #1 Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map cryosparc_P130_J727_008_volume_map.mrc (#1) using 3904 atoms average map value = 0.06366, steps = 108 shifted from previous position = 1.88 rotated from previous position = 10.4 degrees atoms outside contour = 1621, contour level = 0.051689 Position of MBD-CRBN_fitToJ547.pdb (#3) relative to cryosparc_P130_J727_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.97971915 0.19754391 -0.03356770 -22.45445972 -0.19850374 0.97969574 -0.02815171 38.00667615 0.02732493 0.03424408 0.99903988 -7.61051151 Axis 0.15386219 -0.15015554 -0.97661648 Axis point 176.81201202 130.47372722 0.00000000 Rotation angle (degrees) 11.69870689 Shift along axis -1.72925450 > show #!16 models > hide #!16 models > hide #!3 models > show #!3 models > show #!21 models > hide #!21 models > show #!21 models > close #16 > hide #!21 models > show #!21 models > volume #21 level 0.0623 > volume #21 level 0.4246 > volume #21 level 0.05915 > volume #1 level 0.03059 > transparency #1.1#21.1 0 > transparency #1.1#21.1 50 > hide #!21 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > volume #1 level 0.04829 > volume #1 level 0.05509 > show #!2 models > ui tool show ""Side View"" > view > select ::name=""MSH"" 80 atoms, 90 bonds, 2 residues, 2 models selected > view sel > select add #3 3944 atoms, 4044 bonds, 6 pseudobonds, 480 residues, 4 models selected > select subtract #3 40 atoms, 45 bonds, 1 residue, 1 model selected > select add #4 36811 atoms, 37154 bonds, 19 pseudobonds, 2307 residues, 3 models selected > select subtract #4 Nothing selected > hide #!2 models > volume #1 level 0.08981 > volume #2 level 0.08839 > volume #1 level 0.06462 > volume #2 level 0.06995 > view > show #!21 models > open > ""/Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J444_mask > (1).mrc"" Opened cryosparc_P130_J444_mask (1).mrc as #16, grid size 512,512,512, pixel 0.647, shown at level 5e-05, step 2, values float32 > hide #!21 models > hide #!16 models > show #!16 models > hide #!16 models > show #!21 models > volume #1 level 0.03195 > volume #2 level 0.04624 > volume #2 level 0.04558 > volume #2 level 0.04294 > volume #2 level 0.04228 > volume #2 level 0.03372 > volume #2 level 0.03306 > volume #2 level 0.0324 > volume #1 level 0.02242 > volume #2 level 0.01791 > volume #2 level 0.02977 > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J727_008_volume_mask_refine.mrc Opened cryosparc_P130_J727_008_volume_mask_refine.mrc as #17, grid size 480,480,480, pixel 0.647, shown at level 1, step 2, values float32 > volume #17 step 1 > volume #17 level 1 > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > volume #17 level 1 > hide #!21 models > show #!21 models > volume subtract #17 #21 onGrid #17 Opened volume difference as #18, grid size 480,480,480, pixel 0.647, shown at step 1, values float32 > volume #18 level 1 > volume #17 level 1 > show #!21 models > volume #21 level 0.08872 > volume #21 level 0.1756 > volume #21 level 0.2957 > hide #!17 models > volume #21 step 1 > hide #!18 models > show #!17 models > volume #21 level 0.464 > volume #21 level 0.6728 > volume #21 level 0.8688 > volume #21 level 0.04621 > volume #21 level 0.03697 > hide #!17 models > hide #!21 models > hide #!2 models > select add #3 3904 atoms, 3999 bonds, 6 pseudobonds, 479 residues, 3 models selected > Molmap sel 20 onGrid #1 Unknown command: Molmap sel 20 onGrid #1 > molmap sel 20 onGrid #1 Opened MBD-CRBN_fitToJ547.pdb map 20 as #19, grid size 480,480,480, pixel 0.647, shown at level 0.0305, step 1, values float32 > volume #9 step 1 > select subtract #3 Nothing selected > volume #19 level 0.0123 > volume #19 level 0.001 > volume #19 level 0.005 > volume #19 level 0.008 > molmap sel 18 onGrid #1 No atoms specified > select add #3 3904 atoms, 3999 bonds, 6 pseudobonds, 479 residues, 3 models selected > molmap sel 18 onGrid #1 Opened MBD-CRBN_fitToJ547.pdb map 18 as #19, grid size 480,480,480, pixel 0.647, shown at level 0.0345, step 1, values float32 > volume #19 level 0.005848 > volume #19 level 0.005 No map chosen to save > save > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/FocusMask_J727_1pt8_0pt005.mrc > models #19 > show #!17 models > hide #!17 models > show #!17 models > close #21 > volume subtract #17 #19 onGrid #19 Opened volume difference as #20, grid size 480,480,480, pixel 0.647, shown at step 1, values float32 > show #!17 models > hide #!17 models > show #!19 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/SubtractionMask_to_J727.mrc > models #20 > save > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs > volume #20 level 1 > volume #20 level 0.999 > volume #20 level 0.9 > volume #20 level 0.9999 > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > hide #!20 models > select subtract #3 Nothing selected > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J780_volume_map.mrc Opened cryosparc_P130_J780_volume_map.mrc as #21, grid size 480,480,480, pixel 0.647, shown at level 0.00884, step 2, values float32 > surface dust #1 size 6.47 > surface dust #21 size 6.47 > hide #!1 models > volume #21 step 1 > volume #21 level 0.01688 > hide #!20 models > volume #21 level 0.02369 > volume #21 level 0.02864 > transparency #21.1 50 > volume #21 level 0.04905 > volume #21 level 0.05524 > select ::name=""MSH"" 80 atoms, 90 bonds, 2 residues, 2 models selected > view sel > select add #3 3944 atoms, 4044 bonds, 6 pseudobonds, 480 residues, 4 models selected > select subtract #3 40 atoms, 45 bonds, 1 residue, 1 model selected > select add #4 36811 atoms, 37154 bonds, 19 pseudobonds, 2307 residues, 3 models selected > select subtract #4 Nothing selected > volume #21 level 0.07132 > volume #21 level 0.09236 > volume #21 level 0.07318 > volume #21 level 0.06266 > volume #21 level 0.07504 > view > hide #!21 models > show #!21 models > show #!1 models > hide #!21 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > close #8 > close #9 > close #7.1 > close #7.2 > close #5 > close #10 > close #11 > close #12 > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!19 models > hide #!19 models > close #14 > close #15 > close #6 > close #16 > volume #17 level 0.9667 > volume #17 level 0.9 > volume #17 level 0.999 > volume #17 level 0.9 > close #18 > volume #1 level 0.04352 > volume #1 level 0.005 > volume #1 level 0.001 > volume #1 level 0.0001 > volume #1 level 0.01439 > volume #1 level 0.0212 > hide #!19 models > volume #1 level 0.02324 > volume #1 level 0.04026 > show #!19 models > hide #!19 models > show #!19 models > volume #1 level 0.02256 > volume #19 level 0.0001 > volume #19 level 0.001 > volume #19 level 0.005 > volume #19 level 0.008 > volume #19 level 0.009 > volume #19 level 0.01 > volume #19 level 0.001 > volume #19 level 0.005 > volume #19 level 0.001 > volume #19 level 0.0001 > volume #19 level 0.00015 > volume #19 level 0.00018 > volume #19 level 0.0001 > hide #!19 models > hide #!17 models > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J781_005_volume_map.mrc Opened cryosparc_P130_J781_005_volume_map.mrc as #5, grid size 480,480,480, pixel 0.647, shown at level 0.0039, step 2, values float32 > volume #5 step 1 > volume #5 level 0.01444 > volume #5 color #0433ff > transparency #5.1 50 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > volume #5 color #00fdff > volume #5 color #73fdff > transparency #5.1 50 > volume #5 level 0.04682 > volume #5 level 0.07092 > volume #5 level 0.05058 > volume #5 level 0.05209 > fitmap #3 inMap #5 Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map cryosparc_P130_J781_005_volume_map.mrc (#5) using 3904 atoms average map value = 0.07471, steps = 48 shifted from previous position = 0.229 rotated from previous position = 0.403 degrees atoms outside contour = 1270, contour level = 0.052091 Position of MBD-CRBN_fitToJ547.pdb (#3) relative to cryosparc_P130_J781_005_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.97856834 0.20280037 -0.03572136 -22.71274225 -0.20394417 0.97846130 -0.03194156 39.65488282 0.02847420 0.03854216 0.99885119 -8.28539272 Axis 0.16871494 -0.15366317 -0.97361332 Axis point 179.37286301 129.40513553 0.00000000 Rotation angle (degrees) 12.05696130 Shift along axis -1.85870508 > fitmap #3 inMap #5 Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map cryosparc_P130_J781_005_volume_map.mrc (#5) using 3904 atoms average map value = 0.07471, steps = 40 shifted from previous position = 0.0126 rotated from previous position = 0.0141 degrees atoms outside contour = 1269, contour level = 0.052091 Position of MBD-CRBN_fitToJ547.pdb (#3) relative to cryosparc_P130_J781_005_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.97856552 0.20278494 -0.03588565 -22.69365915 -0.20392989 0.97847017 -0.03176052 39.62183801 0.02867248 0.03839790 0.99885108 -8.30324920 Axis 0.16794748 -0.15454132 -0.97360702 Axis point 179.23595677 129.32276315 0.00000000 Rotation angle (degrees) 12.05614671 Shift along axis -1.85045239 > volume #5 level 0.06188 > fitmap #3 inMap #5 Fit molecule MBD-CRBN_fitToJ547.pdb (#3) to map cryosparc_P130_J781_005_volume_map.mrc (#5) using 3904 atoms average map value = 0.07471, steps = 44 shifted from previous position = 0.00785 rotated from previous position = 0.00726 degrees atoms outside contour = 1628, contour level = 0.06188 Position of MBD-CRBN_fitToJ547.pdb (#3) relative to cryosparc_P130_J781_005_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.97857725 0.20272151 -0.03592429 -22.67795136 -0.20387094 0.97847906 -0.03186474 39.62981845 0.02869150 0.03850603 0.99884637 -8.31720436 Axis 0.16848584 -0.15470695 -0.97348769 Axis point 179.33230739 129.27667864 0.00000000 Rotation angle (degrees) 12.05396407 Shift along axis -1.85522583 > open > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/CS_jobs/cryosparc_P130_J782_map_locres.mrc Opened cryosparc_P130_J782_map_locres.mrc as #6, grid size 480,480,480, pixel 0.647, shown at level 0.00227, step 2, values float32 > hide #!5 models > show #!5 models > hide #!6 models > volume #6 step 1 > show #!6 models > hide #!6 models > ui tool show ""Color Zone"" > ui tool show ""Surface Color"" > key red-white-blue :0.0 :0.5 :1.0 showTool true > ui mousemode right ""color key"" > color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > color sample #5.1 map #6 palette 2.588,#0000ff:17.44,#00aaff:32.3,#00ffa9 Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > color sample #5.1 map #6 palette > 2.588,#0000ff:3,#00aaff:3.5,#00ffa9:4,#00ff00:4.5,#aaff00:5,#ffaa00:5.5,#ff0000 Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > color sample #5.1 map #6 palette > 2.588,#0000ff:3.2,#00aaff:3.6,#00ffa9:4.2,#00ff00:4.8,#aaff00:5.2,#ffaa00:6,#ff0000 Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > color sample #5.1 map #6 palette > 2.588,#0000ff:3.2,#0091ff:3.6,#00ffda:4.2,#00ff48:4.8,#48ff00:5.2,#daff00:6,#ff9100:6.5,#ff0000 Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > color sample #5.1 map #6 palette > 2.588,#0000ff:3.2,#0091ff:3.6,#00ffda:4.2,#00ff48:4.8,#48ff00:5.2,#daff00:6,#ff9100:6.5,#ff0000 Map values for surface ""surface"": minimum 2.588, mean 3.414, maximum 32.3 > save > /Users/zmotiwal@amgen.com/Desktop/EM_MSH_CRBN_8750/Processing_3769924/924_chimera4-S2merged.cxs > key blue:2.59 #0091ff:3.20 #00ffda:3.60 #00ff48:4.20 #48ff00:4.80 > #daff00:5.20 #ff9100:6.00 red:6.50 showTool true > ui mousemode right translate > show #13 models > key blue:2.59 #0091ff:3.20 #00ffda:3.60 #00ff48:4.20 #48ff00:4.80 > #daff00:5.20 #ff9100:6.00 red:6.50 showTool true > ui mousemode right ""color key"" > key numericLabelSpacing equal > key fontSize 11 > key fontSize 10 > ui mousemode right translate > volume #5 level 0.0461 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 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 M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AY001HWLL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 13 days, 22 hours, 30 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 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 DELL P2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL U3223QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 ChimeraX-Clipper: 0.24.0 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX