id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16389 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-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: Segmentation fault Thread 0x000000036eeaf000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000036dea3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000036ce97000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000036be8b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000036ae7f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000369e73000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000368e67000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000367e5b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000366e4f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000365e43000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000364e37000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000363e2b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000362e1f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000361e13000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000360e07000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001e9ed0f40 (most recent call first): 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, scipy._lib._ccallback_c, 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scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, 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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, 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Bytes before following region: 4307369623\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100bd4000-100bd8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000169"",""rawCodes"":[1,361],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000169""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":78342}, ""vmregioninfo"" : ""0x169 is not in any region. 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""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6475575296, ""size"" : 577528, ""uuid"" : ""aaa5636d-6f3f-3fa7-9f4a-cf966f0308fe"", ""path"" : ""\/usr\/lib\/libc++.1.dylib"", ""name"" : ""libc++.1.dylib"" } ], ""sharedCache"" : { ""base"" : 6472040448, ""size"" : 4214358016, ""uuid"" : ""bb3df3d3-38bd-304c-9233-e43de95f1903"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=8.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 720K 38 \nColorSync 656K 31 \nCoreAnimation 2320K 110 \nCoreGraphics 96K 6 \nCoreServices 624K 2 \nCoreUI image data 5456K 43 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 7.4G 184 \nMALLOC guard page 192K 12 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{ }, ""deploymentId"" : 240000032 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields 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/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/SMARCA/M-32792/Prelim-DataQC.cxs format session Opened cryosparc_P150_J139_005_volume_map.mrc gaussian as #4, grid size 360,360,360, pixel 0.648, shown at level 0.0206, step 1, values float32 Opened cryosparc_P150_J133_006_volume_map.mrc as #3, grid size 360,360,360, pixel 0.648, shown at level 0.00704, step 2, values float32 Opened cryosparc_P150_J133_006_volume_map.mrc gaussian as #5, grid size 360,360,360, pixel 0.648, shown at level 0.0198, step 1, values float32 Opened E3_ligase_complex_AMPH-19559_final_map.mrc as #6, grid size 300,300,300, pixel 0.731, shown at level 0.136, step 2, values float32 Opened E3_ligase_complex_AMPH-19559_final_map.mrc gaussian as #7, grid size 300,300,300, pixel 0.731, shown at level 0.0455, step 1, values float32 Opened cryosparc_P150_J139_005_volume_map.mrc as #8, grid size 360,360,360, pixel 0.648, shown at level 0.00757, step 2, values float32 opened ChimeraX session The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_2/protein.pdb Chain information for protein.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available > close #10 > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_1/state1_ligandPose1.sdf > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_ligandPose2.sdf > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_protein2.pdb Chain information for state1_protein2.pdb #12 --- Chain | Description A | No description available B | No description available C | No description available > close #10-11#12 > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_1/state1_protein1.pdb Chain information for state1_protein1.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available > show #!1 models > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_1/state1_ligandPose1.sdf > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_protein2.pdb Chain information for state1_protein2.pdb #12 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_1/docking_2/state1_ligandPose2.sdf > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_1/state2_protein1.pdb Chain information for state2_protein1.pdb #14 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_1/state2_ligandPose1.sdf > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_2/state2_protein2.pdb Chain information for state2_protein2.pdb #16 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/SMARCA/M32792-CompDocking_LigandInRawEMmaps/state_2/docking_2/state2_ligandPose2.sdf > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!5 models > hide #!14 models > hide #15 models > hide #!16 models > hide #17 models > hide #!1 models > hide #!10 models > hide #!12 models > volume #4 level 0.01566 > show #!1 models > hide #!4 models > select up 20 atoms, 17 bonds, 4 residues, 2 models selected > select up 24 atoms, 22 bonds, 4 residues, 2 models selected > select up 154 atoms, 156 bonds, 22 residues, 2 models selected > select up 2474 atoms, 2548 bonds, 314 residues, 2 models selected > select down 154 atoms, 156 bonds, 22 residues, 2 models selected > select down 24 atoms, 22 bonds, 4 residues, 2 models selected > select down 20 atoms, 17 bonds, 4 residues, 2 models selected > select ~sel & ##selected 16240 atoms, 16559 bonds, 14 pseudobonds, 2051 residues, 5 models selected > select ~sel & ##selected 20 atoms, 17 bonds, 4 residues, 2 models selected > select ~sel 97587 atoms, 98711 bonds, 59 pseudobonds, 7156 residues, 36 models selected > select ~sel 20 atoms, 17 bonds, 4 residues, 2 models selected > select ~sel & ##selected 16240 atoms, 16559 bonds, 14 pseudobonds, 2051 residues, 5 models selected > select ~sel & ##selected 20 atoms, 17 bonds, 4 residues, 2 models selected > ui mousemode right select > select #1/B:179 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/B:178 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #1/B:179 12 atoms, 10 bonds, 2 residues, 1 model selected > select add #1/B:56 19 atoms, 16 bonds, 3 residues, 1 model selected > select add #1/B:55 28 atoms, 24 bonds, 4 residues, 1 model selected > select subtract #1/B:56 21 atoms, 18 bonds, 3 residues, 1 model selected > show #!4 models > hide #!4 models > select add #1/B:181 35 atoms, 33 bonds, 4 residues, 1 model selected > select add #1/B:52 43 atoms, 40 bonds, 5 residues, 1 model selected > select subtract #1/B:52 35 atoms, 33 bonds, 4 residues, 1 model selected > style sel ball Changed 35 atom styles > style sel ball Changed 35 atom styles > select add #1/B:177 41 atoms, 38 bonds, 5 residues, 1 model selected > style sel ball Changed 41 atom styles > select add #1/B:182 49 atoms, 45 bonds, 6 residues, 1 model selected > select add #1/B:56 56 atoms, 51 bonds, 7 residues, 1 model selected > style sel ball Changed 56 atom styles > select #1/B:180 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #1/B:181 18 atoms, 18 bonds, 2 residues, 1 model selected > style sel ball Changed 18 atom styles > style sel ball Changed 18 atom styles > style sel stick Changed 18 atom styles > style sel stick Changed 18 atom styles > show sel atoms > show #!4 models > hide #!4 models > select add #1/B:184 27 atoms, 26 bonds, 3 residues, 1 model selected > show sel atoms > show #!4 models > hide #!4 models > select add #1/B:59 35 atoms, 33 bonds, 4 residues, 1 model selected > show sel atoms > show #!4 models > hide #11 models > hide #13 models > hide #!4 models > select add #1/C:1407 44 atoms, 41 bonds, 5 residues, 1 model selected > show #!4 models > hide #!4 models > select add #1/B:55 53 atoms, 49 bonds, 6 residues, 1 model selected > show sel atoms > style sel ball Changed 53 atom styles > style sel stick Changed 53 atom styles > show #!4 models > hide #!4 models > select add #1/B:47 59 atoms, 54 bonds, 7 residues, 1 model selected > style sel stick Changed 59 atom styles > style sel stick Changed 59 atom styles > select add #1/B:48 66 atoms, 61 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 66 atom styles > style sel ball Changed 66 atom styles > style sel ball Changed 66 atom styles > style sel stick Changed 66 atom styles > select clear > select #1/B:178 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/B:177@CA 1 atom, 1 residue, 1 model selected > select #1/B:178@CA 1 atom, 1 residue, 1 model selected > select add #1/B:178@CB 2 atoms, 1 residue, 1 model selected > select clear > select #1/B:178 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #1/B:177@CA 7 atoms, 5 bonds, 2 residues, 1 model selected > select add #1/B:179@CB 8 atoms, 6 bonds, 3 residues, 1 model selected > select add #1/B:179@SG 9 atoms, 6 bonds, 3 residues, 1 model selected > select add #1/B:177@SG 10 atoms, 6 bonds, 3 residues, 1 model selected > select add #1/B:177@CB 11 atoms, 6 bonds, 3 residues, 1 model selected > color sel byhetero > show #!4 models > save > /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CryoEM_QC_DockedCompounds.cxs > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!12 models > hide #!12 models > select clear > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #!10 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker BDup_fit_J139.pdb, chain A (#1) with state1_protein1.pdb, chain A (#10), sequence alignment score = 3750.7 RMSD between 740 pruned atom pairs is 0.193 angstroms; (across all 740 pairs: 0.193) > matchmaker #12 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker BDup_fit_J139.pdb, chain A (#1) with state1_protein2.pdb, chain A (#12), sequence alignment score = 3750.7 RMSD between 740 pruned atom pairs is 0.193 angstroms; (across all 740 pairs: 0.193) > show #!10 models > hide #!1 models > show #!1 models > hide #!1 models > show #11 models > hide #11 models > show #13 models > hide #!10 models > show #!10 models > show #11 models > show #!1 models > hide #!10 models > hide #11 models > hide #13 models > show #13 models > show #11 models > hide #11 models > hide #13 models > show #11 models > show #15 models > hide #!1 models > hide #!4 models > hide #15 models > show #15 models > show #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #15 models > show #13 models Drag select of 4 cryosparc_P150_J139_005_volume_map.mrc gaussian , 2 bonds, 1 atoms > select clear > show #!2 models > hide #!1 models > show #15 models > show #!5 models > hide #!4 models > hide #13 models > hide #15 models > hide #11 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!5 models > show #!4 models > hide #!4 models > show #!3 models > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/tarunnarwani/Desktop/movie1.mp4 Movie saved to /Users/tarunnarwani/Desktop/movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/tarunnarwani/Desktop/movie2.mp4 Movie saved to /Users/tarunnarwani/Desktop/movie2.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/tarunnarwani/Desktop/movie3.mp4 Movie saved to /Users/tarunnarwani/Desktop/movie3.mp4 > save /Users/tarunnarwani/Desktop/image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/tarunnarwani/Desktop/movie4.mp4 Movie saved to /Users/tarunnarwani/Desktop/movie4.mp4 > volume #3 level 0.02074 > ui mousemode right windowing > ui mousemode right ""contour level"" > ui mousemode right ""play map series"" > ui mousemode right ""contour level"" > ui mousemode right ""move planes"" > ui mousemode right ""rotate slab"" > ui mousemode right ""play map series"" Drag select of 3 cryosparc_P150_J133_006_volume_map.mrc > ui mousemode right ""play map series"" > volume #3 level 0.002471 > volume #3 level 0.004131 > volume #3 level 0.01534 > ui mousemode right ""crop volume"" > ui mousemode right ""tape measure"" > ui mousemode right ""mark maximum"" > ui tool show ""Side View"" > show #!1 models > ui mousemode right select > volume #3 level 0.009529 > volume #3 level 0.0003946 > volume #3 level 0.002886 > volume #3 level 0.01493 > show #11 models ===== 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 - 88.1 OpenGL renderer: Apple M3 Pro 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: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AY0010LB/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 39 days, 16 hours, 52 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: No Connection Type: Internal DELL P2422H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL P2422H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz 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-Clipper: 0.23.1 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-ISOLDE: 1.8 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-maskChains: 1.4 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-QScore: 1.1 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-StarMap: 1.2.15 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 pyqtgraph: 0.13.7 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 Send2Trash: 1.8.3 SEQCROW: 1.8.12 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 Window Toolkit duplicate all ChimeraX