id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16617 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 0x0000000323daf000 (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 0x0000000322da3000 (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 0x0000000321d97000 (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 0x0000000320d8b000 (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 0x000000031fd7f000 (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 0x000000031ed73000 (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 0x000000031dd67000 (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 0x000000031cd5b000 (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 0x000000031bd4f000 (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 0x000000031ad43000 (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 0x0000000319d37000 (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 0x0000000318d2b000 (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 0x0000000317d1f000 (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 0x0000000316d13000 (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 0x0000000315d07000 (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, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, 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.pdb_lib._load_libs, chimerax.surface._surface, 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, lxml._elementpath, lxml.etree, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, 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Bytes before following region: 4363124376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104100000-104104000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000168"",""rawCodes"":[1,360],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000168""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":43803}, ""vmregioninfo"" : ""0x168 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CondensedMap- > State1.mrc format mrc Opened CondensedMap-State1.mrc as #1, grid size 360,360,360, pixel 0.648, shown at level 0.00859, step 2, values float32 > 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 > open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/SMARCA/M-19559/E3_ligase_complex_AMPH-19559_half1_map.mrc format mrc No such file/path: /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- QC/DATA/SMARCA/M-19559/E3_ligase_complex_AMPH-19559_half1_map.mrc > open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CondensedMap- > State1.mrc format mrc Opened CondensedMap-State1.mrc as #10, grid size 360,360,360, pixel 0.648, shown at level 0.00859, step 2, values float32 > toolshed show Downloading bundle ChimeraX_LigandRecognizer-0.2-py3-none-any.whl Installed ChimeraX-LigandRecognizer (0.2) > close session > open ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/TEAD/Second round_5A/12182027_Amphista_model_8S7E_8Q68_fit.pdb"" Chain information for 12182027_Amphista_model_8S7E_8Q68_fit.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available 58 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/2grc.pdb 2grc.pdb title: 1.5 A structure of bromodomain from human BRG1 protein, A central atpase of swi/SNF remodeling complex [more info...] Chain information for 2grc.pdb #2 --- Chain | Description | UniProt A | probable global transcription activator SNF2L4 | SMCA4_HUMAN 1448-1575 > close #2 > close #1 > open ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/TEAD/Second round_5A/12182024_Amphista_Glacios_3Dclass1.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182024_Amphista_Glacios_3Dclass2.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182024_Amphista_Glacios_3Dclass3.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182024_Amphista_Glacios_3Dclass4.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182024_Amphista_Glacios_3Drefine.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182024_Amphista_Glacios_deepEMhancer.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182024_Amphista_Glacios_postprocess.mrc"" > ""/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second > round_5A/12182027_Amphista_model_8S7E_8Q68_fit.pdb"" Opened 12182024_Amphista_Glacios_3Dclass1.mrc as #1, grid size 160,160,160, pixel 1.9, shown at level 1.02e-05, step 1, values float32 Opened 12182024_Amphista_Glacios_3Dclass2.mrc as #2, grid size 160,160,160, pixel 1.9, shown at level 1.79e-06, step 1, values float32 Opened 12182024_Amphista_Glacios_3Dclass3.mrc as #3, grid size 160,160,160, pixel 1.9, shown at level 1.11e-05, step 1, values float32 Opened 12182024_Amphista_Glacios_3Dclass4.mrc as #4, grid size 160,160,160, pixel 1.9, shown at level 8.58e-06, step 1, values float32 Opened 12182024_Amphista_Glacios_3Drefine.mrc as #5, grid size 320,320,320, pixel 0.95, shown at level 0.00115, step 2, values float32 Opened 12182024_Amphista_Glacios_deepEMhancer.mrc as #6, grid size 320,320,320, pixel 0.95, shown at level 0.00113, step 2, values float32 Opened 12182024_Amphista_Glacios_postprocess.mrc as #7, grid size 320,320,320, pixel 0.95, shown at level 0.00895, step 2, values float32 Chain information for 12182027_Amphista_model_8S7E_8Q68_fit.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available 58 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!1 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!8 models > surface dust #7 size 9.5 > ui tool show ""Map Statistics"" > measure mapstats #!7 Map 12182024_Amphista_Glacios_postprocess.mrc #7, step 2, minimum -0.07711, maximum 0.1442, mean 2.224e-05, SD 0.003721, RMS 0.003721 > volume gaussian #7 bfactor 200 Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #9, grid size 320,320,320, pixel 0.95, shown at step 1, values float32 > surface dust #9 size 9.5 > volume #9 level 0.03798 > show #!8 models > color #8 #ffd70085 > color #8 gold > color #9 #ffffb280 models > color #9 #ffffb27c models > color #9 #ffffb27a models > volume #9 level 0.02755 > volume #7 level 0.04413 > volume #7 color #b2b2b283 > volume #7 color #b2b2b282 > transparency #7.1 0 > volume #!7 style surface > transparency #7.1 50 > lighting simple > lighting soft > lighting simple > lighting full > lighting simple > lighting soft > lighting simple > volume #9 level 0.01287 > volume gaussian #7 bfactor 500 Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #10, grid size 320,320,320, pixel 0.95, shown at step 1, values float32 > surface dust #9 size 9.5 > surface dust #10 size 9.5 > volume #10 level 0.00193 > volume #9 level 0.005044 > volume #9 level 0.007327 > volume #9 level 0.01059 > save /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM- > QC/DATA/TEAD/TEAD-33353_QC_lowRes.cxs > volume #9 level 0.02592 > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > volume gaussian #7 bfactor 50 Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #11, grid size 320,320,320, pixel 0.95, shown at step 1, values float32 > surface dust #11 size 9.5 > close #11 > volume #10 level 0.003282 > hide #!8 models > show #!8 models > hide #!10 models > select add #8 9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,-7.0879,0,1,0,-95.424,0,0,1,15.923 > show #!9 models > select subtract #8 Nothing selected > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #8 inMap #9 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms average map value = 0.0001173, steps = 68 shifted from previous position = 2.63 rotated from previous position = 2.5 degrees atoms outside contour = 9225, contour level = 0.025916 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99907078 0.03464922 0.02563226 -13.95349461 -0.03448119 0.99938105 -0.00696877 -89.23650384 -0.02585786 0.00607847 0.99964715 20.46990590 Axis 0.14965739 0.59061371 -0.79295530 Axis point -1372.49318712 59.13081900 0.00000000 Rotation angle (degrees) 2.49833508 Shift along axis -71.02426682 Average map value = 0.0001173 for 9225 atoms, 9225 outside contour > fitmap #8 inMap #9 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms average map value = 0.0001174, steps = 44 shifted from previous position = 0.00819 rotated from previous position = 0.0172 degrees atoms outside contour = 9225, contour level = 0.025916 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99906040 0.03488088 0.02572239 -13.99697307 -0.03471659 0.99937402 -0.00680628 -89.21845569 -0.02594369 0.00590689 0.99964595 20.50558129 Axis 0.14511744 0.58975483 -0.79443701 Axis point -1366.07525796 69.34971193 0.00000000 Rotation angle (degrees) 2.51053116 Shift along axis -70.93861284 > select add #8 9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected > view matrix models > #8,0.99906,0.034881,0.025722,-8.3619,-0.034717,0.99937,-0.0068063,-11.745,-0.025944,0.0059069,0.99965,-1.3901 > fitmap #8 inMap #9 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms average map value = 0.01963, steps = 152 shifted from previous position = 18.7 rotated from previous position = 3.15 degrees atoms outside contour = 6156, contour level = 0.025916 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99992934 -0.01142249 -0.00329146 2.27394680 0.01142241 0.99993476 -0.00004104 -1.74537512 0.00329171 0.00000344 0.99999458 -0.67996791 Axis 0.00187064 -0.27689963 0.96089703 Axis point 157.95429147 198.12642221 0.00000000 Rotation angle (degrees) 0.68110696 Shift along axis -0.16583167 > select subtract #8 Nothing selected > select add #8 9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected > view matrix models > #8,0.99993,-0.011422,-0.0032915,-3.5695,0.011422,0.99993,-4.1036e-05,-62.845,0.0032917,3.4372e-06,0.99999,-2.4981 > fitmap #8 inMap #9 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms average map value = 1.363e-05, steps = 196 shifted from previous position = 19.4 rotated from previous position = 6 degrees atoms outside contour = 9225, contour level = 0.025916 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99431729 -0.05928567 -0.08842135 20.10376186 0.05599766 0.99766045 -0.03921596 -79.98971064 0.09053943 0.03404172 0.99531089 -29.43601181 Axis 0.32540047 -0.79491900 0.51207258 Axis point 635.65737995 0.00000000 -16.09347900 Rotation angle (degrees) 6.46322218 Shift along axis 55.05373958 > show #!6 models > fitmap #8 inMap #6 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_deepEMhancer.mrc (#6) using 9225 atoms average map value = -2.05e-07, steps = 108 shifted from previous position = 2.8 rotated from previous position = 3.77 degrees atoms outside contour = 9225, contour level = 0.0011304 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_deepEMhancer.mrc (#6) coordinates: Matrix rotation and translation 0.98548173 -0.10928181 -0.12993553 37.97855608 0.10485094 0.99366348 -0.04048668 -86.45732218 0.13353665 0.02627502 0.99069551 -32.98473542 Axis 0.19294358 -0.76144356 0.61885093 Axis point 502.45375084 0.00000000 157.82069091 Rotation angle (degrees) 9.96277668 Shift along axis 52.74745576 > hide #!8 models > show #!8 models > hide #!6 models > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.96604,-0.25116,0.060748,329.53,-0.24323,0.96321,0.1143,-51.849,-0.087219,0.095641,-0.99159,288.6 > view matrix models > #8,-0.93896,-0.34014,0.051598,339.78,-0.33368,0.93692,0.10412,-32.592,-0.083758,0.080546,-0.99323,290.52 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.93896,-0.34014,0.051598,336.16,-0.33368,0.93692,0.10412,15.724,-0.083758,0.080546,-0.99323,301.02 > fitmap #8 inMap #9 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms average map value = 0.01249, steps = 196 shifted from previous position = 26.1 rotated from previous position = 17.6 degrees atoms outside contour = 7377, contour level = 0.025916 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation -0.99485298 -0.05640899 0.08417581 298.41439918 -0.05770550 0.99824838 -0.01304770 8.37561434 -0.08329235 -0.01783795 -0.99636549 322.22824158 Axis -0.02859139 0.99956123 -0.00773840 Axis point 156.08973708 0.00000000 154.88477744 Rotation angle (degrees) 175.19465315 Shift along axis -2.65367532 > select subtract #8 Nothing selected > hide #!8 models > show #!8 models > undo > ui mousemode right ""rotate selected models"" > select add #8 9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected > view matrix models > #8,0.63145,-0.73347,-0.25158,198.47,0.74744,0.6621,-0.054305,-59.744,0.20641,-0.15375,0.96631,2.7575 > view matrix models > #8,0.66766,-0.70845,-0.22876,185.82,0.72104,0.69184,-0.038128,-62.479,0.18528,-0.13949,0.97274,2.9451 > ui mousemode right ""translate selected models"" > fitmap #8 inMap #9 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms average map value = 0.01963, steps = 224 shifted from previous position = 9.7 rotated from previous position = 47.5 degrees atoms outside contour = 6156, contour level = 0.025916 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99992784 -0.01156045 -0.00326680 2.29250872 0.01155956 0.99993314 -0.00029013 -1.73205577 0.00326994 0.00025235 0.99999462 -0.71324265 Axis 0.02257300 -0.27199657 0.96203343 Axis point 154.82316121 197.65867302 0.00000000 Rotation angle (degrees) 0.68849522 Shift along axis -0.16330125 > select subtract #8 Nothing selected > open > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/Cluster0-TCF.pdb > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/FBXO22-cluster0_B.pdb > /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/SKP1-cluster0_A.pdb Summary of feedback from opening /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/Cluster0-TCF.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 6196 messages similar to the above omitted Chain information for Cluster0-TCF.pdb #11 --- Chain | Description A | No description available B | No description available C | No description available Chain information for FBXO22-cluster0_B.pdb #12 --- Chain | Description B | No description available Chain information for SKP1-cluster0_A.pdb #13 --- Chain | Description A | No description available > hide #11 models > hide #13 models > select add #12 6264 atoms, 6322 bonds, 403 residues, 1 model selected > view matrix models #12,1,0,0,28.299,0,1,0,126.57,0,0,1,133.32 > view matrix models #12,1,0,0,74.356,0,1,0,168.28,0,0,1,152.09 > view matrix models #12,1,0,0,133.54,0,1,0,164.03,0,0,1,161.43 > view matrix models #12,1,0,0,169.31,0,1,0,154.78,0,0,1,157.95 > select subtract #12 Nothing selected > select add #12 6264 atoms, 6322 bonds, 403 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #12 inMap #9 Fit molecule FBXO22-cluster0_B.pdb (#12) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 6264 atoms average map value = 0.01064, steps = 248 shifted from previous position = 24.3 rotated from previous position = 31.5 degrees atoms outside contour = 5083, contour level = 0.025916 Position of FBXO22-cluster0_B.pdb (#12) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.90868714 -0.41082603 0.07422710 166.52223980 0.41179179 0.85278525 -0.32122397 135.28017747 0.06866740 0.32245820 0.94408977 151.96432014 Axis 0.61623678 0.00532264 0.78754295 Axis point -278.21123987 132.65002846 0.00000000 Rotation angle (degrees) 31.48454427 Shift along axis 223.01560662 > hide #!9 models > show #!9 models > hide #!9 models > hide #!8 models > show #!8 models > hide #12 models > show #!9 models > hide #!9 models > show #!9 models > hide #!8 models > show #12 models > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.77426,0.24415,0.58388,166.01,0.60207,0.00013087,-0.79844,136.29,-0.19501,0.96974,-0.14689,148.54 > view matrix models > #12,-0.26602,0.63325,0.72679,161.77,0.90962,0.41448,-0.028195,138.15,-0.3191,0.6536,-0.68628,147.62 > view matrix models > #12,-0.15284,0.67533,0.7215,162.15,0.93603,0.3331,-0.1135,138.22,-0.31698,0.658,-0.68305,147.63 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.15284,0.67533,0.7215,150.14,0.93603,0.3331,-0.1135,139.31,-0.31698,0.658,-0.68305,145.63 > fitmap #12 inMap #9 Fit molecule FBXO22-cluster0_B.pdb (#12) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 6264 atoms average map value = 0.01432, steps = 92 shifted from previous position = 7.55 rotated from previous position = 14.3 degrees atoms outside contour = 4754, contour level = 0.025916 Position of FBXO22-cluster0_B.pdb (#12) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation -0.32330010 0.51175524 0.79597966 145.55673879 0.87726895 0.47745562 0.04934891 143.14383578 -0.35479040 0.71424275 -0.60330844 141.25704059 Axis 0.48237030 0.83486605 0.26517460 Axis point 50.81561189 -0.00000000 39.28555144 Rotation angle (degrees) 136.43362582 Shift along axis 227.17595615 > select subtract #12 Nothing selected > show #!8 models > hide #!9 models > hide #12 models > hide #!8 models > show #!9 models > show #13 models > select add #13 2536 atoms, 2559 bonds, 160 residues, 1 model selected > view matrix models #13,1,0,0,169.68,0,1,0,134.62,0,0,1,100.38 > view matrix models #13,1,0,0,129.92,0,1,0,158.38,0,0,1,103.69 > view matrix models #13,1,0,0,125.66,0,1,0,170.68,0,0,1,115.53 > view matrix models #13,1,0,0,131.81,0,1,0,169.76,0,0,1,115.57 > fitmap #13 inMap #9 Fit molecule SKP1-cluster0_A.pdb (#13) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 2536 atoms average map value = 0.0115, steps = 116 shifted from previous position = 4.35 rotated from previous position = 11 degrees atoms outside contour = 2123, contour level = 0.025916 Position of SKP1-cluster0_A.pdb (#13) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation 0.99400424 -0.10375006 0.03451810 132.62134676 0.10788845 0.98193472 -0.15544864 164.32868551 -0.01776672 0.15824072 0.98724071 117.10946969 Axis 0.82117189 0.13687051 0.55402453 Axis point 0.00000000 18.26009484 882.18276290 Rotation angle (degrees) 11.01120915 Shift along axis 196.27819317 > ui mousemode right ""rotate selected models"" > view matrix models > #13,-0.16768,-0.76567,-0.62099,158.3,0.98541,-0.14877,-0.082648,136.5,-0.029107,-0.62579,0.77945,113.34 > view matrix models > #13,-0.33663,-0.65511,-0.6764,163.2,0.93274,-0.3305,-0.14411,136.83,-0.12914,-0.67941,0.7223,115.58 > ui mousemode right ""translate selected models"" > view matrix models > #13,-0.33663,-0.65511,-0.6764,151.15,0.93274,-0.3305,-0.14411,134.13,-0.12914,-0.67941,0.7223,110.91 > view matrix models > #13,-0.33663,-0.65511,-0.6764,151.93,0.93274,-0.3305,-0.14411,132.36,-0.12914,-0.67941,0.7223,109.65 > fitmap #13 inMap #9 Fit molecule SKP1-cluster0_A.pdb (#13) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 2536 atoms average map value = 0.01541, steps = 156 shifted from previous position = 7.59 rotated from previous position = 25.6 degrees atoms outside contour = 1886, contour level = 0.025916 Position of SKP1-cluster0_A.pdb (#13) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates: Matrix rotation and translation -0.49270313 -0.79679422 -0.34980366 152.17213174 0.85426248 -0.51945687 -0.02000428 128.10938210 -0.16576862 -0.30868031 0.93660943 122.14498317 Axis -0.17120156 -0.10914341 0.97917197 Axis point 48.46787857 117.27732412 0.00000000 Rotation angle (degrees) 122.53232085 Shift along axis 79.56654352 > hide #13 models > show #!8 models > color #9 #ffffb20d models > color #9 #ffffb234 models > color #9 #ffffb236 models > lighting simple > lighting soft > lighting full > color #8 gold > show #!10 models > hide #!9 models > volume #10 level 0.02995 > volume #10 level 0.01517 > volume #10 level -0.004033 > volume #10 level 0.002368 > volume #10 level 0.003892 > volume #10 level 0.02294 > ui tool show ""Ramachandran Plot"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/cbook.py"", line 298, in process func(*args, **kwargs) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/isolde/validation/ramaplot/ramaplot.py"", line 309, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 192, in step_to self._new_camera_position(residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 281, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 266, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 425, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) ^ UnboundLocalError: cannot access local variable 'o' where it is not associated with a value > ui tool show ""Side View"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/cbook.py"", line 298, in process func(*args, **kwargs) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/isolde/validation/ramaplot/ramaplot.py"", line 309, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 192, in step_to self._new_camera_position(residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 281, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 266, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 425, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) ^ UnboundLocalError: cannot access local variable 'o' where it is not associated with a value Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/cbook.py"", line 298, in process func(*args, **kwargs) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/isolde/validation/ramaplot/ramaplot.py"", line 309, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 192, in step_to self._new_camera_position(residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 281, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 266, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 425, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) ^ UnboundLocalError: cannot access local variable 'o' where it is not associated with a value Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/matplotlib/cbook.py"", line 298, in process func(*args, **kwargs) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site- packages/chimerax/isolde/validation/ramaplot/ramaplot.py"", line 309, in on_pick get_stepper(self.current_model).step_to(picked_rama.residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 192, in step_to self._new_camera_position(residue) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 281, in _new_camera_position interpolate_camera(session, 0, frames=1) File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 266, in interpolate_camera ncp, fcp = _get_clip_points(session, dist) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/tarunnarwani/Library/Application Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py"", line 425, in _get_clip_points return (o+vd*dist*0.5, o+vd*dist*1.5) ^ UnboundLocalError: cannot access local variable 'o' where it is not associated with a value > volume #10 level 0.0301 > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #8/B Alignment identifier is 8/B > select #8/B:26-36,38-47,49-62,82-92,130-139,202-209,236-245,298-312,339-349 1645 atoms, 1647 bonds, 100 residues, 1 model selected > select #8/B:56 16 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:56 16 atoms, 15 bonds, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!9 models > show #!9 models > hide #!8 models > show #!10 models > show #!8 models > hide #!9 models > show #!9 models > hide #!10 models > view matrix models > #8,0.99993,-0.01156,-0.0032668,2.3088,0.01156,0.99993,-0.00029013,-1.7053,0.0032699,0.00025235,0.99999,-0.7365 > select clear > view > hide #!9 models > show #!9 models > hide #!9 models > show #!7 models > hide #!7 models > show #!5 models > hide #!5 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!6 models > volume gaussian #6 bfactor 100 Opened 12182024_Amphista_Glacios_deepEMhancer.mrc gaussian as #14, grid size 320,320,320, pixel 0.95, shown at step 1, values float32 > volume #10 level 0.02782 > volume #10 level -0.006166 > volume #10 level 0.005263 > volume #10 level 0.02386 > show #13 models > ui mousemode right ""translate selected models"" > select add #13 2536 atoms, 2559 bonds, 160 residues, 1 model selected > view matrix models > #13,-0.4927,-0.79679,-0.3498,165.94,0.85426,-0.51946,-0.020004,179.7,-0.16577,-0.30868,0.93661,169.79 > 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 #11 to #8/A pairing bs Parameters --- Chain pairing | bs 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 12182027_Amphista_model_8S7E_8Q68_fit.pdb, chain A (#8) with Cluster0-TCF.pdb, chain A (#11), sequence alignment score = 576 RMSD between 79 pruned atom pairs is 1.051 angstroms; (across all 128 pairs: 3.301) > hide #13 models > select #8/B:20 14 atoms, 13 bonds, 1 residue, 1 model selected > ui mousemode right select > select up 105 atoms, 105 bonds, 7 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #8/B:403 23 atoms, 22 bonds, 1 residue, 1 model selected > select up 71 atoms, 70 bonds, 5 residues, 1 model selected > select up 312 atoms, 315 bonds, 20 residues, 1 model selected > select up 333 atoms, 335 bonds, 22 residues, 1 model selected > select up 1803 atoms, 1822 bonds, 119 residues, 1 model selected > select up 1858 atoms, 1876 bonds, 123 residues, 1 model selected > select up 2222 atoms, 2242 bonds, 147 residues, 1 model selected > select up 2236 atoms, 2255 bonds, 148 residues, 1 model selected > select up 2650 atoms, 2673 bonds, 173 residues, 1 model selected > select up 2717 atoms, 2740 bonds, 177 residues, 1 model selected > select up 3722 atoms, 3757 bonds, 244 residues, 1 model selected > select up 3748 atoms, 3782 bonds, 246 residues, 1 model selected > select up 5189 atoms, 5236 bonds, 335 residues, 1 model selected > show #!10 models > ui mousemode right ""rotate selected models"" > hide #!8 models > show #!8 models > select add #8 9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected > select subtract #8 Nothing selected > select add #8 9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected > view matrix models > #8,-0.050776,-0.98234,-0.1801,332.24,-0.9675,0.093113,-0.23511,316.58,0.24773,0.16231,-0.95514,231.81 > view matrix models > #8,-0.40316,-0.91029,0.093985,334.57,-0.88572,0.36231,-0.29024,272.9,0.23015,-0.20026,-0.95233,287.18 > view matrix models > #8,-0.40533,0.91417,-0.00064002,81.984,0.88635,0.39316,0.24456,-83.877,0.22382,0.098558,-0.96964,247 > view matrix models > #8,0.63897,0.7332,0.23265,-86.807,0.72105,-0.67626,0.15088,112.15,0.26796,0.071341,-0.96079,242.88 > view matrix models > #8,-0.86854,-0.49287,-0.052056,366.8,-0.49091,0.86998,-0.04636,101.34,0.068137,-0.014711,-0.99757,291.67 > view matrix models > #8,-0.88027,-0.46419,-0.098213,371.34,-0.46362,0.88553,-0.029953,92.414,0.10087,0.019167,-0.99471,281.25 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.88027,-0.46419,-0.098213,371.21,-0.46362,0.88553,-0.029953,93.111,0.10087,0.019167,-0.99471,288.61 > view matrix models > #8,-0.88027,-0.46419,-0.098213,383.15,-0.46362,0.88553,-0.029953,155.98,0.10087,0.019167,-0.99471,290.72 > view matrix models > #8,-0.88027,-0.46419,-0.098213,383.74,-0.46362,0.88553,-0.029953,157.98,0.10087,0.019167,-0.99471,284.77 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.42759,0.86906,-0.2488,10.478,-0.90377,0.41684,-0.097187,304.24,0.019252,0.26642,0.96367,-33.182 > view matrix models > #8,0.77352,0.60123,-0.20047,-10.647,-0.63227,0.75383,-0.17881,225.51,0.043614,0.26507,0.96324,-36.659 > volume #10 level 0.02553 > view matrix models > #8,0.76877,0.63484,-0.077293,-33.348,-0.63567,0.7453,-0.20113,230.63,-0.070078,0.20376,0.97651,-12.231 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.76877,0.63484,-0.077293,-41.29,-0.63567,0.7453,-0.20113,160.36,-0.070078,0.20376,0.97651,-14.162 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.67531,0.73297,-0.081904,-40.626,-0.73298,0.65467,-0.1848,186.11,-0.081831,0.18483,0.97936,-10.016 > view matrix models > #8,0.92495,0.34942,0.14956,-57.551,-0.33478,0.93529,-0.11468,73.385,-0.17995,0.056001,0.98208,23.493 > view matrix models > #8,0.99272,-0.099665,0.067645,10.116,0.10567,0.99014,-0.091933,-5.6452,-0.057816,0.098412,0.99346,-3.1669 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.99272,-0.099665,0.067645,2.2475,0.10567,0.99014,-0.091933,-2.8917,-0.057816,0.098412,0.99346,-1.1003 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.98714,-0.15251,0.047811,13.821,0.15631,0.98363,-0.089662,-10.05,-0.033353,0.095982,0.99482,-4.7023 > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #8 inMap #10 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) using 9225 atoms average map value = 0.01841, steps = 108 shifted from previous position = 5.56 rotated from previous position = 10.6 degrees atoms outside contour = 6516, contour level = 0.025532 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) coordinates: Matrix rotation and translation 0.99999655 -0.00244054 -0.00097730 0.52642988 0.00244123 0.99999678 0.00070534 -0.49302841 0.00097557 -0.00070772 0.99999928 -0.11313285 Axis -0.25954042 -0.35868970 0.89664958 Axis point 211.23113280 208.89189162 0.00000000 Rotation angle (degrees) 0.15597247 Shift along axis -0.06122614 Average map value = 0.01841 for 9225 atoms, 6516 outside contour The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #4 inMap #10 Fit map 12182024_Amphista_Glacios_3Dclass4.mrc in map 12182024_Amphista_Glacios_postprocess.mrc gaussian using 36656 points correlation = 0.8147, correlation about mean = 0.6883, overlap = 16.21 steps = 56, shift = 1.48, angle = 0.868 degrees Position of 12182024_Amphista_Glacios_3Dclass4.mrc (#4) relative to 12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) coordinates: Matrix rotation and translation 0.99988562 0.00584419 -0.01394988 1.41668665 -0.00585547 0.99998256 -0.00076808 -0.07536794 0.01394514 0.00084968 0.99990240 -3.22359478 Axis 0.05340490 -0.92085783 -0.38622372 Axis point 193.32512548 0.00000000 94.64857300 Rotation angle (degrees) 0.86784733 Shift along axis 1.39008996 Correlation = 0.8147, Correlation about mean = 0.6883, Overlap = 16.21 > fitmap #8 inMap #4 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_3Dclass4.mrc (#4) using 9225 atoms average map value = 0.03868, steps = 56 shifted from previous position = 0.529 rotated from previous position = 0.463 degrees atoms outside contour = 180, contour level = 8.5775e-06 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_3Dclass4.mrc (#4) coordinates: Matrix rotation and translation 0.99985955 -0.00195433 0.01664564 -2.29841881 0.00198688 0.99999615 -0.00193912 0.76665025 -0.01664179 0.00197192 0.99985958 3.60031780 Axis 0.11589162 0.98637224 0.11678583 Axis point 208.72035729 0.00000000 146.17829889 Rotation angle (degrees) 0.96683567 Shift along axis 0.91030116 Average map value = 0.03868 for 9225 atoms, 180 outside contour > fitmap #8 inMap #1 Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map 12182024_Amphista_Glacios_3Dclass1.mrc (#1) using 9225 atoms average map value = 0.04031, steps = 52 shifted from previous position = 0.782 rotated from previous position = 0.702 degrees atoms outside contour = 661, contour level = 1.0157e-05 Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to 12182024_Amphista_Glacios_3Dclass1.mrc (#1) coordinates: Matrix rotation and translation 0.99991779 -0.00315908 0.01242759 -1.22912133 0.00316312 0.99999496 -0.00030561 -0.01164305 -0.01242656 0.00034490 0.99992273 2.25993858 Axis 0.02535732 0.96882574 0.24644209 Axis point 171.03150715 0.00000000 101.08386603 Rotation angle (degrees) 0.73495019 Shift along axis 0.51449666 Average map value = 0.04031 for 9225 atoms, 661 outside contour > hide #!8 models > show #!8 models > hide #!10 models > show #!10 models > volume #10 level 0.002087 > volume #10 level 0.002994 ===== 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: 86 days, 14 hours, 37 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-LigandRecognizer: 0.2 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