id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17319 Crash on Mac waking from sleep chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-arm64-arm-64bit ChimeraX Version: 1.9rc202411082121 (2024-11-08 21:21:14 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000034bfc7000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034afbb000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000349faf000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000348fa3000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000347f97000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000346f8b000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000345f7f000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000344f73000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000343f67000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000342f5b000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000341f4f000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000340f43000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033ff37000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033ef2b000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033df1f000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033cf13000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000033bf07000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000203087ac0 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 126) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-07 21:37:05.00 -0500"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.1.1 (24B2091)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""400D8F0A-155A-49AB-B9FA-628DCB1CB5F3""} { ""uptime"" : 170000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac16,8"", ""coalitionID"" : 1998, ""osVersion"" : { ""train"" : ""macOS 15.1.1"", ""build"" : ""24B2091"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-07 21:36:59.6193 -0500"", ""codeSigningMonitor"" : 2, ""incident"" : ""400D8F0A-155A-49AB-B9FA-628DCB1CB5F3"", ""pid"" : 23914, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-07 09:30:14.2926 -0500"", ""procStartAbsTime"" : 3229846140087, ""procExitAbsTime"" : 4148004828263, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9-rc2024.11.08.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""748C12F4-D50B-50E7-A8AF-353B633C1F65"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""7FA5FDF8-8D67-28A2-72D7-B9E65B3FCACD"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""51D843D1-B804-467F-9D93-B2D566F293A4"", ""sleepWakeUUID"" : ""57D8BBC3-196A-48F9-9695-65F6A8E6B370"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x168 is not in any region. 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Startup Messages --- note | available bundle cache has not been initialized yet > mousemode middleMode center > cofr centerOfView > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh set bgColor black; surface cap false; surface style > mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; > style ions ball; size ballscale 0.2; size stickradius 0.07; cofr > centerofview; clip near -10 far 10 position cofr; color ##~num_residues > #3d60ffff; transparency 50 > alias cootmode_off surface style solid; lighting soft; graphics silhouettes > false; hide atoms; default_mol_display; transparency 0; symclip 40; color > ##~num_residues grey; size stickradius 0.2; > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5; > lighting soft; color byhet > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet > alias caps_off surface cap false > alias caps_on surface cap true > alias rock_movie cofr showpivot false; movie record supersample 3; rock y > 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop > alias publication_figure save Figure.png format png supersample 3 > transparentBackground true width 3000 height 3000 > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add Hide_H command ""~disp @H*"" > buttonpanel Shortcuts add Licorice command licorice > buttonpanel Shortcuts add Ribbons command ""preset ribbons"" > buttonpanel Shortcuts add RockMovie command rock_movie > buttonpanel Shortcuts add SymClip10 command ""symclip 10"" > buttonpanel Shortcuts add SymClip20 command ""symclip 20"" > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add PubFigure command publication_figure > buttonpanel Shortcuts add coot_mode command cootmode > buttonpanel Shortcuts add coot_mesh command cootmode_mesh > buttonpanel Shortcuts add coot_off command cootmode_off > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > ui tool show ""Model Panel"" UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"" Opened P913_J108_DeepEMhancer_zflipped.mrc as #1, grid size 384,384,384, pixel 0.933, shown at level 0.000654, step 2, values float32 > surface dust #1 size 9.33 > volume #1 step 1 > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-0.pdb"" Chain information for AF3_J108_zflip_086-coot-0.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/OPG153/Phenix/RealSpaceRefine_91/AF3_J108_zflip_086-coot-0_real_space_refined_091.pdb"" Chain information for AF3_J108_zflip_086-coot-0_real_space_refined_091.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > style stick Changed 12646 atom styles > volume #1 level 0.00727 > color byhetero > volume #1 color #b2b2b278 > show cartoons > color #2 #5b7beeff > color #3 #eee92cff > color byhetero > volume #1 level 0.01058 > volume #1 level 0.01 > volume #1 level 0.0098 > volume #1 level 0.0093 > volume #1 level 0.009 > volume #1 level 0.005692 > volume #1 level 0.002384 > volume #1 level 0.0025 > volume #1 level 0.0028 > volume #1 level 0.0032 > volume #1 level 0.0035 > volume #1 level 0.0045 > volume #1 level 0.01112 > volume #1 level 0.01442 > volume #1 level 0.07066 > volume #1 level 0.01112 > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-1.pdb"" Chain information for AF3_J108_zflip_086-coot-1.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > style stick Changed 18969 atom styles > color byhetero > show cartoons > view #4/E:94 > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-2.pdb"" Chain information for AF3_J108_zflip_086-coot-2.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available [deleted to fit within ticket limits] Chain information for AF3_J108_zflip_170-coot-2_real_space_refined_178.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/OPG153/Phenix/RealSpaceRefine_170/AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb"" Chain information for AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > show atoms > show cartoons > style stick Changed 12646 atom styles > color byhetero > color #2 #7775eeff > color #2 #53eebaff > color #1 #cdee5bff > color #1 #eece74ff > color byhetero > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"" Opened P913_J108_DeepEMhancer_zflipped.mrc as #3, grid size 384,384,384, pixel 0.933, shown at level 0.000654, step 2, values float32 > surface dust #3 size 9.33 > volume #3 step 1 > volume #3 level 0.003842 > volume #3 color #b2b2b267 > volume #3 color #b2b2b266 > lighting simple > open ""/Users/zhouling95/Documents/Academic/McLellan > Lab/MPXV/OPG153/Phenix/RealSpaceRefine_180/AF3_J108_zflip_170-coot-2_real_space_refined_178_real_space_refined_180.pdb"" Chain information for AF3_J108_zflip_170-coot-2_real_space_refined_178_real_space_refined_180.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > show atoms > style stick Changed 18969 atom styles > show cartoons > color byhetero > hide #2 models > show #2 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > mousemode middleMode center > cofr centerOfView > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh set bgColor black; surface cap false; surface style > mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; > style ions ball; size ballscale 0.2; size stickradius 0.07; cofr > centerofview; clip near -10 far 10 position cofr; color ##~num_residues > #3d60ffff; transparency 50 > alias cootmode_off surface style solid; lighting soft; graphics silhouettes > false; hide atoms; default_mol_display; transparency 0; symclip 40; color > ##~num_residues grey; size stickradius 0.2; > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5; > lighting soft; color byhet > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet > alias caps_off surface cap false > alias caps_on surface cap true > alias rock_movie cofr showpivot false; movie record supersample 3; rock y > 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop > alias publication_figure save Figure.png format png supersample 3 > transparentBackground true width 3000 height 3000 > buttonpanel Shortcuts rows 3 columns 5 > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add Hide_H command ""~disp @H*"" > buttonpanel Shortcuts add Licorice command licorice > buttonpanel Shortcuts add Ribbons command ""preset ribbons"" > buttonpanel Shortcuts add RockMovie command rock_movie > buttonpanel Shortcuts add SymClip10 command ""symclip 10"" > buttonpanel Shortcuts add SymClip20 command ""symclip 20"" > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add PubFigure command publication_figure > buttonpanel Shortcuts add coot_mode command cootmode > buttonpanel Shortcuts add coot_mesh command cootmode_mesh > buttonpanel Shortcuts add coot_off command cootmode_off > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > ui tool show ""Model Panel"" UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2J3LL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1.1 (24B2091) Kernel Version: Darwin 24.1.0 Time since boot: 4 days, 11 hours, 6 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 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 U32J59x: Resolution: 4096 x 2304 UI Looks like: 2048 x 1152 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 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: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.7 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9rc202411082121 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.5 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.11 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.17 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.2.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.8 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.54.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.1 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.1 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX