id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18094 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit 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 0x000070002b893000 (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 0x000070002a890000 (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 0x000070002988d000 (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 0x000070002888a000 (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 0x0000700027887000 (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 0x0000700026884000 (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 0x0000700025881000 (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 0x000070002487e000 (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 0x000070002387b000 (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 0x0000700022878000 (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 0x0000700021875000 (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 0x0000700020872000 (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 0x000070001f86f000 (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 0x000070001e86c000 (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 0x000070001d869000 (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 0x000070001c866000 (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 0x000070001b863000 (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 0x000070001a860000 (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 0x000070001985d000 (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 0x00007ff846ff0fc0 (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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, 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._minpack2, 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 (total: 124) {""app_name"":""ChimeraX"",""timestamp"":""2025-06-30 14:52:19.00 +1000"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""B67BD54C-9601-48BB-9BF7-1B6C7EF2C8C8""} { ""uptime"" : 520000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 68190, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-06-30 14:52:14.6100 +1000"", ""codeSigningMonitor"" : 0, ""incident"" : ""B67BD54C-9601-48BB-9BF7-1B6C7EF2C8C8"", ""pid"" : 37624, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-06-26 12:29:13.9101 +1000"", ""procStartAbsTime"" : 441016384683813, ""procExitAbsTime"" : 529487818685601, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""C3BA8B9E-1138-5FA2-8C81-49936FF253EE"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""324B8216-C495-C2F1-1769-3322C698A086"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 18, ""bridgeVersion"" : {""build"":""21P5077"",""train"":""8.5""}, ""sleepWakeUUID"" : ""99AB5B2D-4BC8-48ED-BE0A-F2C317F8200B"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX Could not find virtual screen for QCocoaScreen(0x6000023f1290, ""DELL P2422H"", QRect(1536,61 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/dongju/Downloads/cryosparc_P161_J106_005_volume_map.mrc Opened cryosparc_P161_J106_005_volume_map.mrc as #1, grid size 288,288,288, pixel 0.75, shown at level 0.0371, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > volume #1 level 0.05798 > volume #1 level 0.04754 > volume #1 level 0.06319 > volume #1 level 0.05276 > open /Users/dongju/Downloads/cryosparc_P161_J104_007_volume_map.mrc Opened cryosparc_P161_J104_007_volume_map.mrc as #2, grid size 288,288,288, pixel 0.75, shown at level 0.0404, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #2 step 1 > volume #2 level 0.06461 > volume #1 level 0.07885 > volume #2 level 0.08474 > volume #2 level 0.06863 > volume #1 level 0.06841 > volume #2 level 0.1129 > volume #1 level 0.1102 > volume #2 level 0.09279 > volume #2 level 0.05655 > volume #1 level 0.06319 > volume #1 level 0.09973 > volume #1 level 0.06319 > volume #1 level 0.05276 > volume #1 level 0.08407 > open /Users/dongju/Downloads/cryosparc_P161_J107_006_volume_map.mrc Opened cryosparc_P161_J107_006_volume_map.mrc as #3, grid size 288,288,288, pixel 0.75, shown at level 0.0443, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #3 step 1 > volume #3 level 0.076 > volume #3 level 0.05488 > view > volume #3 level 0.06544 > volume #3 level 0.08127 > volume #3 level 0.076 > volume #3 level 0.07072 > volume #3 level 0.06544 > volume #3 level 0.02849 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/dongju/Downloads/cryosparc_P161_J109_005_volume_map.mrc Opened cryosparc_P161_J109_005_volume_map.mrc as #4, grid size 288,288,288, pixel 0.75, shown at level 0.0433, step 2, values float32 > hide #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 step 1 > volume #4 level 0.06187 > volume #4 level 0.05442 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 level 0.07676 > volume #4 level 0.06932 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 level 0.03209 > volume #4 level 0.03953 > volume #4 level 0.04698 > volume #4 level 0.06932 > volume #4 level 0.07676 > open ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/GPR3_8ww2_after_ISOLDE_004-coot-0.pdb"" Chain information for GPR3_8ww2_after_ISOLDE_004-coot-0.pdb #5 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > select add #5 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 2 models selected > hide sel atoms > show sel cartoons > select ::name=""OLA"" 53 atoms, 52 bonds, 1 residue, 1 model selected > show sel atoms > hide #!4 models > ui mousemode right select > select clear > show #!4 models > volume #4 color #b2b2ff98 > select add #5 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 2 models selected Drag select of 4 cryosparc_P161_J109_005_volume_map.mrc , 6 residues > select clear > select /R:214 10 atoms, 9 bonds, 1 residue, 1 model selected > select clear > select add #5 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #5,1,0,0,-2.0271,0,1,0,4.1947,0,0,1,10.623 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.80629,-0.25719,-0.53268,102.95,0.29293,0.95596,-0.018159,-21.201,0.51389,-0.1414,0.84612,-14.174 > view matrix models > #5,0.83272,-0.19695,-0.51748,92.122,0.39237,0.86932,0.30054,-56.961,0.39067,-0.45331,0.80118,36.816 > view matrix models > #5,0.99758,-0.029461,-0.063035,8.0571,0.050194,0.93209,0.35873,-32.431,0.048186,-0.36102,0.93131,50.602 > view matrix models > #5,0.96063,0.21629,-0.17439,-1.8327,-0.15034,0.93249,0.32841,-7.3612,0.23365,-0.28926,0.9283,23.156 > ui mousemode right select > select clear > volume #4 level 0.0507 > select add #5 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #5,0.96063,0.21629,-0.17439,-8.4208,-0.15034,0.93249,0.32841,-74.751,0.23365,-0.28926,0.9283,26.59 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.96091,0.17814,-0.21193,-0.44022,-0.12667,0.96356,0.2356,-70.692,0.24617,-0.19955,0.94846,13.652 > view matrix models > #5,-0.86919,-0.33323,-0.36534,269.28,0.36549,-0.93058,-0.02076,101.85,-0.33306,-0.15157,0.93064,73.708 > view matrix models > #5,-0.91004,-0.062288,-0.40981,250.03,0.079701,-0.99649,-0.025529,140.46,-0.40678,-0.055894,0.91181,73.714 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.91004,-0.062288,-0.40981,267.3,0.079701,-0.99649,-0.025529,203.57,-0.40678,-0.055894,0.91181,75.699 > view matrix models > #5,-0.91004,-0.062288,-0.40981,248.99,0.079701,-0.99649,-0.025529,208.15,-0.40678,-0.055894,0.91181,71.528 > view matrix models > #5,-0.91004,-0.062288,-0.40981,251.64,0.079701,-0.99649,-0.025529,207.24,-0.40678,-0.055894,0.91181,65.141 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.90393,-0.089717,-0.41817,254.75,0.075865,-0.99588,0.049673,199.57,-0.4209,0.013176,0.90701,59.942 > select subtract #5 Nothing selected > ui tool show ""Fit in Map"" > fitmap #5 inMap #4 Fit molecule GPR3_8ww2_after_ISOLDE_004-coot-0.pdb (#5) to map cryosparc_P161_J109_005_volume_map.mrc (#4) using 15424 atoms average map value = 0.0704, steps = 412 shifted from previous position = 7.8 rotated from previous position = 18.1 degrees atoms outside contour = 7906, contour level = 0.050702 Position of GPR3_8ww2_after_ISOLDE_004-coot-0.pdb (#5) relative to cryosparc_P161_J109_005_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.97562205 0.08842047 -0.20085674 223.45640432 -0.11301394 -0.98697877 0.11445853 214.28134897 -0.18812086 0.13436788 0.97291100 18.93953371 Axis 0.09816449 -0.06279518 -0.99318704 Axis point 118.13143748 100.79731333 0.00000000 Rotation angle (degrees) 174.17973925 Shift along axis -10.33085087 > volume #4 level 0.07333 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for GPR3_8ww2_after_ISOLDE_004-coot-0.pdb --- Chain | Description 5.2/A | No description available 5.2/B | No description available 5.2/G | No description available 5.2/N | No description available 5.2/R | No description available > clipper associate #4 toModel #5 Opened cryosparc_P161_J109_005_volume_map.mrc as #5.1.1.1, grid size 288,288,288, pixel 0.75, shown at step 1, values float32 > ui tool show ""Ramachandran Plot"" > isolde sim start /A-R Loading residue template for OLA from internal database Loading residue template for PLM from internal database Loading residue template for Y01 from internal database ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim No map chosen to save > save ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/GPR3_8ww2_after_ISOLDE_with_local_refined_map.pdb"" > ui mousemode right select > select clear > open 8X2K 8x2k title: a lipid receptor complex structure [more info...] Chain information for 8x2k #4 --- Chain | Description | UniProt A | Soluble cytochrome b562,G-protein coupled receptor 3 | C562_ECOLX -105--1, GPR3_HUMAN 1-330 B | Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 26-394 C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 E | scfv16 | Non-standard residues in 8x2k #4 --- 5YM — (Z)-N-(2-hydroxyethyl)octadec-9-enamide > hide #!5 models > hide #!5.1 models > hide #!5.2 models > style #!4 stick Changed 8570 atom styles > select #4/E 1803 atoms, 1849 bonds, 1 pseudobond, 236 residues, 2 models selected > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > show #!4 cartoons > hide #!4 atoms > select ::name=""OLA"" 53 atoms, 52 bonds, 1 residue, 1 model selected > show #!4 atoms > hide #!4 atoms > select ::name=""Y01"" 84 atoms, 87 bonds, 1 residue, 1 model selected > hide #!4 atoms > show #!4 atoms > hide #!4 atoms > select ::name=""PLM"" 49 atoms, 48 bonds, 1 residue, 1 model selected > show #!4 atoms > hide #!4 atoms > select ::name=""Y01"" 84 atoms, 87 bonds, 1 residue, 1 model selected > show #!4 atoms > hide #!4 atoms > select ::name=""HOH"" 8 atoms, 4 bonds, 4 residues, 2 models selected > show sel & #!4 atoms > select clear > select ::name=""OLA"" 53 atoms, 52 bonds, 1 residue, 1 model selected > show #!4 atoms > select clear > open /Users/dongju/Downloads/cryosparc_P161_J107_006_volume_map.mrc Opened cryosparc_P161_J107_006_volume_map.mrc as #6, grid size 288,288,288, pixel 0.75, shown at level 0.0443, step 2, values float32 > select #6 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.73345,0.65334,-0.18762,141.09,0.1515,0.42619,0.89186,-53.169,0.66265,0.6257,-0.41157,15.256 > view matrix models > #6,-0.73281,0.65369,-0.18888,141.12,0.15181,0.42766,0.8911,-53.281,0.66328,0.62433,-0.41263,15.456 > view matrix models > #6,-0.73251,0.65386,-0.18948,141.14,0.15196,0.42837,0.89073,-53.335,0.66358,0.62368,-0.41314,15.553 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.73251,0.65386,-0.18948,177.19,0.15196,0.42837,0.89073,-22.897,0.66358,0.62368,-0.41314,34.499 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.96181,0.26424,-0.071368,232.46,0.11777,0.6349,0.76357,-27.698,0.24707,0.726,-0.64177,94.971 > view matrix models > #6,-0.89916,0.43652,0.031084,195.02,0.35766,0.69208,0.62698,-45.349,0.25217,0.57487,-0.77842,126.39 > view matrix models > #6,-0.82853,0.55937,-0.025287,179.91,0.39191,0.61157,0.68731,-47.001,0.39992,0.55955,-0.72593,105.82 > ui mousemode right select > select clear > volume #6 level 0.04887 > volume #6 step 1 > volume #6 level 0.05942 > open ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/cryosparc_P161_J109_005_volume_map_local_refined.mrc"" Opened cryosparc_P161_J109_005_volume_map_local_refined.mrc as #7, grid size 288,288,288, pixel 0.75, shown at level 0.0433, step 2, values float32 > volume #7 step 1 > select #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.10829,0.64861,-0.75338,136.51,0.43162,-0.65201,-0.62337,207.25,-0.89553,-0.39267,-0.20935,280.91 > view matrix models > #7,0.85375,0.38219,0.3536,-66.705,-0.1078,-0.53466,0.83816,87.13,0.5094,-0.7537,-0.41527,189.01 > view matrix models > #7,0.17581,0.98168,-0.073426,-9.628,0.5821,-0.043519,0.81195,-40.961,0.79388,-0.18549,-0.57909,112.94 > volume #7 level 0.05815 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.17581,0.98168,-0.073426,-15.078,0.5821,-0.043519,0.81195,-23.212,0.79388,-0.18549,-0.57909,109.13 > view matrix models > #7,0.17581,0.98168,-0.073426,-42.117,0.5821,-0.043519,0.81195,17.854,0.79388,-0.18549,-0.57909,121.72 > view matrix models > #7,0.17581,0.98168,-0.073426,-66.958,0.5821,-0.043519,0.81195,31.669,0.79388,-0.18549,-0.57909,149.31 > view matrix models > #7,0.17581,0.98168,-0.073426,-95.107,0.5821,-0.043519,0.81195,-14.801,0.79388,-0.18549,-0.57909,112.64 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.69545,0.69425,-0.18541,45.513,0.47208,0.63594,0.6105,-55.837,0.54175,0.33704,-0.77001,103.58 > view matrix models > #7,-0.89376,0.35898,-0.26893,114.29,0.16902,0.82491,0.5394,-35.592,0.41548,0.43664,-0.79795,109.49 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.89376,0.35898,-0.26893,143.7,0.16902,0.82491,0.5394,9.3094,0.41548,0.43664,-0.79795,155.68 > view matrix models > #7,-0.89376,0.35898,-0.26893,195.74,0.16902,0.82491,0.5394,-44.28,0.41548,0.43664,-0.79795,169.22 > view matrix models > #7,-0.89376,0.35898,-0.26893,232.2,0.16902,0.82491,0.5394,-23.125,0.41548,0.43664,-0.79795,135.92 > view matrix models > #7,-0.89376,0.35898,-0.26893,227.89,0.16902,0.82491,0.5394,-26.588,0.41548,0.43664,-0.79795,135.89 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.46183,0.81971,-0.33881,136.82,0.57119,0.56709,0.59342,-48.084,0.67857,0.080536,-0.73011,139.1 > view matrix models > #7,-0.86477,0.26182,-0.4285,253.69,0.024563,0.87435,0.48468,-10.028,0.50156,0.40861,-0.76255,125.54 > view matrix models > #7,-0.94906,-0.056844,-0.30994,285.14,-0.19463,0.87929,0.4347,19.183,0.24781,0.47288,-0.84556,155.67 > view matrix models > #7,-0.80992,0.37234,-0.45321,238.11,0.058308,0.81996,0.56945,-17.278,0.58364,0.43478,-0.68581,104.88 > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.04438, steps = 108 shifted from previous position = 4.35 rotated from previous position = 2.21 degrees atoms outside contour = 5087, contour level = 0.058148 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.81517704 0.09266454 0.57175142 129.93727547 0.39454705 0.81152293 0.43100251 -124.17877772 -0.42405074 0.57692618 -0.69809538 189.54106528 Axis 0.13887742 0.94771760 0.28730543 Axis point 104.39574238 0.00000000 93.19490419 Rotation angle (degrees) 148.30693874 Shift along axis -45.18488225 > view matrix models > #7,-0.81501,0.37973,-0.43768,236.08,0.13773,0.86065,0.49022,-21.563,0.56284,0.33925,-0.75374,125.57 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.81501,0.37973,-0.43768,233.5,0.13773,0.86065,0.49022,-21.891,0.56284,0.33925,-0.75374,119.17 > view matrix models > #7,-0.81501,0.37973,-0.43768,233.91,0.13773,0.86065,0.49022,-22.071,0.56284,0.33925,-0.75374,120.31 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.941,0.13143,-0.31184,261.24,-0.023249,0.89421,0.44705,-3.2309,0.3376,0.42792,-0.8384,144.76 > view matrix models > #7,-0.90657,-0.22062,-0.35981,302.29,-0.37011,0.82531,0.42647,44.932,0.20287,0.51979,-0.82985,148.32 > view matrix models > #7,-0.83297,0.41452,-0.36651,223.91,0.15086,0.80743,0.57035,-26.66,0.53235,0.41979,-0.7351,112.54 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.83297,0.41452,-0.36651,224.68,0.15086,0.80743,0.57035,-23.537,0.53235,0.41979,-0.7351,113.73 > view matrix models > #7,-0.83297,0.41452,-0.36651,217.96,0.15086,0.80743,0.57035,-20.916,0.53235,0.41979,-0.7351,114.13 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.87486,0.46034,-0.15066,192.93,0.31253,0.77413,0.55049,-32.705,0.37005,0.43452,-0.82113,140.09 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.87486,0.46034,-0.15066,195.01,0.31253,0.77413,0.55049,-33.672,0.37005,0.43452,-0.82113,140.15 > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.04806, steps = 140 shifted from previous position = 2.63 rotated from previous position = 3.49 degrees atoms outside contour = 4997, contour level = 0.058148 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.88393234 0.29296046 0.36446921 136.72106596 0.44554358 0.76427538 0.46623393 -130.26637807 -0.14196674 0.57450616 -0.80609437 159.58318850 Axis 0.20054476 0.93803440 0.28261859 Axis point 95.01291068 0.00000000 88.66283440 Rotation angle (degrees) 164.33898827 Shift along axis -49.67447350 > ui mousemode right select > select clear > volume #7 color #ffb2b295 > volume #7 color #ffb2b27b > volume #7 color #ffb2b27a > save ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/GPR3_8x2k_after_ISOLDE_with_local_refined_map.pdb"" > hide #!4 models > select clear > show #!4 models Drag select of 28 atoms, 10 residues, 24 bonds, 7 cryosparc_P161_J109_005_volume_map_local_refined.mrc > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #7 level 0.06539 > volume #7 level 0.06177 Drag select of 7 cryosparc_P161_J109_005_volume_map_local_refined.mrc > select clear > hide #!4 models > volume #7 color #ffb2b2 Drag select of 7 cryosparc_P161_J109_005_volume_map_local_refined.mrc > select clear > volume #7 level 0.04728 > show #!4 models > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.04806, steps = 44 shifted from previous position = 0.0181 rotated from previous position = 0.142 degrees atoms outside contour = 4221, contour level = 0.04728 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.88504407 0.29202289 0.36251846 137.28110685 0.44359757 0.76517938 0.46660659 -130.19087019 -0.14113184 0.57377970 -0.80675812 159.66869859 Axis 0.19966212 0.93829400 0.28238167 Axis point 95.14503014 0.00000000 88.70239295 Rotation angle (degrees) 164.43174189 Shift along axis -49.65996247 > volume #7 color #f761af > volume #7 color #f761af70 > ui mousemode right ""translate selected models"" > ui mousemode right select > select add #4 6767 atoms, 6888 bonds, 5 pseudobonds, 878 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99976,0.010313,0.019193,-7.1446,-0.010894,0.99948,0.030403,-3.2833,-0.018869,-0.030605,0.99935,3.9006 > view matrix models > #4,0.99976,0.010313,0.019193,-9.7927,-0.010894,0.99948,0.030403,-3.7937,-0.018869,-0.030605,0.99935,3.0925 > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.04807, steps = 68 shifted from previous position = 0.705 rotated from previous position = 0.106 degrees atoms outside contour = 4222, contour level = 0.04728 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.88575849 0.29185989 0.36090126 137.63750347 0.44261337 0.76522125 0.46747177 -130.20720847 -0.13973305 0.57380680 -0.80698230 159.50421253 Axis 0.19929972 0.93831991 0.28255152 Axis point 95.20915381 0.00000000 88.67634517 Rotation angle (degrees) 164.52774861 Shift along axis -49.67674275 > view matrix models > #4,0.99972,0.010471,0.02104,-8.3389,-0.011109,0.99947,0.030444,-3.8922,-0.02071,-0.030669,0.99932,4.1192 > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.04806, steps = 72 shifted from previous position = 1.2 rotated from previous position = 0.0775 degrees atoms outside contour = 4220, contour level = 0.04728 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.88540679 0.29168663 0.36190295 137.46528417 0.44293299 0.76554867 0.46663219 -130.15661309 -0.14094395 0.57345806 -0.80701962 159.72842999 Axis 0.19935535 0.93839836 0.28225160 Axis point 95.19053057 0.00000000 88.72393577 Rotation angle (degrees) 164.45897620 Shift along axis -49.65070756 > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.04806, steps = 40 shifted from previous position = 0.0106 rotated from previous position = 0.0449 degrees atoms outside contour = 4214, contour level = 0.04728 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.88569835 0.29141057 0.36141156 137.61382341 0.44236387 0.76597762 0.46646812 -130.11325993 -0.14089943 0.57302545 -0.80733462 159.83350870 Axis 0.19909168 0.93851763 0.28204107 Axis point 95.22949468 0.00000000 88.75787293 Rotation angle (degrees) 164.47797923 Shift along axis -49.63620691 > ui mousemode right select > select clear > volume #7 color #f88bc6ba Drag select of 7 cryosparc_P161_J109_005_volume_map_local_refined.mrc > select clear > hide #!4 models > volume #7 level 0.05453 Drag select of 7 cryosparc_P161_J109_005_volume_map_local_refined.mrc > select clear > volume #7 color #f88bc6 > volume #7 color #5146ee > volume #7 level 0.08713 > select clear > volume #7 level 0.07264 > open > /Users/dongju/Downloads/cryosparc_P161_8ww2_receptor_only_mask_12A_tigher_mask_th0.119_ns6_ngs8.mrc Opened cryosparc_P161_8ww2_receptor_only_mask_12A_tigher_mask_th0.119_ns6_ngs8.mrc as #8, grid size 288,288,288, pixel 0.75, shown at level 0.717, step 2, values float32 > open ""/Users/dongju/Downloads/cryosparc_P161_J97_005_volume_map (1).mrc"" Opened cryosparc_P161_J97_005_volume_map (1).mrc as #9, grid size 288,288,288, pixel 0.75, shown at level 0.0477, step 2, values float32 > select add #8 2 models selected > select add #9 4 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.15608,-0.96037,0.23094,172.49,-0.70522,0.055359,0.70682,100.27,-0.6916,-0.27318,-0.66863,300,#9,0.15608,-0.96037,0.23094,172.49,-0.70522,0.055359,0.70682,100.27,-0.6916,-0.27318,-0.66863,300 > view matrix models > #8,0.92597,-0.2811,0.25211,10.457,-0.36461,-0.83921,0.40348,196.32,0.098154,-0.46553,-0.87957,258.64,#9,0.92597,-0.2811,0.25211,10.457,-0.36461,-0.83921,0.40348,196.32,0.098154,-0.46553,-0.87957,258.64 > view matrix models > #8,-0.57565,0.81761,-0.011919,87.163,0.57452,0.41478,0.70561,-80.591,0.58186,0.39933,-0.7085,90.448,#9,-0.57565,0.81761,-0.011919,87.163,0.57452,0.41478,0.70561,-80.591,0.58186,0.39933,-0.7085,90.448 > view matrix models > #8,-0.55509,0.82984,-0.05688,88.797,0.59712,0.44517,0.66729,-81.95,0.57906,0.33644,-0.74263,101.64,#9,-0.55509,0.82984,-0.05688,88.797,0.59712,0.44517,0.66729,-81.95,0.57906,0.33644,-0.74263,101.64 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.55509,0.82984,-0.05688,70.313,0.59712,0.44517,0.66729,-97.005,0.57906,0.33644,-0.74263,85.075,#9,-0.55509,0.82984,-0.05688,70.313,0.59712,0.44517,0.66729,-97.005,0.57906,0.33644,-0.74263,85.075 > view matrix models > #8,-0.55509,0.82984,-0.05688,67.424,0.59712,0.44517,0.66729,-99.544,0.57906,0.33644,-0.74263,83.158,#9,-0.55509,0.82984,-0.05688,67.424,0.59712,0.44517,0.66729,-99.544,0.57906,0.33644,-0.74263,83.158 > ui mousemode right select The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #9 step 1 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #8 step 1 > select clear > hide #!8 models > volume #9 level 0.07484 > select #7 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.87486,0.46034,-0.15066,181.01,0.31253,0.77413,0.55049,-21.957,0.37005,0.43452,-0.82113,142.01 > ui mousemode right select > select clear > show #!8 models > select add #8 2 models selected > select add #9 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.76077,0.6473,-0.047265,108.82,0.50122,0.63222,0.59083,-101.24,0.41232,0.42579,-0.80541,98.403,#9,-0.76077,0.6473,-0.047265,108.82,0.50122,0.63222,0.59083,-101.24,0.41232,0.42579,-0.80541,98.403 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.76077,0.6473,-0.047265,111.46,0.50122,0.63222,0.59083,-104.75,0.41232,0.42579,-0.80541,96.487,#9,-0.76077,0.6473,-0.047265,111.46,0.50122,0.63222,0.59083,-104.75,0.41232,0.42579,-0.80541,96.487 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.88897,0.45764,-0.017338,142.91,0.38243,0.76263,0.52168,-98.565,0.25196,0.45712,-0.85297,115.68,#9,-0.88897,0.45764,-0.017338,142.91,0.38243,0.76263,0.52168,-98.565,0.25196,0.45712,-0.85297,115.68 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.88897,0.45764,-0.017338,150.25,0.38243,0.76263,0.52168,-101.8,0.25196,0.45712,-0.85297,116.06,#9,-0.88897,0.45764,-0.017338,150.25,0.38243,0.76263,0.52168,-101.8,0.25196,0.45712,-0.85297,116.06 > view matrix models > #8,-0.88897,0.45764,-0.017338,155.28,0.38243,0.76263,0.52168,-92.706,0.25196,0.45712,-0.85297,102.4,#9,-0.88897,0.45764,-0.017338,155.28,0.38243,0.76263,0.52168,-92.706,0.25196,0.45712,-0.85297,102.4 > view matrix models > #8,-0.88897,0.45764,-0.017338,153.64,0.38243,0.76263,0.52168,-96.807,0.25196,0.45712,-0.85297,101.78,#9,-0.88897,0.45764,-0.017338,153.64,0.38243,0.76263,0.52168,-96.807,0.25196,0.45712,-0.85297,101.78 > select subtract #8 2 models selected > select subtract #9 Nothing selected > volume #8 color #b2ffb25c > volume #9 level 0.06499 > volume #8 level 0.991 > hide #!8 models > show #!8 models > hide #!8 models > set bgColor white > volume #7 color #4b81e9 > volume #7 level 0.08351 > open /Users/dongju/Downloads/cryosparc_P161_run_class001.mrc Opened cryosparc_P161_run_class001.mrc as #10, grid size 288,288,288, pixel 0.75, shown at level 0.00175, step 2, values float32 > select add #10 2 models selected > view matrix models #10,1,0,0,40.169,0,1,0,100.32,0,0,1,90.763 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.7961,0.56924,0.20541,150.99,0.49425,0.41572,0.76348,21.447,0.34921,0.70933,-0.6123,161.97 > view matrix models > #10,-0.94317,0.30937,0.12129,205.6,0.30075,0.63953,0.7075,24.576,0.14131,0.70377,-0.69623,195.22 > view matrix models > #10,-0.92784,0.37036,0.044213,206.17,0.27734,0.60578,0.74573,26.417,0.24941,0.70418,-0.66478,179.62 > view matrix models > #10,-0.88456,0.4662,-0.014699,197.71,0.36615,0.71357,0.59729,22.061,0.28894,0.52295,-0.80189,211.22 > ui mousemode right select > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #10 step 1 > volume #10 color #e77159 > volume #9 color #e69430 > volume #9 color #e6752a > volume #9 color #ab6fe6 > volume #9 color #9e57e6 > volume #10 color #e05e49 > volume #10 level 0.002553 > select add #7 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.87486,0.46034,-0.15066,176.29,0.31253,0.77413,0.55049,-28.125,0.37005,0.43452,-0.82113,148.31 > ui mousemode right select > select clear > select add #8 2 models selected > select add #9 4 models selected > show #!8 models > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.88897,0.45764,-0.017338,155.88,0.38243,0.76263,0.52168,-90.076,0.25196,0.45712,-0.85297,110.25,#9,-0.88897,0.45764,-0.017338,155.88,0.38243,0.76263,0.52168,-90.076,0.25196,0.45712,-0.85297,110.25 > select subtract #8 2 models selected > select subtract #9 Nothing selected > select add #10 2 models selected > view matrix models > #10,-0.88456,0.4662,-0.014699,195.47,0.36615,0.71357,0.59729,16.015,0.28894,0.52295,-0.80189,204.81 > color #8 #b2ffb280 models > ui mousemode right select > select clear > select add #7 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.87486,0.46034,-0.15066,179.38,0.31253,0.77413,0.55049,-31.498,0.37005,0.43452,-0.82113,147.84 > ui mousemode right select > select clear > hide #!8 models > set bgColor black > set bgColor white > volume #10 level 0.002403 > volume #9 level 0.06129 > volume #7 level 0.07264 > volume #7 level 0.07989 > select add #10 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.88456,0.4662,-0.014699,192.44,0.36615,0.71357,0.59729,10.009,0.28894,0.52295,-0.80189,210.95 > select subtract #10 Nothing selected > select add #7 4 models selected > view matrix models > #7,-0.87486,0.46034,-0.15066,178.1,0.31253,0.77413,0.55049,-33.972,0.37005,0.43452,-0.82113,151.1 > view matrix models > #7,-0.87486,0.46034,-0.15066,183.31,0.31253,0.77413,0.55049,-37.355,0.37005,0.43452,-0.82113,151.46 > select subtract #7 Nothing selected > volume #7 level 0.0509 > volume #9 level 0.05021 > volume #10 level 0.002052 > volume #10 level 0.002754 > volume #9 level 0.06499 > select add #9 3 models selected > select add #10 7 models selected > select subtract #9 4 models selected > select add #7 8 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.88773,0.42265,-0.1825,193.93,0.26966,0.79869,0.53794,-34.628,0.37312,0.42833,-0.82299,152.22,#10,-0.90054,0.43201,-0.048988,200.95,0.32231,0.73895,0.59167,13.441,0.29181,0.51703,-0.80469,211.43 > view matrix models > #7,-0.89101,0.4195,-0.17354,193.89,0.27266,0.80014,0.53425,-34.848,0.36298,0.42871,-0.82732,153.85,#10,-0.90294,0.42789,-0.040145,200.38,0.32493,0.74082,0.58788,13.494,0.28129,0.51778,-0.80795,212.9 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.89101,0.4195,-0.17354,197.48,0.27266,0.80014,0.53425,-29.136,0.36298,0.42871,-0.82732,149.01,#10,-0.90294,0.42789,-0.040145,203.97,0.32493,0.74082,0.58788,19.206,0.28129,0.51778,-0.80795,208.06 > select subtract #7 4 models selected > view matrix models > #10,-0.90294,0.42789,-0.040145,205,0.32493,0.74082,0.58788,19.674,0.28129,0.51778,-0.80795,203.13 > ui mousemode right select > select clear > volume #7 level 0.07626 > volume #10 level 0.002253 > select clear > volume #7 level 0.08713 > volume #7 level 0.07626 > volume #10 level 0.002052 > volume #7 level 0.03641 > volume #10 level 0.0004996 > volume #10 level 0.001351 > volume #9 level 0.04282 > open /Users/dongju/Downloads/emd_37881.map Opened emd_37881.map as #11, grid size 256,256,256, pixel 1.1, shown at level 0.322, step 1, values float32 > volume #11 level 0.669 > volume #11 level 0.8825 > volume #11 level 1.096 > volume #11 color #d58070 Drag select of 11 emd_37881.map > select clear > volume #11 level 1.043 > volume #7 level 0.07989 > volume #9 level 0.07114 > volume #10 level 0.002754 > volume #10 level 0.002102 > volume #10 level 0.002653 > select #10 3 models selected > select clear > volume #7 level 0.1052 > volume #7 level 0.07626 > volume #7 color #6287e7 > ui tool show ""Side View"" > select clear > show #!4 models Drag select of 7 cryosparc_P161_J109_005_volume_map_local_refined.mrc > select clear > fitmap #4 inMap #7 Fit molecule 8x2k (#4) to map cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) using 6767 atoms average map value = 0.09378, steps = 320 shifted from previous position = 4.82 rotated from previous position = 9.25 degrees atoms outside contour = 4718, contour level = 0.076262 Position of 8x2k (#4) relative to cryosparc_P161_J109_005_volume_map_local_refined.mrc (#7) coordinates: Matrix rotation and translation -0.82900919 0.33028107 0.45128504 108.24959084 0.53332062 0.70972345 0.46028443 -132.02544985 -0.16826434 0.62225963 -0.76451296 154.32242988 Axis 0.24110970 0.92223601 0.30223642 Axis point 87.24467129 0.00000000 87.53515003 Rotation angle (degrees) 160.37301375 Shift along axis -49.01673902 > volume #7 level 0.04003 > volume #7 level 0.05453 > open ""/Users/dongju/Downloads/emd_38015 (3).map"" Opened emd_38015 (3).map as #12, grid size 320,320,320, pixel 0.85, shown at level 0.177, step 2, values float32 > volume #12 step 1 > volume #12 level 0.5404 > fitmap #4 inMap #12 Fit molecule 8x2k (#4) to map emd_38015 (3).map (#12) using 6767 atoms average map value = 0.1985, steps = 76 shifted from previous position = 1.43 rotated from previous position = 2.22 degrees atoms outside contour = 5549, contour level = 0.54038 Position of 8x2k (#4) relative to emd_38015 (3).map (#12) coordinates: Matrix rotation and translation 0.98824045 -0.13706882 -0.06777135 21.57985379 0.14128248 0.98803474 0.06185958 -23.61932149 0.05848143 -0.07070704 0.99578132 1.94425330 Axis -0.39791118 -0.37895961 0.83549764 Axis point 174.39990587 148.24790088 0.00000000 Rotation angle (degrees) 9.58892472 Shift along axis 1.98832295 > hide #!4 models > volume #12 level 0.4424 > volume #12 level 0.6383 > volume #12 level 0.4984 > volume #12 level 0.5404 > volume #12 level 0.6383 ===== 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 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 24 days, 1 hour, 55 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX