Opened 4 months ago

Closed 4 months ago

#18094 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

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.  Bytes before following region: 4499775488\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10c352000-10c356000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":37624},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4499775488\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10c352000-10c356000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
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===== Log before crash start =====
Startup Messages  
---  
warning | Could not find virtual screen for QCocoaScreen(0x6000023f1290, "DELL P2422H", QRect(1536,61 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

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

Change History (2)

comment:1 by Eric Pettersen, 4 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Eric Pettersen, 4 months ago

Resolution: → duplicate
Status: assigned → closed
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