Opened 9 months ago

Closed 9 months ago

#16617 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-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000323daf000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000322da3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000321d97000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000320d8b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031fd7f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031ed73000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031dd67000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031cd5b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031bd4f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031ad43000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000319d37000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000318d2b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000317d1f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316d13000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315d07000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001e9ed0f40 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 107)


{"app_name":"ChimeraX","timestamp":"2025-01-14 13:24:08.00 +0000","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"D4E63E48-D121-4E42-8F37-3478F73AD98C"}
{
  "uptime" : 1200000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 242167,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2025-01-14 13:24:05.1895 +0000",
  "codeSigningMonitor" : 1,
  "incident" : "D4E63E48-D121-4E42-8F37-3478F73AD98C",
  "pid" : 43803,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-01-13 10:06:49.2053 +0000",
  "procStartAbsTime" : 30083938786137,
  "procExitAbsTime" : 30924940853512,
  "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":"24620DA0-5988-5B23-9E82-940A82D06194","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "E13F26CC-2B73-1C1F-F7BF-9C3A2414B42E",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 13568,
  "sleepWakeUUID" : "81BD1F33-43F8-4A7F-8D1A-2A508751098F",
  "sip" : "enabled",
  "vmRegionInfo" : "0x168 is not in any region.  Bytes before following region: 4363124376\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104100000-104104000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43803},
  "vmregioninfo" : "0x168 is not in any region.  Bytes before following region: 4363124376\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104100000-104104000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":1},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5369723544},{"value":99},{"value":95},{"value":2},{"value":0},{"value":14237422058713925516},{"value":14237422050797504716},{"value":14757395258967641293},{"value":4294967286},{"value":5369723473},{"value":0},{"value":49},{"value":4294967280},{"value":328},{"value":8394712296},{"value":0},{"value":11},{"value":8219594560,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8219594784,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4386211376,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8225169408,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":8225169408,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6476536864},"cpsr":{"value":1073745920},"fp":{"value":5369723616},"sp":{"value":5369723584},"esr":{"value":1442840704,"description":" 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_postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":244},{"imageOffset":2095464,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":448,"imageIndex":244},{"imageOffset":510204,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":244},{"imageOffset":2095004,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":244},{"imageOffset":515532,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":1856,"imageIndex":244},{"imageOffset":11458836,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":592,"imageIndex":244},{"imageOffset":3274684,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1100,"imageIndex":244},{"imageOffset":3405156,"symbol":"-[NSWindow 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG image                          1408K       75 \nColorSync                          656K       31 \nCoreAnimation                     4496K      246 \nCoreGraphics                        64K        4 \nCoreServices                       624K        2 \nCoreUI image data                 5488K       54 \nDispatch continuations            96.0M        1 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             1.9G      255 \nMALLOC guard page                  192K       12 \nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       1104K       69 \nStack                            411.9M       70 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      360.5M      356 \nVM_ALLOCATE (reserved)           608.0M        4         reserved VM address space (unallocated)\n__AUTH                            2211K      409 \n__AUTH_CONST                      31.9M      627 \n__CTF                               824        1 \n__DATA                            25.1M      871 \n__DATA_CONST                      44.1M      873 \n__DATA_DIRTY                      2033K      235 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       568.0M      241 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2200K        1 \n__TEXT                           995.4M      890 \ndyld private memory                592K        8 \nmapped file                      585.4M      104 \nshared memory                     3296K       34 \n===========                     =======  ======= \nTOTAL                              5.7G     5494 \nTOTAL, minus reserved VM space     5.1G     5494 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "6adeb57a55f13df3622dee06b3c3cc10cf749019",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "64b21a7351cbb02ce3442e4e",
      "factorPackIds" : {
        "REMINDERS_GROCERY" : "6647f0f7b6a75d3dc32993e7"
      },
      "deploymentId" : 240000042
    },
    {
      "rolloutId" : "6297d96be2c9387df974efa4",
      "factorPackIds" : {

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      "deploymentId" : 240000032
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CondensedMap-
> State1.mrc format mrc

Opened CondensedMap-State1.mrc as #1, grid size 360,360,360, pixel 0.648,
shown at level 0.00859, step 2, values float32  

> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/SMARCA/M-32792/Prelim-DataQC.cxs format session

Opened cryosparc_P150_J139_005_volume_map.mrc gaussian as #4, grid size
360,360,360, pixel 0.648, shown at level 0.0206, step 1, values float32  
Opened cryosparc_P150_J133_006_volume_map.mrc as #3, grid size 360,360,360,
pixel 0.648, shown at level 0.00704, step 2, values float32  
Opened cryosparc_P150_J133_006_volume_map.mrc gaussian as #5, grid size
360,360,360, pixel 0.648, shown at level 0.0198, step 1, values float32  
Opened E3_ligase_complex_AMPH-19559_final_map.mrc as #6, grid size
300,300,300, pixel 0.731, shown at level 0.136, step 2, values float32  
Opened E3_ligase_complex_AMPH-19559_final_map.mrc gaussian as #7, grid size
300,300,300, pixel 0.731, shown at level 0.0455, step 1, values float32  
Opened cryosparc_P150_J139_005_volume_map.mrc as #8, grid size 360,360,360,
pixel 0.648, shown at level 0.00757, step 2, values float32  
opened ChimeraX session  

> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/SMARCA/M-19559/E3_ligase_complex_AMPH-19559_half1_map.mrc format mrc

No such file/path: /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
QC/DATA/SMARCA/M-19559/E3_ligase_complex_AMPH-19559_half1_map.mrc  

> open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CondensedMap-
> State1.mrc format mrc

Opened CondensedMap-State1.mrc as #10, grid size 360,360,360, pixel 0.648,
shown at level 0.00859, step 2, values float32  

> toolshed show

Downloading bundle ChimeraX_LigandRecognizer-0.2-py3-none-any.whl  
Installed ChimeraX-LigandRecognizer (0.2)  

> close session

> open "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/TEAD/Second round_5A/12182027_Amphista_model_8S7E_8Q68_fit.pdb"

Chain information for 12182027_Amphista_model_8S7E_8Q68_fit.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/2grc.pdb

2grc.pdb title:  
1.5 A structure of bromodomain from human BRG1 protein, A central atpase of
swi/SNF remodeling complex [more info...]  
  
Chain information for 2grc.pdb #2  
---  
Chain | Description | UniProt  
A | probable global transcription activator SNF2L4 | SMCA4_HUMAN 1448-1575  
  

> close #2

> close #1

> open "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/TEAD/Second round_5A/12182024_Amphista_Glacios_3Dclass1.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Dclass2.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Dclass3.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Dclass4.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Drefine.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_deepEMhancer.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_postprocess.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182027_Amphista_model_8S7E_8Q68_fit.pdb"

Opened 12182024_Amphista_Glacios_3Dclass1.mrc as #1, grid size 160,160,160,
pixel 1.9, shown at level 1.02e-05, step 1, values float32  
Opened 12182024_Amphista_Glacios_3Dclass2.mrc as #2, grid size 160,160,160,
pixel 1.9, shown at level 1.79e-06, step 1, values float32  
Opened 12182024_Amphista_Glacios_3Dclass3.mrc as #3, grid size 160,160,160,
pixel 1.9, shown at level 1.11e-05, step 1, values float32  
Opened 12182024_Amphista_Glacios_3Dclass4.mrc as #4, grid size 160,160,160,
pixel 1.9, shown at level 8.58e-06, step 1, values float32  
Opened 12182024_Amphista_Glacios_3Drefine.mrc as #5, grid size 320,320,320,
pixel 0.95, shown at level 0.00115, step 2, values float32  
Opened 12182024_Amphista_Glacios_deepEMhancer.mrc as #6, grid size
320,320,320, pixel 0.95, shown at level 0.00113, step 2, values float32  
Opened 12182024_Amphista_Glacios_postprocess.mrc as #7, grid size 320,320,320,
pixel 0.95, shown at level 0.00895, step 2, values float32  
Chain information for 12182027_Amphista_model_8S7E_8Q68_fit.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!8 models

> surface dust #7 size 9.5

> ui tool show "Map Statistics"

> measure mapstats #!7

Map 12182024_Amphista_Glacios_postprocess.mrc #7, step 2, minimum -0.07711,
maximum 0.1442, mean 2.224e-05, SD 0.003721, RMS 0.003721  

> volume gaussian #7 bfactor 200

Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #9, grid size
320,320,320, pixel 0.95, shown at step 1, values float32  

> surface dust #9 size 9.5

> volume #9 level 0.03798

> show #!8 models

> color #8 #ffd70085

> color #8 gold

> color #9 #ffffb280 models

> color #9 #ffffb27c models

> color #9 #ffffb27a models

> volume #9 level 0.02755

> volume #7 level 0.04413

> volume #7 color #b2b2b283

> volume #7 color #b2b2b282

> transparency #7.1 0

> volume #!7 style surface

> transparency #7.1 50

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting simple

> volume #9 level 0.01287

> volume gaussian #7 bfactor 500

Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #10, grid size
320,320,320, pixel 0.95, shown at step 1, values float32  

> surface dust #9 size 9.5

> surface dust #10 size 9.5

> volume #10 level 0.00193

> volume #9 level 0.005044

> volume #9 level 0.007327

> volume #9 level 0.01059

> save /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/TEAD/TEAD-33353_QC_lowRes.cxs

> volume #9 level 0.02592

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!8 models

> volume gaussian #7 bfactor 50

Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #11, grid size
320,320,320, pixel 0.95, shown at step 1, values float32  

> surface dust #11 size 9.5

> close #11

> volume #10 level 0.003282

> hide #!8 models

> show #!8 models

> hide #!10 models

> select add #8

9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #8,1,0,0,-7.0879,0,1,0,-95.424,0,0,1,15.923

> show #!9 models

> select subtract #8

Nothing selected  

> ui tool show "Fit in Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #8 inMap #9

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms  
average map value = 0.0001173, steps = 68  
shifted from previous position = 2.63  
rotated from previous position = 2.5 degrees  
atoms outside contour = 9225, contour level = 0.025916  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99907078 0.03464922 0.02563226 -13.95349461  
-0.03448119 0.99938105 -0.00696877 -89.23650384  
-0.02585786 0.00607847 0.99964715 20.46990590  
Axis 0.14965739 0.59061371 -0.79295530  
Axis point -1372.49318712 59.13081900 0.00000000  
Rotation angle (degrees) 2.49833508  
Shift along axis -71.02426682  
  
Average map value = 0.0001173 for 9225 atoms, 9225 outside contour  

> fitmap #8 inMap #9

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms  
average map value = 0.0001174, steps = 44  
shifted from previous position = 0.00819  
rotated from previous position = 0.0172 degrees  
atoms outside contour = 9225, contour level = 0.025916  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99906040 0.03488088 0.02572239 -13.99697307  
-0.03471659 0.99937402 -0.00680628 -89.21845569  
-0.02594369 0.00590689 0.99964595 20.50558129  
Axis 0.14511744 0.58975483 -0.79443701  
Axis point -1366.07525796 69.34971193 0.00000000  
Rotation angle (degrees) 2.51053116  
Shift along axis -70.93861284  
  

> select add #8

9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected  

> view matrix models
> #8,0.99906,0.034881,0.025722,-8.3619,-0.034717,0.99937,-0.0068063,-11.745,-0.025944,0.0059069,0.99965,-1.3901

> fitmap #8 inMap #9

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms  
average map value = 0.01963, steps = 152  
shifted from previous position = 18.7  
rotated from previous position = 3.15 degrees  
atoms outside contour = 6156, contour level = 0.025916  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99992934 -0.01142249 -0.00329146 2.27394680  
0.01142241 0.99993476 -0.00004104 -1.74537512  
0.00329171 0.00000344 0.99999458 -0.67996791  
Axis 0.00187064 -0.27689963 0.96089703  
Axis point 157.95429147 198.12642221 0.00000000  
Rotation angle (degrees) 0.68110696  
Shift along axis -0.16583167  
  

> select subtract #8

Nothing selected  

> select add #8

9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected  

> view matrix models
> #8,0.99993,-0.011422,-0.0032915,-3.5695,0.011422,0.99993,-4.1036e-05,-62.845,0.0032917,3.4372e-06,0.99999,-2.4981

> fitmap #8 inMap #9

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms  
average map value = 1.363e-05, steps = 196  
shifted from previous position = 19.4  
rotated from previous position = 6 degrees  
atoms outside contour = 9225, contour level = 0.025916  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99431729 -0.05928567 -0.08842135 20.10376186  
0.05599766 0.99766045 -0.03921596 -79.98971064  
0.09053943 0.03404172 0.99531089 -29.43601181  
Axis 0.32540047 -0.79491900 0.51207258  
Axis point 635.65737995 0.00000000 -16.09347900  
Rotation angle (degrees) 6.46322218  
Shift along axis 55.05373958  
  

> show #!6 models

> fitmap #8 inMap #6

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_deepEMhancer.mrc (#6) using 9225 atoms  
average map value = -2.05e-07, steps = 108  
shifted from previous position = 2.8  
rotated from previous position = 3.77 degrees  
atoms outside contour = 9225, contour level = 0.0011304  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_deepEMhancer.mrc (#6) coordinates:  
Matrix rotation and translation  
0.98548173 -0.10928181 -0.12993553 37.97855608  
0.10485094 0.99366348 -0.04048668 -86.45732218  
0.13353665 0.02627502 0.99069551 -32.98473542  
Axis 0.19294358 -0.76144356 0.61885093  
Axis point 502.45375084 0.00000000 157.82069091  
Rotation angle (degrees) 9.96277668  
Shift along axis 52.74745576  
  

> hide #!8 models

> show #!8 models

> hide #!6 models

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.96604,-0.25116,0.060748,329.53,-0.24323,0.96321,0.1143,-51.849,-0.087219,0.095641,-0.99159,288.6

> view matrix models
> #8,-0.93896,-0.34014,0.051598,339.78,-0.33368,0.93692,0.10412,-32.592,-0.083758,0.080546,-0.99323,290.52

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.93896,-0.34014,0.051598,336.16,-0.33368,0.93692,0.10412,15.724,-0.083758,0.080546,-0.99323,301.02

> fitmap #8 inMap #9

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms  
average map value = 0.01249, steps = 196  
shifted from previous position = 26.1  
rotated from previous position = 17.6 degrees  
atoms outside contour = 7377, contour level = 0.025916  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
-0.99485298 -0.05640899 0.08417581 298.41439918  
-0.05770550 0.99824838 -0.01304770 8.37561434  
-0.08329235 -0.01783795 -0.99636549 322.22824158  
Axis -0.02859139 0.99956123 -0.00773840  
Axis point 156.08973708 0.00000000 154.88477744  
Rotation angle (degrees) 175.19465315  
Shift along axis -2.65367532  
  

> select subtract #8

Nothing selected  

> hide #!8 models

> show #!8 models

> undo

> ui mousemode right "rotate selected models"

> select add #8

9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected  

> view matrix models
> #8,0.63145,-0.73347,-0.25158,198.47,0.74744,0.6621,-0.054305,-59.744,0.20641,-0.15375,0.96631,2.7575

> view matrix models
> #8,0.66766,-0.70845,-0.22876,185.82,0.72104,0.69184,-0.038128,-62.479,0.18528,-0.13949,0.97274,2.9451

> ui mousemode right "translate selected models"

> fitmap #8 inMap #9

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms  
average map value = 0.01963, steps = 224  
shifted from previous position = 9.7  
rotated from previous position = 47.5 degrees  
atoms outside contour = 6156, contour level = 0.025916  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99992784 -0.01156045 -0.00326680 2.29250872  
0.01155956 0.99993314 -0.00029013 -1.73205577  
0.00326994 0.00025235 0.99999462 -0.71324265  
Axis 0.02257300 -0.27199657 0.96203343  
Axis point 154.82316121 197.65867302 0.00000000  
Rotation angle (degrees) 0.68849522  
Shift along axis -0.16330125  
  

> select subtract #8

Nothing selected  

> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/Cluster0-TCF.pdb
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/FBXO22-cluster0_B.pdb
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/SKP1-cluster0_A.pdb

Summary of feedback from opening
/Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/Cluster0-TCF.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
6196 messages similar to the above omitted  
  
Chain information for Cluster0-TCF.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for FBXO22-cluster0_B.pdb #12  
---  
Chain | Description  
B | No description available  
  
Chain information for SKP1-cluster0_A.pdb #13  
---  
Chain | Description  
A | No description available  
  

> hide #11 models

> hide #13 models

> select add #12

6264 atoms, 6322 bonds, 403 residues, 1 model selected  

> view matrix models #12,1,0,0,28.299,0,1,0,126.57,0,0,1,133.32

> view matrix models #12,1,0,0,74.356,0,1,0,168.28,0,0,1,152.09

> view matrix models #12,1,0,0,133.54,0,1,0,164.03,0,0,1,161.43

> view matrix models #12,1,0,0,169.31,0,1,0,154.78,0,0,1,157.95

> select subtract #12

Nothing selected  

> select add #12

6264 atoms, 6322 bonds, 403 residues, 1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #12 inMap #9

Fit molecule FBXO22-cluster0_B.pdb (#12) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 6264 atoms  
average map value = 0.01064, steps = 248  
shifted from previous position = 24.3  
rotated from previous position = 31.5 degrees  
atoms outside contour = 5083, contour level = 0.025916  
  
Position of FBXO22-cluster0_B.pdb (#12) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.90868714 -0.41082603 0.07422710 166.52223980  
0.41179179 0.85278525 -0.32122397 135.28017747  
0.06866740 0.32245820 0.94408977 151.96432014  
Axis 0.61623678 0.00532264 0.78754295  
Axis point -278.21123987 132.65002846 0.00000000  
Rotation angle (degrees) 31.48454427  
Shift along axis 223.01560662  
  

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!8 models

> show #!8 models

> hide #12 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #12 models

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.77426,0.24415,0.58388,166.01,0.60207,0.00013087,-0.79844,136.29,-0.19501,0.96974,-0.14689,148.54

> view matrix models
> #12,-0.26602,0.63325,0.72679,161.77,0.90962,0.41448,-0.028195,138.15,-0.3191,0.6536,-0.68628,147.62

> view matrix models
> #12,-0.15284,0.67533,0.7215,162.15,0.93603,0.3331,-0.1135,138.22,-0.31698,0.658,-0.68305,147.63

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.15284,0.67533,0.7215,150.14,0.93603,0.3331,-0.1135,139.31,-0.31698,0.658,-0.68305,145.63

> fitmap #12 inMap #9

Fit molecule FBXO22-cluster0_B.pdb (#12) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 6264 atoms  
average map value = 0.01432, steps = 92  
shifted from previous position = 7.55  
rotated from previous position = 14.3 degrees  
atoms outside contour = 4754, contour level = 0.025916  
  
Position of FBXO22-cluster0_B.pdb (#12) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
-0.32330010 0.51175524 0.79597966 145.55673879  
0.87726895 0.47745562 0.04934891 143.14383578  
-0.35479040 0.71424275 -0.60330844 141.25704059  
Axis 0.48237030 0.83486605 0.26517460  
Axis point 50.81561189 -0.00000000 39.28555144  
Rotation angle (degrees) 136.43362582  
Shift along axis 227.17595615  
  

> select subtract #12

Nothing selected  

> show #!8 models

> hide #!9 models

> hide #12 models

> hide #!8 models

> show #!9 models

> show #13 models

> select add #13

2536 atoms, 2559 bonds, 160 residues, 1 model selected  

> view matrix models #13,1,0,0,169.68,0,1,0,134.62,0,0,1,100.38

> view matrix models #13,1,0,0,129.92,0,1,0,158.38,0,0,1,103.69

> view matrix models #13,1,0,0,125.66,0,1,0,170.68,0,0,1,115.53

> view matrix models #13,1,0,0,131.81,0,1,0,169.76,0,0,1,115.57

> fitmap #13 inMap #9

Fit molecule SKP1-cluster0_A.pdb (#13) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 2536 atoms  
average map value = 0.0115, steps = 116  
shifted from previous position = 4.35  
rotated from previous position = 11 degrees  
atoms outside contour = 2123, contour level = 0.025916  
  
Position of SKP1-cluster0_A.pdb (#13) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.99400424 -0.10375006 0.03451810 132.62134676  
0.10788845 0.98193472 -0.15544864 164.32868551  
-0.01776672 0.15824072 0.98724071 117.10946969  
Axis 0.82117189 0.13687051 0.55402453  
Axis point 0.00000000 18.26009484 882.18276290  
Rotation angle (degrees) 11.01120915  
Shift along axis 196.27819317  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.16768,-0.76567,-0.62099,158.3,0.98541,-0.14877,-0.082648,136.5,-0.029107,-0.62579,0.77945,113.34

> view matrix models
> #13,-0.33663,-0.65511,-0.6764,163.2,0.93274,-0.3305,-0.14411,136.83,-0.12914,-0.67941,0.7223,115.58

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.33663,-0.65511,-0.6764,151.15,0.93274,-0.3305,-0.14411,134.13,-0.12914,-0.67941,0.7223,110.91

> view matrix models
> #13,-0.33663,-0.65511,-0.6764,151.93,0.93274,-0.3305,-0.14411,132.36,-0.12914,-0.67941,0.7223,109.65

> fitmap #13 inMap #9

Fit molecule SKP1-cluster0_A.pdb (#13) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 2536 atoms  
average map value = 0.01541, steps = 156  
shifted from previous position = 7.59  
rotated from previous position = 25.6 degrees  
atoms outside contour = 1886, contour level = 0.025916  
  
Position of SKP1-cluster0_A.pdb (#13) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
-0.49270313 -0.79679422 -0.34980366 152.17213174  
0.85426248 -0.51945687 -0.02000428 128.10938210  
-0.16576862 -0.30868031 0.93660943 122.14498317  
Axis -0.17120156 -0.10914341 0.97917197  
Axis point 48.46787857 117.27732412 0.00000000  
Rotation angle (degrees) 122.53232085  
Shift along axis 79.56654352  
  

> hide #13 models

> show #!8 models

> color #9 #ffffb20d models

> color #9 #ffffb234 models

> color #9 #ffffb236 models

> lighting simple

> lighting soft

> lighting full

> color #8 gold

> show #!10 models

> hide #!9 models

> volume #10 level 0.02995

> volume #10 level 0.01517

> volume #10 level -0.004033

> volume #10 level 0.002368

> volume #10 level 0.003892

> volume #10 level 0.02294

> ui tool show "Ramachandran Plot"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process  
func(*args, **kwargs)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to  
self._new_camera_position(residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position  
interpolate_camera(session, 0, frames=1)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera  
ncp, fcp = _get_clip_points(session, dist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points  
return (o+vd*dist*0.5, o+vd*dist*1.5)  
^  
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value  

> ui tool show "Side View"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process  
func(*args, **kwargs)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to  
self._new_camera_position(residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position  
interpolate_camera(session, 0, frames=1)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera  
ncp, fcp = _get_clip_points(session, dist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points  
return (o+vd*dist*0.5, o+vd*dist*1.5)  
^  
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process  
func(*args, **kwargs)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to  
self._new_camera_position(residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position  
interpolate_camera(session, 0, frames=1)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera  
ncp, fcp = _get_clip_points(session, dist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points  
return (o+vd*dist*0.5, o+vd*dist*1.5)  
^  
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process  
func(*args, **kwargs)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to  
self._new_camera_position(residue)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position  
interpolate_camera(session, 0, frames=1)  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera  
ncp, fcp = _get_clip_points(session, dist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points  
return (o+vd*dist*0.5, o+vd*dist*1.5)  
^  
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value  

> volume #10 level 0.0301

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> sequence chain #8/B

Alignment identifier is 8/B  

> select #8/B:26-36,38-47,49-62,82-92,130-139,202-209,236-245,298-312,339-349

1645 atoms, 1647 bonds, 100 residues, 1 model selected  

> select #8/B:56

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #8/B:56

16 atoms, 15 bonds, 1 residue, 1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!10 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!10 models

> view matrix models
> #8,0.99993,-0.01156,-0.0032668,2.3088,0.01156,0.99993,-0.00029013,-1.7053,0.0032699,0.00025235,0.99999,-0.7365

> select clear

> view

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!7 models

> hide #!7 models

> show #!5 models

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!6 models

> volume gaussian #6 bfactor 100

Opened 12182024_Amphista_Glacios_deepEMhancer.mrc gaussian as #14, grid size
320,320,320, pixel 0.95, shown at step 1, values float32  

> volume #10 level 0.02782

> volume #10 level -0.006166

> volume #10 level 0.005263

> volume #10 level 0.02386

> show #13 models

> ui mousemode right "translate selected models"

> select add #13

2536 atoms, 2559 bonds, 160 residues, 1 model selected  

> view matrix models
> #13,-0.4927,-0.79679,-0.3498,165.94,0.85426,-0.51946,-0.020004,179.7,-0.16577,-0.30868,0.93661,169.79

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #11 to #8/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 12182027_Amphista_model_8S7E_8Q68_fit.pdb, chain A (#8) with
Cluster0-TCF.pdb, chain A (#11), sequence alignment score = 576  
RMSD between 79 pruned atom pairs is 1.051 angstroms; (across all 128 pairs:
3.301)  
  

> hide #13 models

> select #8/B:20

14 atoms, 13 bonds, 1 residue, 1 model selected  

> ui mousemode right select

> select up

105 atoms, 105 bonds, 7 residues, 1 model selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #8/B:403

23 atoms, 22 bonds, 1 residue, 1 model selected  

> select up

71 atoms, 70 bonds, 5 residues, 1 model selected  

> select up

312 atoms, 315 bonds, 20 residues, 1 model selected  

> select up

333 atoms, 335 bonds, 22 residues, 1 model selected  

> select up

1803 atoms, 1822 bonds, 119 residues, 1 model selected  

> select up

1858 atoms, 1876 bonds, 123 residues, 1 model selected  

> select up

2222 atoms, 2242 bonds, 147 residues, 1 model selected  

> select up

2236 atoms, 2255 bonds, 148 residues, 1 model selected  

> select up

2650 atoms, 2673 bonds, 173 residues, 1 model selected  

> select up

2717 atoms, 2740 bonds, 177 residues, 1 model selected  

> select up

3722 atoms, 3757 bonds, 244 residues, 1 model selected  

> select up

3748 atoms, 3782 bonds, 246 residues, 1 model selected  

> select up

5189 atoms, 5236 bonds, 335 residues, 1 model selected  

> show #!10 models

> ui mousemode right "rotate selected models"

> hide #!8 models

> show #!8 models

> select add #8

9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected  

> select subtract #8

Nothing selected  

> select add #8

9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected  

> view matrix models
> #8,-0.050776,-0.98234,-0.1801,332.24,-0.9675,0.093113,-0.23511,316.58,0.24773,0.16231,-0.95514,231.81

> view matrix models
> #8,-0.40316,-0.91029,0.093985,334.57,-0.88572,0.36231,-0.29024,272.9,0.23015,-0.20026,-0.95233,287.18

> view matrix models
> #8,-0.40533,0.91417,-0.00064002,81.984,0.88635,0.39316,0.24456,-83.877,0.22382,0.098558,-0.96964,247

> view matrix models
> #8,0.63897,0.7332,0.23265,-86.807,0.72105,-0.67626,0.15088,112.15,0.26796,0.071341,-0.96079,242.88

> view matrix models
> #8,-0.86854,-0.49287,-0.052056,366.8,-0.49091,0.86998,-0.04636,101.34,0.068137,-0.014711,-0.99757,291.67

> view matrix models
> #8,-0.88027,-0.46419,-0.098213,371.34,-0.46362,0.88553,-0.029953,92.414,0.10087,0.019167,-0.99471,281.25

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.88027,-0.46419,-0.098213,371.21,-0.46362,0.88553,-0.029953,93.111,0.10087,0.019167,-0.99471,288.61

> view matrix models
> #8,-0.88027,-0.46419,-0.098213,383.15,-0.46362,0.88553,-0.029953,155.98,0.10087,0.019167,-0.99471,290.72

> view matrix models
> #8,-0.88027,-0.46419,-0.098213,383.74,-0.46362,0.88553,-0.029953,157.98,0.10087,0.019167,-0.99471,284.77

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.42759,0.86906,-0.2488,10.478,-0.90377,0.41684,-0.097187,304.24,0.019252,0.26642,0.96367,-33.182

> view matrix models
> #8,0.77352,0.60123,-0.20047,-10.647,-0.63227,0.75383,-0.17881,225.51,0.043614,0.26507,0.96324,-36.659

> volume #10 level 0.02553

> view matrix models
> #8,0.76877,0.63484,-0.077293,-33.348,-0.63567,0.7453,-0.20113,230.63,-0.070078,0.20376,0.97651,-12.231

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.76877,0.63484,-0.077293,-41.29,-0.63567,0.7453,-0.20113,160.36,-0.070078,0.20376,0.97651,-14.162

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.67531,0.73297,-0.081904,-40.626,-0.73298,0.65467,-0.1848,186.11,-0.081831,0.18483,0.97936,-10.016

> view matrix models
> #8,0.92495,0.34942,0.14956,-57.551,-0.33478,0.93529,-0.11468,73.385,-0.17995,0.056001,0.98208,23.493

> view matrix models
> #8,0.99272,-0.099665,0.067645,10.116,0.10567,0.99014,-0.091933,-5.6452,-0.057816,0.098412,0.99346,-3.1669

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.99272,-0.099665,0.067645,2.2475,0.10567,0.99014,-0.091933,-2.8917,-0.057816,0.098412,0.99346,-1.1003

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.98714,-0.15251,0.047811,13.821,0.15631,0.98363,-0.089662,-10.05,-0.033353,0.095982,0.99482,-4.7023

> ui tool show "Fit in Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #8 inMap #10

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) using 9225 atoms  
average map value = 0.01841, steps = 108  
shifted from previous position = 5.56  
rotated from previous position = 10.6 degrees  
atoms outside contour = 6516, contour level = 0.025532  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) coordinates:  
Matrix rotation and translation  
0.99999655 -0.00244054 -0.00097730 0.52642988  
0.00244123 0.99999678 0.00070534 -0.49302841  
0.00097557 -0.00070772 0.99999928 -0.11313285  
Axis -0.25954042 -0.35868970 0.89664958  
Axis point 211.23113280 208.89189162 0.00000000  
Rotation angle (degrees) 0.15597247  
Shift along axis -0.06122614  
  
Average map value = 0.01841 for 9225 atoms, 6516 outside contour  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #4 inMap #10

Fit map 12182024_Amphista_Glacios_3Dclass4.mrc in map
12182024_Amphista_Glacios_postprocess.mrc gaussian using 36656 points  
correlation = 0.8147, correlation about mean = 0.6883, overlap = 16.21  
steps = 56, shift = 1.48, angle = 0.868 degrees  
  
Position of 12182024_Amphista_Glacios_3Dclass4.mrc (#4) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) coordinates:  
Matrix rotation and translation  
0.99988562 0.00584419 -0.01394988 1.41668665  
-0.00585547 0.99998256 -0.00076808 -0.07536794  
0.01394514 0.00084968 0.99990240 -3.22359478  
Axis 0.05340490 -0.92085783 -0.38622372  
Axis point 193.32512548 0.00000000 94.64857300  
Rotation angle (degrees) 0.86784733  
Shift along axis 1.39008996  
  
Correlation = 0.8147, Correlation about mean = 0.6883, Overlap = 16.21  
  

> fitmap #8 inMap #4

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_3Dclass4.mrc (#4) using 9225 atoms  
average map value = 0.03868, steps = 56  
shifted from previous position = 0.529  
rotated from previous position = 0.463 degrees  
atoms outside contour = 180, contour level = 8.5775e-06  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_3Dclass4.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99985955 -0.00195433 0.01664564 -2.29841881  
0.00198688 0.99999615 -0.00193912 0.76665025  
-0.01664179 0.00197192 0.99985958 3.60031780  
Axis 0.11589162 0.98637224 0.11678583  
Axis point 208.72035729 0.00000000 146.17829889  
Rotation angle (degrees) 0.96683567  
Shift along axis 0.91030116  
  
Average map value = 0.03868 for 9225 atoms, 180 outside contour  

> fitmap #8 inMap #1

Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_3Dclass1.mrc (#1) using 9225 atoms  
average map value = 0.04031, steps = 52  
shifted from previous position = 0.782  
rotated from previous position = 0.702 degrees  
atoms outside contour = 661, contour level = 1.0157e-05  
  
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_3Dclass1.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99991779 -0.00315908 0.01242759 -1.22912133  
0.00316312 0.99999496 -0.00030561 -0.01164305  
-0.01242656 0.00034490 0.99992273 2.25993858  
Axis 0.02535732 0.96882574 0.24644209  
Axis point 171.03150715 0.00000000 101.08386603  
Rotation angle (degrees) 0.73495019  
Shift along axis 0.51449666  
  
Average map value = 0.04031 for 9225 atoms, 661 outside contour  

> hide #!8 models

> show #!8 models

> hide #!10 models

> show #!10 models

> volume #10 level 0.002087

> volume #10 level 0.002994


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: Z1AY0010LB/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 86 days, 14 hours, 37 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL P2422H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2422H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-LigandRecognizer: 0.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-maskChains: 1.4
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    pyqtgraph: 0.13.7
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.12
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 9 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, 9 months ago

Resolution: → duplicate
Status: assigned → closed
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