id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16576	Graphics crash, macOS 15.2, Radeon Pro Vega 56	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.2-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: Aborted

Thread 0x000070002e2ae000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002d2ab000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002c2a8000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/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 ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002b2a5000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002a2a2000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002929f000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002829c000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700027299000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700026296000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700025293000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700024290000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002328d000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070002228a000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700021287000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700020284000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001f281000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001e27e000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001d27b000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001c278000 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00007ff8498164c0 (most recent call first):
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 556 in swap_buffers
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback
  File ""/opt/sbgrid/i386-mac/chimerax/1.8/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 ""/opt/sbgrid/i386-mac/chimerax/1.8/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 ""/opt/sbgrid/i386-mac/chimerax/1.8/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.pdb_lib._load_libs, 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, chimerax.surface._surface, 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 (total: 53)


{""app_name"":""ChimeraX"",""timestamp"":""2025-01-07 16:14:17.00 -0500"",""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 15.2 (24C101)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""3421FC72-7DCC-468F-AD48-0E01365314CD""}
{
  ""uptime"" : 11000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""iMacPro1,1"",
  ""coalitionID"" : 469,
  ""osVersion"" : {
    ""train"" : ""macOS 15.2"",
    ""build"" : ""24C101"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2025-01-07 16:13:55.4540 -0500"",
  ""codeSigningMonitor"" : 0,
  ""incident"" : ""3421FC72-7DCC-468F-AD48-0E01365314CD"",
  ""pid"" : 2139,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2025-01-07 12:07:57.9113 -0500"",
  ""procStartAbsTime"" : 81281993985,
  ""procExitAbsTime"" : 11973535904611,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/programs\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX"",
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    ""path"" : ""\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib"",
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    ""CFBundleShortVersionString"" : ""21.0.27"",
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    ""path"" : ""\/usr\/lib\/dyld"",
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  ""legacyInfo"" : {
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    ""queue"" : ""com.apple.main-thread""
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},
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}
===== 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/navid/Downloads/cryosparc_P21_J871_008_volume_map.mrc

Opened cryosparc_P21_J871_008_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.847, shown at level 0.0716, step 2, values float32  

> open /Users/navid/Downloads/cryosparc_P21_J870_009_volume_map.mrc

Opened cryosparc_P21_J870_009_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.847, shown at level 0.0586, step 2, values float32  

> volume #0-100 step 1

> volume #1 level 0.1915

> volume #2 level 0.1897

> ui dockable false Log

> ui dockable false ""Model Panel""

> ui dockable false ""Volume Viewer""

> volume #2 level 0.3208

> volume #2 level 0.325

> volume #1 level 0.3114

> open /Users/navid/Downloads/cryosparc_P21_J872_010_volume_map.mrc

Opened cryosparc_P21_J872_010_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.847, shown at level 0.053, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.2669

> open ""/Users/navid/Library/CloudStorage/GoogleDrive-nav2686@gmail.com/My
> Drive/Science/Projects/RNAP/RNAP_WhiB1_20250101_ALIGNED_J642_512BOX.pdb""

Chain information for RNAP_WhiB1_20250101_ALIGNED_J642_512BOX.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
J | No description available  
M | No description available  
O | No description available  
P | No description available  
Z | No description available  
  

> hide atoms

> show cartoons

> fitmap #4 inMap #1

Fit molecule RNAP_WhiB1_20250101_ALIGNED_J642_512BOX.pdb (#4) to map
cryosparc_P21_J871_008_volume_map.mrc (#1) using 60060 atoms  
average map value = 0.1439, steps = 88  
shifted from previous position = 1.65  
rotated from previous position = 0.235 degrees  
atoms outside contour = 57771, contour level = 0.3114  
  
Position of RNAP_WhiB1_20250101_ALIGNED_J642_512BOX.pdb (#4) relative to
cryosparc_P21_J871_008_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999188 -0.00133214 0.00380231 -0.36117172  
0.00132911 0.99999880 0.00079830 -2.07042204  
-0.00380337 -0.00079324 0.99999245 1.30348219  
Axis -0.19377065 0.92599719 0.32400948  
Axis point 463.76858913 0.00000000 168.59097220  
Rotation angle (degrees) 0.23530031  
Shift along axis -1.42487991  
  

> show atoms

> style stick

Changed 60060 atom styles  

> volume #1 color #b2b2b280

> open /Users/navid/Downloads/cryosparc_P21_J1046_002_volume_map.mrc

Opened cryosparc_P21_J1046_002_volume_map.mrc as #5, grid size 512,512,512,
pixel 0.847, shown at level 0.0508, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.1028

> volume #5 level 0.08244

> volume #5 level 0.313

> open /Users/navid/Downloads/cryosparc_P21_J1032_006_volume_map.mrc

Opened cryosparc_P21_J1032_006_volume_map.mrc as #6, grid size 512,512,512,
pixel 0.847, shown at level 0.0569, step 2, values float32  

> volume #6 step 1

> volume #6 level 0.1236

> volume #6 level 0.1183

> open /Users/navid/Downloads/cryosparc_P21_J1034_007_volume_map.mrc

Opened cryosparc_P21_J1034_007_volume_map.mrc as #7, grid size 512,512,512,
pixel 0.847, shown at level 0.0633, step 2, values float32  

> volume #7 step 1

> volume #7 level 0.1206


===== 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  

> open /Users/navid/Downloads/cryosparc_P21_J1076_003_volume_map.mrc

Opened cryosparc_P21_J1076_003_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.847, shown at level 0.0496, step 2, values float32  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro Vega 56 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: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: 8-Core Intel Xeon W
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 1 MB
      L3 Cache: 11 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.12093.0.0,0)
      OS Loader Version: 582~2898

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 4 hours, 12 minutes

Graphics/Displays:

    Radeon Pro Vega 56:

      Chipset Model: Radeon Pro Vega 56
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6867
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XL-018
      Option ROM Version: 113-D05001A1XL-018
      EFI Driver Version: 01.01.114
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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-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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Graphics		nonchimerax						all	ChimeraX