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Opened 4 days ago
Closed 3 days ago
#19884 closed defect (duplicate)
Crash in expose event dispatched from within QOpenGLContext.makeCurrent(), macOS 26
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x00000003110c7000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003100bb000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030f0af000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030e0a3000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030d097000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030c08b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030b07f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030a073000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000309067000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030805b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030704f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000306043000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000305037000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000207223080 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 143 in render
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, cython.cimports.libc.math, 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._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, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.connect_structure._cs, chimerax.atom_search.ast, chimerax.chem_group._chem_group, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, PIL._imaging, kiwisolver._cext, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 122)
{"app_name":"ChimeraX","timestamp":"2026-02-23 15:11:40.00 +0200","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3 (25D125)","roots_installed":0,"name":"ChimeraX","incident_id":"F907CAF8-FEDD-42A8-9A54-1DFB125F5DEB"}
{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 1011626602,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 18554,
"osVersion" : {
"train" : "macOS 26.3",
"build" : "25D125",
"releaseType" : "User"
},
"captureTime" : "2026-02-23 15:09:51.7270 +0200",
"codeSigningMonitor" : 2,
"incident" : "F907CAF8-FEDD-42A8-9A54-1DFB125F5DEB",
"pid" : 16293,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-02-23 13:24:43.9350 +0200",
"procStartAbsTime" : 4044923528847,
"procExitAbsTime" : 4196310242713,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7153AE3B-C72D-5E6A-802F-76E7C91C4E5A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "31622414-D700-AB9C-C51E-CAAD8E597596",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "575EC0E3-5A59-4C85-82FE-D6A5E505DE42",
"wakeTime" : 19851,
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Model: Mac16,8, BootROM 13822.81.10, proc 14:10:4 processors, 48 GB, SMC
Graphics: Apple M4 Pro, Apple M4 Pro, Built-In
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4388), wl0: Dec 6 2025 00:30:14 version 23.41.8.0.41.51.201 FWID 01-990604ea
IO80211_driverkit-1540.16 "IO80211_driverkit-1540.16" Jan 27 2026 21:04:24
AirPort:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2
> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel
> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse_and_help command "mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/avenka/Phenix/cryosparc_P1_J559_008_volume_map_zflip.mrc format
> mrc
Opened cryosparc_P1_J559_008_volume_map_zflip.mrc as #1, grid size
512,512,512, pixel 0.828, shown at level 0.0114, step 1, values float32
> open
> /Users/avenka/Phenix/RealSpaceRefine_27/cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
Summary of feedback from opening
/Users/avenka/Phenix/RealSpaceRefine_27/cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 801
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "25" on line 159
Bad residue range for struct_conf "26" on line 160
Bad residue range for struct_conf "64" on line 198
Bad residue range for struct_conf "71" on line 205
Bad residue range for struct_conf "72" on line 206
Invalid sheet range for struct_sheet_range "12 1" on line 791
Invalid sheet range for struct_sheet_range "13 1" on line 792
Invalid sheet range for struct_sheet_range "14 1" on line 793
Invalid sheet range for struct_sheet_range "15 1" on line 794
Invalid sheet range for struct_sheet_range "16 1" on line 795
1 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for
cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif #2
---
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
> select ~sel & ##selected
Nothing selected
> phenix location /Applications/Phenix/phenix-1.21.2-5419
Using Phenix installation /Applications/Phenix/phenix-1.21.2-5419
> runscript /Users/avenka/Chimera/chimera_startup.py
> hide surfaces
> show cartoons
> hide atoms
> show atoms
> hide atoms
> style ball
Changed 25786 atom styles
> hide #!1 models
> show surfaces
> hide surfaces
> show #!1 models
> color #1 #d783ffff models
> color #1 #ff85ffff models
> color #1 #ff8ad8ff models
> color #1 #005493ff models
> color #1 #0096ffff models
> color #1 #00fdffff models
> color #1 #73fdffff models
> color #1 #73fcd6ff models
> color #1 #73fa79ff models
> color #1 #ff9300ff models
> color #1 #941100ff models
> color #1 #945200ff models
> color #1 #424242ff models
> color #1 #5e5e5eff models
> color #1 #797979ff models
> color #1 #919191ff models
> color #1 #9191919a models
> color #1 #91919180 models
> color #1 #d783ffff models
> color #1 #d783ff7d models
> color #1 #942193ff models
> color #1 #941751ff models
> color #1 #009193ff models
> color #1 #005493ff models
> color #1 #919191ff models
> color #1 #941100ff models
> color #1 #945200ff models
> color #1 #94520090 models
> color #1 #94520080 models
> volume #1 level 0.04573
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 68
shifted from previous position = 0.821
rotated from previous position = 1.17 degrees
atoms outside contour = 12796, contour level = 0.045734
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994527 -0.01021184 -0.00227366 1.96900846
0.01025000 0.99979510 0.01745561 -6.34297659
0.00209494 -0.01747796 0.99984505 3.58169120
Axis -0.85789511 -0.10728378 0.50249993
Axis point 0.00000000 178.98483963 360.61639686
Rotation angle (degrees) 1.16662538
Shift along axis 0.79109534
> volume #1 level 0.1012
> select add #2
25786 atoms, 26051 bonds, 509 pseudobonds, 1592 residues, 3 models selected
> select subtract #2
6 models selected
> select add #2
25786 atoms, 26051 bonds, 509 pseudobonds, 1592 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010212,-0.0022737,0.031366,0.01025,0.9998,0.017456,-8.2915,0.0020949,-0.017478,0.99985,8.724
> select subtract #2
6 models selected
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 88
shifted from previous position = 5.84
rotated from previous position = 0.011 degrees
atoms outside contour = 20045, contour level = 0.10123
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994638 -0.01012733 -0.00216334 1.92778569
0.01016384 0.99979366 0.01758815 -6.36017685
0.00198477 -0.01760920 0.99984298 3.62136214
Axis -0.86186460 -0.10157332 0.49686242
Axis point 0.00000000 180.33141256 359.20595398
Rotation angle (degrees) 1.17002116
Shift along axis 0.78385279
> surface dust #1 size 8.28
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 40
shifted from previous position = 0.00236
rotated from previous position = 0.00378 degrees
atoms outside contour = 20046, contour level = 0.10123
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994683 -0.01009279 -0.00211335 1.90807689
0.01012846 0.99979356 0.01761382 -6.36000891
0.00193514 -0.01763429 0.99984263 3.63628925
Axis -0.86312655 -0.09913591 0.49516122
Axis point 0.00000000 180.98546204 358.78838914
Rotation angle (degrees) 1.16999547
Shift along axis 0.78414287
> volume style mesh
> volume style image
> volume style surface
> ui mousemode right select
> lighting full
> lighting simple
> ui tool show "Selection Inspector"
> ui tool show "Side View"
> view
> color bfactor
25786 atoms, 1592 residues, 6 surfaces, atom bfactor range 57.2 to 422
> hbonds reveal true
777 hydrogen bonds found
> ~hbonds
> show atoms
> hide cartoons
> volume #1 change image level -0.003346,0 level 0.01135,0.8 level 0.5315,1
> volume #1 level 0.08508
> hide #!2 models
> volume #1 level 0.09226
> volume #1 level 0.112
> select clear
> ui mousemode right translate
> show #!2 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 98 residues in model #2 to IUPAC-IUB
standards.
Chain information for
cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
2.2/C | No description available
2.2/D | No description available
2.2/E | No description available
2.2/F | No description available
> clipper associate #1 toModel #2
Opened cryosparc_P1_J559_008_volume_map_zflip.mrc as #2.1.1.1, grid size
512,512,512, pixel 0.828, shown at step 1, values float32
> isolde sim start /A-F
ISOLDE: started sim
Average map value = 0.08309 for 25786 atoms, 20876 outside contour
> fitmap #2.2 inMap #2.1.1.1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif
(#2.2) to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#2.1.1.1) using
25786 atoms
average map value = 0.08347, steps = 28
shifted from previous position = 0.0454
rotated from previous position = 0.0658 degrees
atoms outside contour = 20827, contour level = 0.15353
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.cif (#2.2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#2.1.1.1) coordinates:
Matrix rotation and translation
0.99999939 -0.00108136 0.00022404 0.14591462
0.00108129 0.99999937 0.00031622 -0.33515581
-0.00022439 -0.00031598 0.99999992 0.10594800
Axis -0.27518468 0.19519460 0.94136733
Axis point 308.98415648 133.27645773 0.00000000
Rotation angle (degrees) 0.06581413
Shift along axis -0.00583809
===== Log before crash end =====
Log:
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2
> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel
> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse_and_help command "mousemode alt right
> contour ; mousemode right clip ; mousemode alt left 'translate selected
> models' ; mousemode shift left 'rotate selected models' ; mousemode alt
> control left 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/avenka/Phenix/cryosparc_P1_J559_008_volume_map_zflip.mrc format
> mrc
Opened cryosparc_P1_J559_008_volume_map_zflip.mrc as #1, grid size
512,512,512, pixel 0.828, shown at level 0.0114, step 1, values float32
> open
> /Users/avenka/Phenix/RealSpaceRefine_27/cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb
> format pdb
Chain information for
cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb #2
---
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
> show cartoons
> hide atoms
> style ball
Changed 25786 atom styles
> style stick
Changed 25786 atom styles
> hide #!1 models
> show surfaces
> hide surfaces
> show atoms
> hide cartoons
> color bychain
> show #!1 models
> color #1 #d783ffff models
> color #1 #d783ff8b models
> color #1 #d783ff80 models
> volume #1 level 0.01648
> volume #1 level 0.02538
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 68
shifted from previous position = 0.821
rotated from previous position = 1.17 degrees
atoms outside contour = 8771, contour level = 0.025381
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994521 -0.01021839 -0.00227399 1.97042028
0.01025655 0.99979500 0.01745768 -6.34467796
0.00209514 -0.01748005 0.99984502 3.58202075
Axis -0.85778227 -0.10726970 0.50269553
Axis point 0.00000000 178.97302423 360.67277228
Rotation angle (degrees) 1.16691793
Shift along axis 0.79106592
> show cartoons
> hide atoms
> select add #2
25786 atoms, 26051 bonds, 2 pseudobonds, 1592 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010218,-0.002274,1.3303,0.010257,0.99979,0.017458,-8.9578,0.0020951,-0.01748,0.99985,10.246
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06156, steps = 72
shifted from previous position = 4.61
rotated from previous position = 1.93 degrees
atoms outside contour = 9283, contour level = 0.025381
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99984993 0.01620662 0.00612007 -7.59530758
-0.01619696 0.99986750 -0.00162492 -0.12875742
-0.00614559 0.00152554 0.99997995 3.81445331
Axis 0.09055572 0.35255976 -0.93139749
Axis point 81.69913135 445.46285237 0.00000000
Rotation angle (degrees) 0.99671863
Shift along axis -4.28596546
> hide sel cartoons
> show sel atoms
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06156, steps = 48
shifted from previous position = 0.00504
rotated from previous position = 0.0204 degrees
atoms outside contour = 9281, contour level = 0.025381
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99984740 0.01633957 0.00617993 -7.63691974
-0.01632781 0.99986479 -0.00194989 -0.02450475
-0.00621096 0.00184869 0.99997900 3.75754808
Axis 0.10808541 0.35257195 -0.92952168
Axis point 88.28911915 439.59092347 0.00000000
Rotation angle (degrees) 1.00686157
Shift along axis -4.32680169
> view matrix models
> #2,0.99985,0.01634,0.0061799,-8.4953,-0.016328,0.99986,-0.0019499,0.26563,-0.006211,0.0018487,0.99998,5.2844
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98843,-0.11248,0.10178,0.13568,0.099762,0.98745,0.12243,-48.371,-0.11427,-0.11086,0.98724,54.234
> view matrix models
> #2,0.63006,-0.76993,-0.10113,255.66,0.76942,0.60136,0.21531,-129.97,-0.10495,-0.21347,0.9713,76.94
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.63006,-0.76993,-0.10113,257.72,0.76942,0.60136,0.21531,-132.42,-0.10495,-0.21347,0.9713,71.456
> view matrix models
> #2,0.63006,-0.76993,-0.10113,264.48,0.76942,0.60136,0.21531,-128.34,-0.10495,-0.21347,0.9713,71.469
> volume #1 level 0.1091
> show sel cartoons
> hide sel atoms
> view matrix models
> #2,0.63006,-0.76993,-0.10113,250.76,0.76942,0.60136,0.21531,-123.77,-0.10495,-0.21347,0.9713,73.583
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97871,-0.19968,-0.047526,47.848,0.20018,0.87734,0.43611,-107.88,-0.045388,-0.43634,0.89864,122.61
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97871,-0.19968,-0.047526,57.636,0.20018,0.87734,0.43611,-110.74,-0.045388,-0.43634,0.89864,124.98
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98872,-0.14471,0.038759,25.68,0.11074,0.88022,0.46146,-97.878,-0.10089,-0.45196,0.88631,142.57
> view matrix models
> #2,0.9695,-0.21272,-0.12171,78.164,0.22228,0.97239,0.07112,-56.85,0.10322,-0.096004,0.99001,3.714
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 136
shifted from previous position = 3.56
rotated from previous position = 14.2 degrees
atoms outside contour = 20515, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994652 -0.01011729 -0.00214235 1.91990026
0.01015348 0.99979335 0.01761124 -6.36409519
0.00196372 -0.01763205 0.99984261 3.63015046
Axis -0.86245665 -0.10048175 0.49605639
Axis point 0.00000000 180.61080679 359.00929382
Rotation angle (degrees) 1.17074434
Shift along axis 0.78440398
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010117,-0.0021423,-1.2187,0.010153,0.99979,0.017611,-6.0876,0.0019637,-0.017632,0.99984,7.8602
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96448,0.12654,-0.23188,27.254,-0.12118,0.99193,0.037306,19.05,0.23473,-0.007883,0.97203,-37.347
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96448,0.12654,-0.23188,30.279,-0.12118,0.99193,0.037306,11.811,0.23473,-0.007883,0.97203,-36.32
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.93584,-0.091789,-0.34027,104.65,0.01548,0.97526,-0.22051,41.628,0.3521,0.20109,0.91411,-91.867
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.93584,-0.091789,-0.34027,100.83,0.01548,0.97526,-0.22051,49.27,0.3521,0.20109,0.91411,-92.095
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.0537, steps = 104
shifted from previous position = 6.6
rotated from previous position = 6.34 degrees
atoms outside contour = 21452, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.96360151 -0.01430515 -0.26695972 68.80085531
-0.03886002 0.98046720 -0.19280551 52.65581295
0.26450336 0.19616174 0.94422378 -77.91044535
Axis 0.59019074 -0.80640359 -0.03725778
Axis point 338.53102992 0.00000000 209.24942069
Rotation angle (degrees) 19.24005259
Shift along axis 1.04656143
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99902,0.0012894,-0.044248,10.389,0.0012188,0.9984,0.056612,-12.943,0.04425,-0.05661,0.99742,9.4238
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 88
shifted from previous position = 6.3
rotated from previous position = 3.35 degrees
atoms outside contour = 20522, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994638 -0.01011859 -0.00220417 1.93224659
0.01015569 0.99979478 0.01752883 -6.34113208
0.00202635 -0.01755028 0.99984393 3.61412347
Axis -0.86111578 -0.10384993 0.49768946
Axis point 0.00000000 180.23797807 359.16430702
Rotation angle (degrees) 1.16710440
Shift along axis 0.79334922
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99995,-0.010119,-0.0022042,1.5273,0.010156,0.99979,0.017529,-5.1177,0.0020263,-0.01755,0.99984,7.492
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98704,-0.081136,-0.13842,48.104,0.070566,0.99432,-0.079638,4.0723,0.1441,0.068839,0.98717,-37.639
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98704,-0.081136,-0.13842,47.525,0.070566,0.99432,-0.079638,3.9883,0.1441,0.068839,0.98717,-36.599
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98739,-0.083732,-0.13436,47.118,0.07423,0.99447,-0.074245,2.0281,0.13983,0.063336,0.98815,-34.771
> view matrix models
> #2,0.9669,-0.097398,-0.23585,76.013,0.06576,0.98818,-0.13849,18.88,0.24655,0.11839,0.96187,-63.053
> open /Users/avenka/Downloads/cryosparc_P1_J559_008_volume_map.mrc format mrc
Opened cryosparc_P1_J559_008_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.828, shown at level 0.0114, step 1, values float32
> hide #!1 models
> volume #3 level 0.09771
> view matrix models
> #2,-0.57582,-0.78641,-0.22358,541.49,-0.62569,0.5999,-0.49863,322.25,0.52626,-0.14723,-0.83748,318.23
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.57582,-0.78641,-0.22358,590.46,-0.62569,0.5999,-0.49863,246.32,0.52626,-0.14723,-0.83748,326.76
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.2554,-0.87338,-0.41471,581.71,-0.87874,0.38858,-0.27717,295.97,0.40322,0.29364,-0.86671,267.93
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.2554,-0.87338,-0.41471,531.08,-0.87874,0.38858,-0.27717,369.97,0.40322,0.29364,-0.86671,245.53
> color #3 #ffffb280 models
> color #3 #945200ff models
> color #3 #94520084 models
> color #3 #94520080 models
> fitmap #2 inMap #3
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map.mrc (#3) using 25786 atoms
average map value = 0.05534, steps = 132
shifted from previous position = 4.61
rotated from previous position = 10.4 degrees
atoms outside contour = 21465, contour level = 0.097709
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.09187478 -0.86703126 -0.48970993 513.31700694
-0.89143621 0.29076595 -0.34755812 405.93202181
0.44373473 0.40461334 -0.79961712 201.83015587
Axis 0.62731587 -0.77849889 -0.02035389
Axis point 377.03500646 0.00000000 205.13923181
Rotation angle (degrees) 143.16477796
Shift along axis 1.88624623
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.083275,-0.84732,-0.52452,514.89,-0.86996,0.31853,-0.37644,401.85,0.48604,0.42496,-0.76366,180.99
> view matrix models
> #2,0.01237,-0.80206,-0.59712,500.89,-0.74479,0.39106,-0.5407,395.62,0.66718,0.45142,-0.59253,100.61
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.01237,-0.80206,-0.59712,513.64,-0.74479,0.39106,-0.5407,403.62,0.66718,0.45142,-0.59253,90.903
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.046374,-0.85805,-0.51146,499.67,-0.84064,0.24306,-0.484,442.29,0.53961,0.4524,-0.71004,142.81
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.046374,-0.85805,-0.51146,485.94,-0.84064,0.24306,-0.484,440.17,0.53961,0.4524,-0.71004,147.05
> view matrix models
> #2,0.046374,-0.85805,-0.51146,486.65,-0.84064,0.24306,-0.484,440.48,0.53961,0.4524,-0.71004,146.86
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.6008,-0.72474,-0.33733,304.73,-0.79821,-0.56685,-0.20379,538.81,-0.043515,0.3917,-0.91906,327.31
> view matrix models
> #2,-0.2162,-0.81429,-0.53869,538.89,-0.91399,0.36282,-0.18162,366.45,0.34334,0.45309,-0.8227,212.29
> view matrix models
> #2,0.11003,-0.8337,-0.54115,474.54,-0.88871,0.16127,-0.42916,455.78,0.44506,0.52814,-0.72318,153.99
> fitmap #2 inMap #3
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map.mrc (#3) using 25786 atoms
average map value = 0.05966, steps = 136
shifted from previous position = 3.37
rotated from previous position = 12.6 degrees
atoms outside contour = 20775, contour level = 0.097709
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.15285460 -0.84843563 -0.50674692 463.93388237
-0.76689194 0.22158013 -0.60231138 456.37223157
0.62330749 0.48068620 -0.61678890 101.06362099
Axis 0.69097788 -0.72100124 0.05202679
Axis point 416.71588201 0.00000000 223.26552193
Rotation angle (degrees) 128.40214273
Shift along axis -3.21887912
> hide #!3 models
> show #!1 models
> runscript /Users/avenka/Chimera/chimera_startup.py
[Repeated 1 time(s)]FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> runscript /Users/avenka/Chimera/chimera_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> phenix location /Applications/Phenix/phenix-1.21.2-5419
Using Phenix installation /Applications/Phenix/phenix-1.21.2-5419
> view matrix models
> #2,0.37912,0.89926,0.21819,-100.2,-0.84492,0.43256,-0.31465,367.64,-0.37733,-0.065065,0.92379,95.073
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.37912,0.89926,0.21819,-102.41,-0.84492,0.43256,-0.31465,364.1,-0.37733,-0.065065,0.92379,116.57
> view matrix models
> #2,0.37912,0.89926,0.21819,-97.95,-0.84492,0.43256,-0.31465,366.74,-0.37733,-0.065065,0.92379,119.27
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.86692,0.18176,0.46412,-105.41,-0.36181,0.86993,0.33514,35.161,-0.34284,-0.45846,0.81992,215.51
> view matrix models
> #2,0.95112,0.044574,0.3056,-60.893,-0.056164,0.99799,0.029234,9.6969,-0.30369,-0.044969,0.95171,93.586
> view matrix models
> #2,0.9994,-0.031829,-0.013831,13.127,0.030364,0.99495,-0.095663,18.811,0.016806,0.095186,0.99532,-12.387
> view matrix models
> #2,0.96779,0.040366,-0.24849,55.157,-0.076511,0.98753,-0.13757,51.888,0.23984,0.15215,0.95882,-63.432
> view matrix models
> #2,0.96724,-0.24698,0.058649,48.838,0.24958,0.96744,-0.042008,-33.291,-0.046365,0.05527,0.99739,8.7539
Average map value = 0.04623 for 25786 atoms, 22347 outside contour
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06195, steps = 128
shifted from previous position = 12.2
rotated from previous position = 9.75 degrees
atoms outside contour = 20858, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99208033 -0.12229480 -0.02864614 34.34093797
0.12308916 0.99200529 0.02783080 -33.67161185
0.02501356 -0.03113642 0.99920210 1.28512125
Axis -0.22854516 -0.20797427 0.95105931
Axis point 289.98274086 262.72939976 0.00000000
Rotation angle (degrees) 7.41213390
Shift along axis 0.37660010
> view matrix models
> #2,0.99843,-0.0027311,0.055991,-9.8315,0.010553,0.99011,-0.13989,26.414,-0.055055,0.14026,0.98858,-14.942
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99843,-0.0027311,0.055991,-10.925,0.010553,0.99011,-0.13989,29.952,-0.055055,0.14026,0.98858,-8.0729
> view matrix models
> #2,0.99843,-0.0027311,0.055991,-17.462,0.010553,0.99011,-0.13989,35.365,-0.055055,0.14026,0.98858,-8.3464
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98588,-0.077829,-0.14829,44.465,0.053032,0.98497,-0.16438,32.703,0.15885,0.1542,0.97519,-53.525
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98588,-0.077829,-0.14829,48.279,0.053032,0.98497,-0.16438,29.396,0.15885,0.1542,0.97519,-52.84
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98786,-0.13066,-0.083988,44.999,0.14392,0.97335,0.17855,-60.86,0.058421,-0.18847,0.98034,38.053
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98786,-0.13066,-0.083988,46.482,0.14392,0.97335,0.17855,-60.595,0.058421,-0.18847,0.98034,37.278
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96337,-0.25119,-0.093886,78.674,0.26085,0.959,0.11082,-67.812,0.0622,-0.13125,0.9894,22.719
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96337,-0.25119,-0.093886,80.549,0.26085,0.959,0.11082,-70.825,0.0622,-0.13125,0.9894,21.371
> ui mousemode right translate
> select subtract #2
6 models selected
> show atoms
> hide cartoons
> fitmap #2 inMap #1
Fit molecule cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
to map cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) using 25786 atoms
average map value = 0.06467, steps = 152
shifted from previous position = 4.88
rotated from previous position = 16.1 degrees
atoms outside contour = 20515, contour level = 0.10909
Position of cryosparc_P1_J559_008_volume_map_real_space_refined_027.pdb (#2)
relative to cryosparc_P1_J559_008_volume_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99994659 -0.01010822 -0.00215449 1.92046438
0.01014460 0.99979352 0.01760702 -6.36320804
0.00197606 -0.01762793 0.99984266 3.62598808
Axis -0.86254020 -0.10111454 0.49578246
Axis point 0.00000000 180.42349393 359.01162573
Rotation angle (degrees) 1.17035379
Shift along axis 0.78463643
> volume #1 level 0.05067
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: Z1FF000KKKS/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 Performance and 4 Efficiency)
Memory: 48 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 7 days, 23 hours, 11 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 4
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: Yes
Connection Type: Internal
P27h-20:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
LEN P27h-10:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-ChopChopMF: 1.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-clix: 0.2.5
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-crai: 0.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.4.12
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RMF: 0.16
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cripser: 0.0.22
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
DiffFit: 0.7.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
finufft: 2.4.1
fonttools: 4.58.4
fsspec: 2025.7.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
pandas: 2.3.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 26.0.1
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt5: 5.15.11
PyQt5-Qt5: 5.15.18
PyQt5_sip: 12.17.2
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.7
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
torch: 2.2.0
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 days ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 |
comment:2 by , 3 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 → Crash in expose event dispatched from within QOpenGLContext.makeCurrent(), macOS 26 |
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This ChimeraX crash is caused by a bug in the Qt window toolkit version 6.8.2 when redrawing the status line. It has only been observed with macOS 26. We have no way to fix this and are hoping a new Qt window toolkit version will fix it. The ChimeraX daily build is using Qt 6.10.2 and this crash has not been reported in that Qt version, although it was reported once a month ago in Qt 6.10.1 (#19773). You may want to try the daily build of ChimeraX is crashing more than this one time.
This crash is in Qt QOpenGLContext.makeCurrent() which catastrophically dispatches an expose event and later crashes on swap_buffers. This may have been fixed in Qt 6.9 and ChimeraX 1.11.