![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Closed 2 months ago
#18603 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fb7220c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 118)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,13",
"coalitionID" : 10454,
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"build" : "24G84",
"releaseType" : "User"
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"captureTime" : "2025-08-21 16:41:06.5882 -0700",
"codeSigningMonitor" : 1,
"incident" : "3CA22345-C71D-45A7-9774-375DACDD2BCA",
"pid" : 40910,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-21 14:37:48.9486 -0700",
"procStartAbsTime" : 6612778836633,
"procExitAbsTime" : 6752095838176,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "22A027BA-0761-EF5A-B287-9A07B43A388A",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "1B62F6C1-3FE1-4FCE-8036-28E6EFFE17F6",
"sip" : "enabled",
"vmRegionInfo" : "0x2617b87134f8 is not in any region. Bytes after previous region: 41402284193017 Bytes before following region: 63669795736328\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":40910},
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"uuid" : "bcc13c1e-fb0b-3997-8606-38716d6d27bf",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_hausdorff.cpython-311-darwin.so",
"name" : "_hausdorff.cpython-311-darwin.so"
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{
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"uuid" : "b022000b-cfb9-332f-8c69-0b86e44dcef4",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ufuncs.cpython-311-darwin.so",
"name" : "_ufuncs.cpython-311-darwin.so"
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"uuid" : "5aa07cfb-914e-38bc-9e47-54882d97d620",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/libsf_error_state.dylib",
"name" : "libsf_error_state.dylib"
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{
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"uuid" : "3138361d-7680-3f2c-9f0a-010f1094a543",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ufuncs_cxx.cpython-311-darwin.so",
"name" : "_ufuncs_cxx.cpython-311-darwin.so"
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{
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"uuid" : "2f1b4b18-a1b2-33d4-a797-d83844dcf802",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_special_ufuncs.cpython-311-darwin.so",
"name" : "_special_ufuncs.cpython-311-darwin.so"
},
{
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"size" : 98304,
"uuid" : "5337aa3d-50d9-39a6-b22f-ea9c39a6776c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_gufuncs.cpython-311-darwin.so",
"name" : "_gufuncs.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
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"size" : 131072,
"uuid" : "44fab445-4a90-39f0-932e-98f1d5342229",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_specfun.cpython-311-darwin.so",
"name" : "_specfun.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5993971712,
"size" : 32768,
"uuid" : "09589b0b-38f8-372a-b5ff-185089c86fa5",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_comb.cpython-311-darwin.so",
"name" : "_comb.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 6440288256,
"size" : 65536,
"uuid" : "04579fae-e25e-310b-9d9a-eb6567460a9a",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ellip_harm_2.cpython-311-darwin.so",
"name" : "_ellip_harm_2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13588332544,
"size" : 425984,
"uuid" : "790f202f-d1d8-3b1a-a2a4-6cedbfc5ae6f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_pybind.cpython-311-darwin.so",
"name" : "_distance_pybind.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13587120128,
"size" : 638976,
"uuid" : "1054ddef-4190-3041-95be-e16119344536",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/transform\/_rotation.cpython-311-darwin.so",
"name" : "_rotation.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 6008619008,
"size" : 32768,
"uuid" : "d08bc19e-a473-3d91-9401-19d68cabbac8",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_direct.cpython-311-darwin.so",
"name" : "_direct.cpython-311-darwin.so"
},
{
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"uuid" : "6e4a96ad-04b8-3e8a-b91d-087e62306246",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
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"uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"uuid" : "dfea8794-80ce-37c3-8f6a-108aa1d0b1b0",
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"name" : "libsystem_c.dylib"
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"uuid" : "fd19a599-8750-31f9-924f-c2810c938371",
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"name" : "libsystem_platform.dylib"
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"name" : "AppKit",
"CFBundleVersion" : "2575.70.52"
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{
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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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{
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"uuid" : "24ce0d89-4114-30c2-a81a-3db1f5931cff",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
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"CFBundleShortVersionString" : "6.9",
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"size" : 5500928,
"uuid" : "8d45baee-6cc0-3b89-93fd-ea1c8e15c6d7",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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"uuid" : "1a037942-11e0-3fc8-aad2-20b11e7ae1a4",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
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"size" : 636280,
"uuid" : "3247e185-ced2-36ff-9e29-47a77c23e004",
"path" : "\/usr\/lib\/dyld",
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"path" : "\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit",
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"size" : 278112,
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"name" : "IOGPU",
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=3.0G written=70.7M(2%) resident=2136K(0%) swapped_out=68.6M(2%) unallocated=3.0G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 16.8M 1 \nCG image 2384K 71 \nCG raster data 384K 8 \nColorSync 624K 33 \nCoreAnimation 3776K 140 \nCoreGraphics 48K 3 \nCoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)\nCoreImage 128K 3 \nCoreServices 624K 2 \nCoreUI image data 5344K 37 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.2G 125 \nMALLOC guard page 288K 18 \nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 47 \nStack 204.6M 47 \nVM_ALLOCATE 279.6M 217 \nVM_ALLOCATE (reserved) 384.0M 2 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 36.5M 1158 \n__DATA_CONST 38.0M 1168 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 655.5M 220 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1188 \n__TEXT (graphics) 80K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 10.7M 87 \nmapped file 635.5M 95 \npage table in kernel 2136K 1 \nshared memory 3216K 26 \n=========== ======= ======= \nTOTAL 5.9G 6702 \nTOTAL, minus reserved VM space 5.6G 6702 \n",
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/rotimi/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/ARPA-H_APECx_alphaviruses/structures/SINV-
> EEEV_EEEV-179Fab/EEEV_EEEV-179_ASUplus_J726_real_space_refined_007.pdb
Chain information for EEEV_EEEV-179_ASUplus_J726_real_space_refined_007.pdb #1
---
Chain | Description
A D G J | No description available
B C E K | No description available
F | No description available
H | No description available
I | No description available
L | No description available
> cartoon
> hide target a
> open /Users/rotimi/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/Alphaviruses/EM-work/nsEM/EEEV_E3-E2-E1_v2/Map-
> fits.cxs
Opened cryosparc_P572_J206_003_volume_map.mrc as #2, grid size 216,216,216,
pixel 2, shown at level 0.0974, step 1, values float32
Opened cryosparc_P572_J207_003_volume_map.mrc as #3, grid size 216,216,216,
pixel 2, shown at level 0.0948, step 1, values float32
Opened cryosparc_P572_J206_003_volume_map.mrc z flip as #4, grid size
216,216,216, pixel 2, shown at level 0.0974, step 1, values float32
Opened cryosparc_P572_J207_003_volume_map.mrc z flip as #5, grid size
216,216,216, pixel 2, shown at level 0.0948, step 1, values float32
> set bgColor #ffffff00
opened ChimeraX session
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> show #!4 models
> hide #!4 models
> close #2
> close #4
> close #5
> rename #3 id #2
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #!2 models
> show #1 models
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> hide #!2 models
> show #!2 models
> hide #1 models
> volume #2 style surface
> hide #!2 models
> show #1 models
> show #!2 models
> volume #2 style mesh
> hide #!2 models
> show #!2 models
> hide #1 models
> volume #2 style surface
> ui tool show "Color Actions"
> color dark gray
> show #1 models
> hide #1 models
> show #1 models
> hide #!2 models
> close session
> open "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs" format session
Opened cryosparc_P572_J207_003_volume_map.mrc as #2, grid size 216,216,216,
pixel 2, shown at level 0.0948, step 1, values float32
opened ChimeraX session
> hide #1 models
> volume #2 style surface
> show #1 models
> volume #2 style mesh
> volume #2 style surface
> hide #1 models
> select add #2
2 models selected
> color sel light gray
> select subtract #2
Nothing selected
> select add #2
2 models selected
> color sel dark gray
> lighting soft
> lighting simple
> lighting full
> lighting soft
> show #1 models
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> volume #2 style mesh
> lighting soft
> lighting simple
> lighting soft
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> volume #2 style surface
> volume #2 style mesh
> volume #2 style surface
> lighting soft
> volume #2 style mesh
> show #1 models
> graphics silhouettes true
> volume #2 level 0.07991
> volume #2 level 0.094
> volume #2 level 0.093
> volume #2 level 0.09
> volume #2 level 0.091
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> volume #2 style surface
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting soft
> hide #1 models
> select add #2
2 models selected
> color sel dark gray
> color sel gray
> color sel dim gray
> color sel gray
> lighting soft
> lighting simple
> color sel dark gray
> select subtract #2
Nothing selected
> select add #2
2 models selected
> select subtract #2
Nothing selected
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> cartoon style #1 xsection oval modeHelix default
> cartoon style (#1 & coil) xsection oval
> cartoon style #1 xsection barbell modeHelix default
> cartoon style #1 modeHelix tube sides 20
> cartoon hide #1
> cartoon #1
> cartoon style #1 xsection rectangle modeHelix default
> cartoon style (#1 & coil) xsection oval
> cartoon style #1 xsection barbell modeHelix default
> ~ribbon #1
> hide #1 models
> show #1 models
> ~cartoon #1
> cartoon #1
> ribbon #1
> hide #1 models
> show #1 models
> cartoon #1
> ribbon #1
> cartoon style oval
Expected an atoms specifier or a keyword
> cartoon style oval #1
Expected an atoms specifier or a keyword
> cartoon style oval width 1.6 thick 1.6
Expected an atoms specifier or a keyword
> cartoon style oval
Expected an atoms specifier or a keyword
> cartoon style oval #1
Expected an atoms specifier or a keyword
> cartoon_style oval #1
Unknown command: cartoon_style oval #1
> preset ribbon
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> cartoon style width 1.6
> cartoon style width 1.6 oval
Expected a keyword
> licorice
Unknown command: licorice
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> #1
Expected fewer arguments
> nucrib
> close session
> open "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs" format session
Opened cryosparc_P572_J207_003_volume_map.mrc as #2, grid size 216,216,216,
pixel 2, shown at level 0.091, step 1, values float32
opened ChimeraX session
> show #1 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:428
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:428-446
82 atoms, 81 bonds, 19 residues, 1 model selected
> color sel dark gray
> select /A:855
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:855-861
67 atoms, 72 bonds, 7 residues, 1 model selected
> select /A:861
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:856-861
61 atoms, 66 bonds, 6 residues, 1 model selected
> color sel dark gray
> select clear
> select /A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:64-427
2881 atoms, 2969 bonds, 364 residues, 1 model selected
> select /A:447
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:447-764
2448 atoms, 2514 bonds, 318 residues, 1 model selected
> select /A:447
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:447-855
3125 atoms, 3211 bonds, 409 residues, 1 model selected
> color sel cornflower blue
> select clear
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> cartoon style xsection
Missing "xsection" keyword's argument
> close session
> open /Users/rotimi/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/ARPA-H_APECx_alphaviruses/structures/SINV-
> EEEV_EEEV-179Fab/EEEV_EEEV-179_ASUplus_J726_real_space_refined_007.pdb
> format pdb
Chain information for EEEV_EEEV-179_ASUplus_J726_real_space_refined_007.pdb #1
---
Chain | Description
A D G J | No description available
B C E K | No description available
F | No description available
H | No description available
I | No description available
L | No description available
> show target ab
> hide target a
> cartoon
> select /J:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 3 residues, 1 model selected
> select up
3119 atoms, 3212 bonds, 408 residues, 1 model selected
> color sel cornflower blue
> select clear
> select /D:121
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 6 residues, 1 model selected
> select up
3119 atoms, 3211 bonds, 408 residues, 1 model selected
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> close session
> open "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs" format session
Opened cryosparc_P572_J207_003_volume_map.mrc as #2, grid size 216,216,216,
pixel 2, shown at level 0.091, step 1, values float32
opened ChimeraX session
> select /A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:64-427
2881 atoms, 2969 bonds, 364 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel magenta
> color sel pink
> select clear
> select /A:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:64-427
2881 atoms, 2969 bonds, 364 residues, 1 model selected
> color sel light pink
> color sel pink
> color sel light pink
> select clear
> select /A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:1-61
475 atoms, 484 bonds, 61 residues, 1 model selected
> color sel light green
> color sel pale green
> color sel light green
> color sel pale green
> color sel medium spring green
> color sel medium aquamarine
> color sel light green
> color sel pale green
> select clear
> show #!2 models
> hide #!2 models
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> show #!2 models
> volume #2 style mesh
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> volume #2 style surface
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 style mesh
> volume #2 style surface
> volume #2 style mesh
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:1-223
1752 atoms, 1796 bonds, 223 residues, 1 model selected
> select clear
> select /A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:1-63
497 atoms, 506 bonds, 63 residues, 1 model selected
> color sel pale green
> select clear
> volume #2 style surface
> volume #2 style mesh
> turn y 90 #1
Expected 'forever' or an integer >= 1 or a keyword
> turn y 1 90 #1
Expected a keyword
> turn y 1 90
> turn y 1 -90
Missing or invalid "frames" argument: Expected 'forever' or an integer >= 1
> turn y 1 270
> turn y 1 90
> turn y 270
> turn y 60
> turn y 30
> turn y 270
> turn y 45
> turn y 270
> turn y 10
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> turn y 270
> turn y 90
> volume #2 style surface
> volume #2 style mesh
> volume #2 style surface
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> volume #2 style mesh
> ui tool show "Side View"
> volume #2 style surface
> volume #2 style mesh
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
> fitmap #1 inMap #2
Fit molecule fold_2025_06_16_full_mc3_model_4.cif (#1) to map
cryosparc_P572_J207_003_volume_map.mrc (#2) using 6646 atoms
average map value = 0.6324, steps = 40
shifted from previous position = 0.0471
rotated from previous position = 0.0182 degrees
atoms outside contour = 2196, contour level = 0.091
Position of fold_2025_06_16_full_mc3_model_4.cif (#1) relative to
cryosparc_P572_J207_003_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.79802914 -0.13746852 -0.58672982 217.57861974
0.20994283 0.97605871 0.05686289 214.90641387
0.56486590 -0.16855797 0.80778383 219.59232598
Axis -0.18419774 -0.94100136 0.28387962
Axis point -333.20172237 0.00000000 429.03248323
Rotation angle (degrees) 37.72694573
Shift along axis -179.96693173
> save "/Users/rotimi/OneDrive - The Scripps Research
> Institute/Alphaviruses/EM-
> work/nsEM/EEEV_E3-E2-E1_v2/EEEV_E3-E2-E1_v2-apo_analysis.cxs"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,13
Model Number: Z1JD000DNLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 12 days, 15 hours, 21 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 2 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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