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Opened 4 months ago
Closed 4 months ago
#18132 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-15.5-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 0x0000000203d9df00 (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.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.pdb_lib._load_libs, chimerax.surface._surface, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, 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: 116)
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{
"uptime" : 250000,
"procRole" : "Background",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 45603,
"osVersion" : {
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"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-07-04 09:31:20.0682 +1000",
"codeSigningMonitor" : 1,
"incident" : "4C38B7F1-F1F9-4693-922C-2000BA7E23B8",
"pid" : 9979,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-03 16:23:15.7212 +1000",
"procStartAbsTime" : 5843592152467,
"procExitAbsTime" : 6155119423933,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"77DCD3C2-B3FB-5607-AE5D-411764F1182A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DE39C8B4-CC66-2A2E-EF17-D264C275FB84",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","assetIsNotReady","siriAssetIsNotReady"]},
"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=="},
"bootSessionUUID" : "F9F7A61B-C9FF-44F6-A6BD-5E14BBA0FB5F",
"wakeTime" : 2,
"sleepWakeUUID" : "9B6EB722-2487-4B65-93B4-68B502EB22D7",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4338679447\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1029b0000-1029b4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":9979},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4338679447\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1029b0000-1029b4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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"uuid" : "a0f6dde6-2963-373f-88a9-51589256c8a4",
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"name" : "_pava_pybind.cpython-311-darwin.so"
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"uuid" : "e1cdfb1d-5054-3d41-8e5f-3da202f63d7b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_ckdtree.cpython-311-darwin.so",
"name" : "_ckdtree.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_qhull.cpython-311-darwin.so",
"name" : "_qhull.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 13505413120,
"size" : 131072,
"uuid" : "3febe891-f150-3e8a-89be-dcfc7eb50fe1",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_voronoi.cpython-311-darwin.so",
"name" : "_voronoi.cpython-311-darwin.so"
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{
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"arch" : "arm64",
"base" : 5892292608,
"size" : 81920,
"uuid" : "c0df5905-acc4-3e30-8273-a93ba14f1738",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_wrap.cpython-311-darwin.so",
"name" : "_distance_wrap.cpython-311-darwin.so"
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{
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"arch" : "arm64",
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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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"arch" : "arm64",
"base" : 5855510528,
"size" : 16384,
"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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"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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"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",
"base" : 13604618240,
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"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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"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"
},
{
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"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"
},
{
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"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"
},
{
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"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",
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"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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{
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"uuid" : "60485b6f-67e5-38c1-aec9-efd6031ff166",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
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"uuid" : "647b91fc-96d3-3bbb-af08-970df45257c8",
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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/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_lipid_v2.cxs"
Opened POWV_sharp1.mrc as #2, grid size 300,300,300, pixel 0.82, shown at
level 2.51, step 1, values float32
Opened POWV_sharp1.mrc zone as #4, grid size 300,300,300, pixel 0.82, shown at
level 1.21, step 1, values float32
Opened POWV_sharp1.mrc zone as #6, grid size 300,300,300, pixel 0.82, shown at
level 2.02, step 1, values float32
Opened bPOWV_volume_54_1.mrc as #7, grid size 800,800,800, pixel 0.82, shown
at level 1.55, step 1, values float32
Opened POWV_sharp1.mrc zone as #8, grid size 300,300,300, pixel 0.82, shown at
level 1.83, step 1, values float32
Opened POWV_sharp1.mrc zone as #9, grid size 300,300,300, pixel 0.82, shown at
level 2.51, step 1, values float32
Opened POWV_sharp1.mrc zone zone as #10, grid size 300,300,300, pixel 0.82,
shown at level 1.88, step 1, values float32
Opened POWV_sharp1.mrc zone as #11, grid size 300,300,300, pixel 0.82, shown
at level 1.99, step 1, values float32
Opened POWV_sharp1.mrc zone zone as #12, grid size 300,300,300, pixel 0.82,
shown at level 1.65, step 1, values float32
Opened POWV_sharp1.mrc zone zone zone as #13, grid size 300,300,300, pixel
0.82, shown at level 1.68, step 1, values float32
Opened POWV_sharp1.mrc zone as #15, grid size 300,300,300, pixel 0.82, shown
at level 2.51, step 1, values float32
Opened POWV_sharp1.mrc zone zone as #16, grid size 300,300,300, pixel 0.82,
shown at level 1.66, step 1, values float32
opened ChimeraX session
> ui tool show "Map Eraser"
> volume erase #16 center 130.57,134.56,134.03 radius 24.265 outside true
> ui mousemode right translate
> volume #16 level 1.516
> save newPOWV_lipid3.png format png width 2000 height 2000
> transparentBackground true
> save "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_lipid_v3.cxs" includeMaps true
> close #1,3,5,14,17#2,4,6-13,15-16
> open "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_asu.cxs" format session
Opened POWV_sharp1.mrc as #2, grid size 300,300,300, pixel 0.82, shown at
level 2.51, step 1, values float32
Opened POWV_sharp1.mrc zone as #4, grid size 300,300,300, pixel 0.82, shown at
level 1.21, step 1, values float32
Opened POWV_sharp1.mrc zone as #6, grid size 300,300,300, pixel 0.82, shown at
level 2.02, step 1, values float32
Opened bPOWV_volume_54_1.mrc as #7, grid size 800,800,800, pixel 0.82, shown
at level 1.55, step 1, values float32
opened ChimeraX session
> ui tool show "Map Filter"
> volume gaussian #6 sDev 0.44
Opened POWV_sharp1.mrc zone gaussian as #8, grid size 300,300,300, pixel 0.82,
shown at step 1, values float32
> volume gaussian #6 sDev 0.83 modelId #8
Opened POWV_sharp1.mrc zone gaussian as #8, grid size 300,300,300, pixel 0.82,
shown at step 1, values float32
> close #8
> show #!6 models
> toolshed show
> show #5 models
> transparency #6.1 50
> show :154
> style #5 stick
Changed 26361 atom styles
> ui tool show "Map Eraser"
> volume erase #6 center 142.51,136.93,107.35 radius 15.914 outside true
> ui mousemode right translate
> ui tool show "Side View"
> transparency #6.1 50
> color zone #6 near #5 distance 4
> transparency #6.1 50
> show #!2 models
> hide #!6 models
> volume #2 level 2.305
> surface dust #2 size 3
> color zone #2 near #5 distance 4
> transparency #2.1 50
> volume #2 level 1.842
> volume #2 level 2.016
> color zone #2 near #5 distance 4
> transparency #2.1 50
> save newPOWV_glycan.png format png width 2000 height 2000
> transparentBackground true
> save newPOWV_glycan2.png format png width 2000 height 2000
> transparentBackground true
> save "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_glycan.cxs" includeMaps true
> show #!6 models
> hide #!2 models
> close #1,3,5#2,4,6-7
> open "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_asu.cxs" format session
Opened POWV_sharp1.mrc as #2, grid size 300,300,300, pixel 0.82, shown at
level 2.51, step 1, values float32
Opened POWV_sharp1.mrc zone as #4, grid size 300,300,300, pixel 0.82, shown at
level 1.21, step 1, values float32
Opened POWV_sharp1.mrc zone as #6, grid size 300,300,300, pixel 0.82, shown at
level 2.02, step 1, values float32
Opened bPOWV_volume_54_1.mrc as #7, grid size 800,800,800, pixel 0.82, shown
at level 1.55, step 1, values float32
opened ChimeraX session
> show #5 models
> volume #6 level 1.763
> show #3 models
> hide #3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #5 models
> show #5 models
> hide #!6 models
> hide #5 models
> show #!6 models
> show #5 models
> color zone #6 near #5 distance 4
> show #5 atoms
> style #5 stick
Changed 26361 atom styles
> transparency #6.1 50
> ui tool show "Side View"
> view
> nucleotides #5 fill
> style nucleic & #5 stick
Changed 0 atom styles
> nucleotides #5 fill
> style nucleic & #5 stick
Changed 0 atom styles
> nucleotides #5 fill
> style nucleic & #5 stick
Changed 0 atom styles
> nucleotides #5 tube/slab shape box
> select add #5
26361 atoms, 26676 bonds, 1719 residues, 1 model selected
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> select subtract #5
Nothing selected
> nucleotides #5 ladder
> nucleotides #5 atoms
> style nucleic & #5 stick
Changed 0 atom styles
> select add #5
26361 atoms, 26676 bonds, 1719 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> cartoon style sel xsection oval modeHelix default
> hide #!6 models
> select subtract #5
Nothing selected
> style #5 ball
Changed 26361 atom styles
> style #5 stick
Changed 26361 atom styles
> cartoon style (#5 & coil) xsection oval
> cartoon style #5 xsection barbell modeHelix default
> cartoon style #5 modeHelix tube sides 20
> undo
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 12893 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
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
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
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 52063 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
> close #1,3,5#2,4,6-7
> open "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_asu.cxs" format session
Opened POWV_sharp1.mrc as #2, grid size 300,300,300, pixel 0.82, shown at
level 2.51, step 1, values float32
Opened POWV_sharp1.mrc zone as #4, grid size 300,300,300, pixel 0.82, shown at
level 1.21, step 1, values float32
Opened POWV_sharp1.mrc zone as #6, grid size 300,300,300, pixel 0.82, shown at
level 2.02, step 1, values float32
Opened bPOWV_volume_54_1.mrc as #7, grid size 800,800,800, pixel 0.82, shown
at level 1.55, step 1, values float32
opened ChimeraX session
> show #5 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> undo
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide #!6 models
> hide #5 models
> show #5 models
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color #5/A medium purple
> color #5/a #e5daffff
> color #5/B teal
> color #5/B pale turquoise
> color #5/b pale turquoise
> color #5/B teal
> color #5/C tomato
> color #5/c light salmon
> color bfactor #5
26361 atoms, 1719 residues, atom bfactor range 41.1 to 151
> undo
> color #5 byhetero
> show #!6 models
> transparency #6.1 50
> view
> save "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_asu_v3.cxs" includeMaps true
> hide #!6 models
> show #!6 models
> ui tool show "Map Eraser"
> volume erase #6 center 99.768,157.06,123.96 radius 21.653 outside true
> ui mousemode right translate
> volume #7 level 1.442
> show #!7 models
> hide #!7 models
> volume #6 level 1.725
> color zone #6 near #5 distance 4
> color #5 byhetero
> color #5/b pale turquoise
> color #5/B teal
> color zone #6 near #5 distance 4
> transparency #6.1 50
> color #5 byhetero
> view
> delete #5/A,C,c,a
> delete #5/B
> view
> ui mousemode right "map eraser"
> volume erase #6 center 110.29,156.64,133.97 radius 7.5021
> volume erase #6 center 108.41,155.02,138.22 radius 7.5021
> volume erase #6 center 115.23,161.15,133.48 radius 4.5504
> volume erase #6 center 120.98,157.11,131.37 radius 6.3952
> volume zone #2 nearAtoms #5/b range 4 newMap true
Opened POWV_sharp1.mrc zone as #9, grid size 300,300,300, pixel 0.82, shown at
step 1, values float32
> volume zone #2 nearAtoms #5/b range 3 newMap true
Opened POWV_sharp1.mrc zone as #10, grid size 300,300,300, pixel 0.82, shown
at step 1, values float32
> hide #!6 models
> volume zone #2 nearAtoms #5/b range 4 newMap true
Opened POWV_sharp1.mrc zone as #11, grid size 300,300,300, pixel 0.82, shown
at step 1, values float32
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> volume #11 level 1.849
> ui mousemode right translate
> show #!9 models
> hide #!11 models
> volume #9 level 2.872
> volume #10 level 1.497
> hide #!9 models
> surface dust #10 size 3
> color #10 pale turquoise
> transparency #10.1 50
> volume #10 level 1.609
> ui mousemode right rotate
> ui mousemode right translate
> view
> select H
614 atoms, 75 residues, 1 model selected
> hide sel
> volume #10 level 1.362
> ui mousemode right "map eraser"
> ui mousemode right translate
> ui mousemode right "map eraser"
> volume erase #10 center 103.37,160.84,106.95 radius 2.7057
> ui mousemode right zoom
> ui mousemode right translate
> view
Alignment identifier is 5/b
> select #5/b:1
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/b:1-18
268 atoms, 270 bonds, 18 residues, 1 model selected
> select #5/b:57
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #5/b:57-71
244 atoms, 245 bonds, 15 residues, 1 model selected
> select add #5
1204 atoms, 1219 bonds, 75 residues, 1 model selected
> select subtract #5
Nothing selected
> toolshed show
> save "/Users/uqnnewt1/Dropbox/1. Work/1. Chimera
> Sessions/POWV/newPOWV_M_feature.cxs" includeMaps true
===== 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 Pro
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 Pro
Model Identifier: Mac15,6
Model Number: MRX33X/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 10 days, 23 hours, 49 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL P3424WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2422H:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 270
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 , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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