![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15466 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.6.7-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff8447197c0 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 98)
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{
"uptime" : 26000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 3693,
"osVersion" : {
"train" : "macOS 13.6.7",
"build" : "22G720",
"releaseType" : "User"
},
"captureTime" : "2024-06-20 19:08:03.8491 +0200",
"incident" : "711118DA-67DB-4AB5-A022-F3E2C39DA3D4",
"pid" : 5859,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-20 17:25:18.8209 +0200",
"procStartAbsTime" : 19932393148146,
"procExitAbsTime" : 26097384042563,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C49B0C80-CC4D-5A15-89A4-89E2CF0A1104","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "544756B3-75BC-0265-043E-3FA91F148407",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 6364,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "BC83090D-DAE8-4A1A-871D-E645549D9B30",
"sip" : "enabled",
"vmRegionInfo" : "0x40 is not in any region. Bytes before following region: 140737487351744\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff0b000-7ffffff0c000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5859},
"vmregioninfo" : "0x40 is not in any region. Bytes before following region: 140737487351744\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff0b000-7ffffff0c000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"deploymentId" : 240000123
},
{
"rolloutId" : "5f72dc58705eff005a46b3a9",
"factorPackIds" : {
},
"deploymentId" : 240000015
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000004
}
]
}
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/chrst874/Postdoc/Cryo-EM/Masks/Mask selection.cxs" format
> session
opened ChimeraX session
> show LSU_RNA
> select ~sel & ##selected
139150 atoms, 142690 bonds, 5748 pseudobonds, 17243 residues, 4 models
selected
> hide LSU_RNA
> select SSU_RNA & ~#1/A:921-1396
22424 atoms, 25113 bonds, 1086 pseudobonds, 1043 residues, 3 models selected
> show sel
> open /Users/chrst874/Downloads/cryosparc_P2_J81_007_volume_map_sharp.mrc
Opened cryosparc_P2_J81_007_volume_map_sharp.mrc as #2, grid size 576,576,576,
pixel 0.758, shown at level 0.164, step 4, values float32
> hide #!1 models
> volume #2 level 0.2123
> volume #2 step 1
> volume #2 level 0.2709
> lighting full
> vop gaussian #2 sdev 2.27
Opened cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian as #3, grid size
576,576,576, pixel 0.758, shown at step 1, values float32
> show #!1 models
> show #1
> fitmap #1 inMap #3
Fit molecule 7k00.cif (#1) to map cryosparc_P2_J81_007_volume_map_sharp.mrc
gaussian (#3) using 149338 atoms
average map value = 0.02772, steps = 524
shifted from previous position = 72.5
rotated from previous position = 26.6 degrees
atoms outside contour = 126217, contour level = 0.070321
Position of 7k00.cif (#1) relative to
cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian (#3) coordinates:
Matrix rotation and translation
0.96652782 0.13367976 0.21898334 -5.62474097
-0.04141802 0.92363397 -0.38103128 123.30558046
-0.25319662 0.35920748 0.89825468 37.88899460
Axis 0.82680296 0.52739712 -0.19557388
Axis point 0.00000000 -60.01737860 262.32086602
Rotation angle (degrees) 26.59309001
Shift along axis 52.97035764
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.96653,0.13368,0.21898,-42.658,-0.041418,0.92363,-0.38103,139.39,-0.2532,0.35921,0.89825,105.41
> view matrix models
> #1,0.96653,0.13368,0.21898,-56.905,-0.041418,0.92363,-0.38103,146.87,-0.2532,0.35921,0.89825,134.28
> view matrix models
> #1,0.96653,0.13368,0.21898,-149.73,-0.041418,0.92363,-0.38103,177.56,-0.2532,0.35921,0.89825,282.01
> lighting simple
> lighting soft
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.59195,0.77019,-0.2375,-110.12,-0.74556,0.6352,0.20164,247.35,0.30616,0.057707,0.95023,224.9
> view matrix models
> #1,0.9174,-0.060934,0.39327,-138.59,0.21432,0.90831,-0.35921,129.48,-0.33533,0.41383,0.84635,296.97
> lighting simple
> view matrix models
> #1,-0.41909,-0.078334,0.90456,10.906,0.7296,0.56392,0.38687,-44.496,-0.5404,0.8221,-0.17918,456.07
> view matrix models
> #1,-0.011702,0.025494,0.99961,-100.61,0.73861,0.67408,-0.0085453,9.3838,-0.67403,0.73822,-0.026718,466.62
> view matrix models
> #1,0.089014,-0.69599,0.71252,67.487,0.75876,0.51081,0.40417,-43.442,-0.64526,0.50466,0.57356,389.18
> view matrix models
> #1,-0.033013,0.18127,0.98288,-121.94,0.74034,0.66508,-0.097793,27.776,-0.67142,0.72444,-0.15616,493.41
> view matrix models
> #1,0.098538,-0.51917,0.84897,7.4022,-0.94397,-0.3188,-0.085393,512.48,0.31499,-0.79299,-0.52149,659.89
> view matrix models
> #1,0.98983,-0.092286,0.10823,-91.591,-0.1182,-0.95696,0.26505,411.04,0.079114,-0.27515,-0.95814,692.02
> view matrix models
> #1,0.95173,-0.23289,0.19994,-76.522,-0.29832,-0.85518,0.42389,395,0.072261,-0.46307,-0.88337,713.25
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.95173,-0.23289,0.19994,56.25,-0.29832,-0.85518,0.42389,336.7,0.072261,-0.46307,-0.88337,447.64
> fitmap #1 inMap #3
Fit molecule 7k00.cif (#1) to map cryosparc_P2_J81_007_volume_map_sharp.mrc
gaussian (#3) using 149338 atoms
average map value = 0.03607, steps = 1120
shifted from previous position = 6.19
rotated from previous position = 64.2 degrees
atoms outside contour = 120975, contour level = 0.070321
Position of 7k00.cif (#1) relative to
cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian (#3) coordinates:
Matrix rotation and translation
0.54184864 -0.59482204 0.59379018 123.25184509
-0.69207264 0.08511079 0.71679257 193.25558810
-0.47690197 -0.79933902 -0.36554289 507.86969820
Axis -0.81572665 0.57606617 -0.05232389
Axis point 0.00000000 351.07738561 165.80502873
Rotation angle (degrees) 111.67194321
Shift along axis -15.78552864
> lighting soft
> hide #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04296
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> volume #2 level 0.2226
> hide #!2 models
> show #!3 models
> view matrix models
> #1,0.54185,-0.59482,0.59379,113.36,-0.69207,0.085111,0.71679,231.98,-0.4769,-0.79934,-0.36554,365.48
> view matrix models
> #1,0.54185,-0.59482,0.59379,103.83,-0.69207,0.085111,0.71679,261.15,-0.4769,-0.79934,-0.36554,230.59
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.95157,0.0031194,0.3074,-25.3,-0.29016,0.33943,0.89476,107.33,-0.10155,-0.94062,0.3239,55.96
> view matrix models
> #1,0.2926,0.95553,-0.036771,-12.842,-0.67008,0.23232,0.70499,232.54,0.68218,-0.18164,0.70826,-299.12
> lighting simple
> view matrix models
> #1,0.056532,0.30319,0.95125,-39.686,0.054394,-0.9523,0.30029,393.68,0.99692,0.034767,-0.070327,-247.18
> view matrix models
> #1,-0.43936,0.42169,0.79319,59.497,0.81662,-0.18042,0.54825,66.266,0.3743,0.88861,-0.26509,-251.96
> view matrix models
> #1,0.49289,-0.3818,0.78185,37.951,0.84915,0.40704,-0.33655,122.38,-0.18975,0.82979,0.52483,-289.27
> view matrix models
> #1,0.73673,-0.32114,-0.59506,245.66,-0.34279,-0.93594,0.080702,505.23,-0.58286,0.14453,-0.79962,160.79
> view matrix models
> #1,0.63011,-0.48985,-0.6025,297.33,-0.30167,-0.86939,0.39135,426.18,-0.71551,-0.064843,-0.69559,203.31
> view matrix models
> #1,0.9303,-0.21619,-0.29633,134.04,-0.078953,-0.90694,0.4138,388.06,-0.35821,-0.36156,-0.86079,223.77
> vop zflip #3
> volume zflip #3
Expected a density maps specifier or a keyword
> volume flip #3 axis z
Opened cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian z flip as #4, grid
size 576,576,576, pixel 0.758, shown at step 1, values float32
> view matrix models
> #1,0.52982,-0.46652,0.70828,60.729,0.84766,0.26401,-0.46018,172.38,0.027688,0.84419,0.53533,-333.62
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.52982,-0.46652,0.70828,19.028,0.84766,0.26401,-0.46018,99.814,0.027688,0.84419,0.53533,-41.615
> view matrix models
> #1,0.52982,-0.46652,0.70828,74.97,0.84766,0.26401,-0.46018,102.98,0.027688,0.84419,0.53533,-32.703
> volume flip #2 axis z
Opened cryosparc_P2_J81_007_volume_map_sharp.mrc z flip as #5, grid size
576,576,576, pixel 0.758, shown at step 1, values float32
> hide #!4 models
> hide #!5 models
> show #!4 models
> fitmap #1 inMap #4
Fit molecule 7k00.cif (#1) to map cryosparc_P2_J81_007_volume_map_sharp.mrc
gaussian z flip (#4) using 149338 atoms
average map value = 0.06778, steps = 244
shifted from previous position = 7.24
rotated from previous position = 13.1 degrees
atoms outside contour = 25314, contour level = 0.04296
Position of 7k00.cif (#1) relative to
cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian z flip (#4) coordinates:
Matrix rotation and translation
0.39703798 -0.59829171 0.69599417 130.96109092
0.89520295 0.08520064 -0.43743864 122.79336205
0.20241675 0.79673577 0.56942039 -60.22550979
Axis 0.61729315 0.24687107 0.74699655
Axis point 17.24203322 133.24637388 0.00000000
Rotation angle (degrees) 88.51991375
Shift along axis 66.16726562
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
> lighting full
> hide #!4 models
> show #!5 models
> close #2-4
> volume #5 level 0.2519
> hide #!1 models
> show #!1 models
> volume style surface
> lighting soft
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide ~sel
> show #!5 models
> hide #!5 models
> select #1/A:921-1396
10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected
> hide
> select #1/A:921-1396
10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected
> show sel
> show #!5 models
> hide #!5 models
> select sel : select sel : show sel
> select up
43999 atoms, 48246 bonds, 450 pseudobonds, 2806 residues, 3 models selected
> show sel
> select #1/A:921-1396
10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected
> select #1/A & ~sel
24642 atoms, 25176 bonds, 1443 pseudobonds, 3202 residues, 4 models selected
> hide sel
> select #1/A:921-1396
10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected
> select protein
43768 atoms, 44383 bonds, 1 pseudobond, 5587 residues, 2 models selected
> hide sel
> hide
> select #1/A:921-1396
10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected
> show sel
> select zone sel 5 protein residues true
Selected 2975 atoms
> show sel
> select SSU_protein
19000 atoms, 19278 bonds, 2410 residues, 1 model selected
> show sel
> select #1/A:921-1396
10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected
> select zone sel 5 protein residues true
Selected 2975 atoms
> select up
6281 atoms, 6352 bonds, 780 residues, 1 model selected
> select up
10600 atoms, 10756 bonds, 1345 residues, 1 model selected
> select protein & ~sel
33168 atoms, 33627 bonds, 4242 residues, 1 model selected
> hide sel
> hide protein
> select #1/B,C
3424 atoms, 3435 bonds, 477 residues, 1 model selected
> select #1/B,C,G,I,J,M,N,S
8913 atoms, 8886 bonds, 1268 residues, 1 model selected
> show sel
> select #1/A:921
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:921,1396
42 atoms, 45 bonds, 2 pseudobonds, 2 residues, 2 models selected
Drag select of 19101 atoms, 487 pseudobonds
> select clear
Drag select of 19101 atoms, 487 pseudobonds
> name frozen SSU_head sel
> hide sel
> show SSU_head
> save "/Users/chrst874/Postdoc/Cryo-EM/Masks/Mask selection.cxs"
> close session
> open /Users/chrst874/Downloads/cryosparc_P2_J82_class_00_00035_volume.mrc
Opened cryosparc_P2_J82_class_00_00035_volume.mrc as #1, grid size
160,160,160, pixel 2.73, shown at level 0.44, step 1, values float32
> open /Users/chrst874/Downloads/cryosparc_P2_J82_class_01_00035_volume.mrc
Opened cryosparc_P2_J82_class_01_00035_volume.mrc as #2, grid size
160,160,160, pixel 2.73, shown at level 0.479, step 1, values float32
> open /Users/chrst874/Downloads/cryosparc_P2_J82_class_02_00035_volume.mrc
Opened cryosparc_P2_J82_class_02_00035_volume.mrc as #3, grid size
160,160,160, pixel 2.73, shown at level 0.442, step 1, values float32
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> lighting soft
> lighting full
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/chrst874/Downloads/cryosparc_P2_J81_007_volume_map_sharp.mrc
Opened cryosparc_P2_J81_007_volume_map_sharp.mrc as #1, grid size 576,576,576,
pixel 0.758, shown at level 0.164, step 4, values float32
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 577.140.2~22
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 1 day, 2 hours, 38 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP Z27n G2:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 6CM00316BF
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
HP Z27n G2:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 6CM0101JDD
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
Send2Trash: 1.8.2
SEQCROW: 1.8.8
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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