![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16563 closed defect (nonchimerax)
Graphics crash, macOS 15.2, Radeon Pro Vega 56
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.2-x86_64-i386-64bit
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. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
Fatal Python error: Aborted
Current thread 0x00007ff85e7134c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/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, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.graphics._graphics, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath (total: 50)
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{
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"version" : 2,
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"build" : "24C101",
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"captureTime" : "2025-01-06 12:23:48.6835 -0500",
"codeSigningMonitor" : 0,
"incident" : "8D5BB7F3-FC26-4216-9EE4-2DFDCB220257",
"pid" : 6589,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-06 12:22:18.6660 -0500",
"procStartAbsTime" : 3497361603096,
"procExitAbsTime" : 3587382621003,
"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"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "555EFC51-FF05-FCB1-EF9E-2B937C6B784E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "23F4A1EF-9783-46A1-8415-5773685198EB",
"wakeTime" : 933,
"bridgeVersion" : {"build":"22P2093","train":"9.2"},
"sleepWakeUUID" : "6B53770E-3E50-4849-B441-4D32188EEA62",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":6589},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000001\n"],
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===== 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/navid/Downloads/cryosparc_P4_J1551_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1551_005_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.663, shown at level 0.0611, step 2, values float32
> volume #0-100 fastEncloseVolume 1250000
> volume #0-100 fastEncloseVolume 50000
> volume #0-100 step 1 fastEncloseVolume 50000
> volume #1 level 0.1235
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/emd_23375.map
Opened emd_23375.map as #2, grid size 300,300,300, pixel 1.03, shown at level
0.118, step 2, values float32
> open /Users/navid/Downloads/emd_23374.map
Opened emd_23374.map as #3, grid size 300,300,300, pixel 1.03, shown at level
0.216, step 2, values float32
> open /Users/navid/Downloads/emd_23372.map
Opened emd_23372.map as #4, grid size 300,300,300, pixel 1.03, shown at level
0.121, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> ui dockable false "Model Panel"
> ui dockable false Log
> ui autostart false Log
> ui autostart true "Volume Viewer"
> hide #!1 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> volume #4 level 0.3757
> show #!3 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #4 level 0.2909
> open /Users/navid/Downloads/cryosparc_P4_J1503_004_volume_map.mrc
Opened cryosparc_P4_J1503_004_volume_map.mrc as #5, grid size 480,480,480,
pixel 0.663, shown at level 0.0457, step 2, values float32
> open /Users/navid/Downloads/cryosparc_P4_J1507_005_volume_map.mrc
Opened cryosparc_P4_J1507_005_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.663, shown at level 0.0537, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> open /Users/navid/Downloads/emd_23374.map format ccp4
Opened emd_23374.map as #1, grid size 300,300,300, pixel 1.03, shown at level
0.216, step 2, values float32
> open /Users/navid/Downloads/emd_23372.map
> /Users/navid/Downloads/emd_23374.map /Users/navid/Downloads/emd_23375.map
Opened emd_23372.map as #2.1, grid size 300,300,300, pixel 1.03, shown at
level 0.121, step 2, values float32
Opened emd_23374.map as #2.2, grid size 300,300,300, pixel 1.03, shown at
level 0.216, step 2, values float32
Opened emd_23375.map as #2.3, grid size 300,300,300, pixel 1.03, shown at
level 0.118, step 2, values float32
> close #1
> volume #0-100 step 1 fastEncloseVolume 40000
> view center
Expected an objects specifier or a view name or a keyword
> center
Unknown command: center
> view orient
> turn x, 90
Expected an axis vector or a keyword
> turn x 90
> turn y, 1
Expected an axis vector or a keyword
> turn y 1
> ui tool show "Side View"
> ui autostart true "Side View"
> ui dockable false "Side View"
> turn y 1
> volume #0-100 step 1 fastEncloseVolume 60000
> volume #0-100 step 1 fastEncloseVolume 70000
> save /Users/navid/Desktop/img1.png
> save /Users/navid/Desktop/img2.png
> save /Users/navid/Desktop/img3.png
> save /Users/navid/Desktop/img4.png
> volume #0-100 step 1 fastEncloseVolume 100000
> turn y 1
> open /Users/navid/Downloads/cryosparc_P4_J1574_004_volume_map_sharp.mrc
Opened cryosparc_P4_J1574_004_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.663, shown at level 0.0567, step 2, values float32
> close #2.1
> close #2.2
> close #2.3
> volume #0-100 step 1 fastEncloseVolume 100000
> volume #0-100 step 1 fastEncloseVolume 30000
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1575_004_volume_map_sharp.mrc
Opened cryosparc_P4_J1575_004_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 0.663, shown at level 0.0571, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1571_002_volume_map_sharp.mrc
Opened cryosparc_P4_J1571_002_volume_map_sharp.mrc as #4, grid size
480,480,480, pixel 0.663, shown at level 0.058, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1581_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1581_005_volume_map_sharp.mrc as #5, grid size
480,480,480, pixel 0.663, shown at level 0.0641, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> close #1
> close #3
> close #4
> open /Users/navid/Downloads/cryosparc_P4_J1582_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1582_005_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.663, shown at level 0.0672, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> fitmap #1 #5
Missing required "in_map" argument
> fitmap #1 inMap #5
Fit map cryosparc_P4_J1582_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137090 points
correlation = 0.9614, correlation about mean = 0.7312, overlap = 1.049e+04
steps = 52, shift = 0.25, angle = 0.201 degrees
Position of cryosparc_P4_J1582_005_volume_map_sharp.mrc (#1) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999740 0.00221129 -0.00055570 -0.20578402
-0.00221276 0.99999403 -0.00265571 0.89265278
0.00054983 0.00265693 0.99999632 -0.29618172
Axis 0.75880415 -0.15790337 -0.63188827
Axis point 0.00000000 138.08007692 329.27815751
Rotation angle (degrees) 0.20057373
Shift along axis -0.10994889
> open /Users/navid/Downloads/cryosparc_P4_J1583_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1583_005_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 0.663, shown at level 0.0619, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> fitmap #3 inMap #5
Fit map cryosparc_P4_J1583_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137411 points
correlation = 0.9618, correlation about mean = 0.7441, overlap = 8800
steps = 60, shift = 0.185, angle = 0.135 degrees
Position of cryosparc_P4_J1583_005_volume_map_sharp.mrc (#3) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999896 -0.00123205 0.00075254 0.13429319
0.00123346 0.99999749 -0.00187193 0.26362467
-0.00075023 0.00187286 0.99999796 -0.24451352
Axis 0.79192955 0.31779844 0.52139404
Axis point 0.00000000 148.13688523 129.99656920
Rotation angle (degrees) 0.13546718
Shift along axis 0.06264236
> view center
Expected an objects specifier or a view name or a keyword
> orient
Unknown command: orient
> view orient
> center
Unknown command: center
> open /Users/navid/Downloads/cryosparc_P4_J1584_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1584_005_volume_map_sharp.mrc as #4, grid size
480,480,480, pixel 0.663, shown at level 0.0617, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> fitmap #4 inMap #5
Fit map cryosparc_P4_J1584_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137561 points
correlation = 0.9571, correlation about mean = 0.7266, overlap = 9193
steps = 40, shift = 0.152, angle = 0.158 degrees
Position of cryosparc_P4_J1584_005_volume_map_sharp.mrc (#4) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999678 -0.00180904 -0.00177994 0.67938840
0.00180714 0.99999780 -0.00106832 -0.12259903
0.00178186 0.00106510 0.99999785 -0.55841434
Axis 0.38748082 -0.64690840 0.65678622
Axis point 76.96784848 380.59739173 0.00000000
Rotation angle (degrees) 0.15773204
Shift along axis -0.02419853
> open /Users/navid/Downloads/cryosparc_P4_J1585_004_volume_map_sharp.mrc
Opened cryosparc_P4_J1585_004_volume_map_sharp.mrc as #6, grid size
480,480,480, pixel 0.663, shown at level 0.0661, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> fitmap #6 inMap #5
Fit map cryosparc_P4_J1585_004_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137001 points
correlation = 0.9614, correlation about mean = 0.7297, overlap = 1.066e+04
steps = 60, shift = 0.26, angle = 0.139 degrees
Position of cryosparc_P4_J1585_004_volume_map_sharp.mrc (#6) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999708 0.00173710 -0.00168222 -0.05448146
-0.00173734 0.99999848 -0.00013765 0.36874115
0.00168198 0.00014057 0.99999858 -0.04395357
Axis 0.05743252 -0.69446927 -0.71722656
Axis point 121.21161759 24.03969426 0.00000000
Rotation angle (degrees) 0.13877819
Shift along axis -0.22768374
> open /Users/navid/Downloads/cryosparc_P4_J1586_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1586_005_volume_map_sharp.mrc as #7, grid size
480,480,480, pixel 0.663, shown at level 0.0634, step 2, values float32
> fitmap #7 inMap #5
Fit map cryosparc_P4_J1586_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137843 points
correlation = 0.8484, correlation about mean = 0.7893, overlap = 1731
steps = 72, shift = 0.057, angle = 0.188 degrees
Position of cryosparc_P4_J1586_005_volume_map_sharp.mrc (#7) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999548 -0.00200484 -0.00224260 0.70273530
0.00200187 0.99999712 -0.00132601 -0.07020167
0.00224525 0.00132151 0.99999661 -0.61680949
Axis 0.40278881 -0.68277396 0.60957436
Axis point 262.98332074 0.00000000 320.90985491
Rotation angle (degrees) 0.18830222
Shift along axis -0.04500546
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1587_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1587_005_volume_map_sharp.mrc as #8, grid size
480,480,480, pixel 0.663, shown at level 0.0629, step 2, values float32
> fitmap #8 inMap #5
Fit map cryosparc_P4_J1587_005_volume_map_sharp.mrc in map
cryosparc_P4_J1581_005_volume_map_sharp.mrc using 137900 points
correlation = 0.855, correlation about mean = 0.7941, overlap = 1728
steps = 52, shift = 0.153, angle = 0.216 degrees
Position of cryosparc_P4_J1587_005_volume_map_sharp.mrc (#8) relative to
cryosparc_P4_J1581_005_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999354 -0.00323644 -0.00156155 0.73888787
0.00323463 0.99999410 -0.00115875 -0.26275230
0.00156529 0.00115369 0.99999811 -0.56893009
Axis 0.30629197 -0.41416289 0.85711979
Axis point 101.20019342 242.53362032 0.00000000
Rotation angle (degrees) 0.21628588
Shift along axis -0.15250357
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1588_004_volume_map_sharp.mrc
Opened cryosparc_P4_J1588_004_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.663, shown at level 0.065, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1589_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1589_005_volume_map_sharp.mrc as #10, grid size
480,480,480, pixel 0.663, shown at level 0.0631, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1590_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1590_005_volume_map_sharp.mrc as #11, grid size
480,480,480, pixel 0.663, shown at level 0.0606, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1591_006_volume_map_sharp.mrc
Opened cryosparc_P4_J1591_006_volume_map_sharp.mrc as #12, grid size
480,480,480, pixel 0.663, shown at level 0.0606, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> open /Users/navid/Downloads/cryosparc_P4_J1592_005_volume_map_sharp.mrc
Opened cryosparc_P4_J1592_005_volume_map_sharp.mrc as #13, grid size
480,480,480, pixel 0.663, shown at level 0.0609, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> set bgColor white
> lighting soft
> open /Users/navid/Downloads/emd_36410.map
Opened emd_36410.map as #14, grid size 240,240,240, pixel 0.93, shown at level
0.0133, step 1, values float32
> close #2#1,3-13
> volume #0-100 step 1 fastEncloseVolume 40000
> view orient
> close #14
> open /Users/navid/Downloads/emd_36417.map
Opened emd_36417.map as #1, grid size 240,240,240, pixel 0.93, shown at level
0.0155, step 1, values float32
> open /Users/navid/Downloads/emd_38133.map
Opened emd_38133.map as #2, grid size 240,240,240, pixel 0.93, shown at level
0.0132, step 1, values float32
> open /Users/navid/Downloads/emd_36410.map
Opened emd_36410.map as #3, grid size 240,240,240, pixel 0.93, shown at level
0.0133, step 1, values float32
> volume #0-100 step 1 fastEncloseVolume 40000
> turn x, 90
Expected an axis vector or a keyword
> turn x 90
> turn y 1
> volume #3 level 0.01603
> volume #2 level 0.01438
> volume #1 level 0.01247
> open /Users/navid/Downloads/cryosparc_P4_J1602_map.mrc
Opened cryosparc_P4_J1602_map.mrc as #4, grid size 240,240,240, pixel 0.93,
shown at level 0.0106, step 1, values float32
> close #1
> close #2
> close #3
> volume #0-100 step 1 fastEncloseVolume 100000
> volume #0-100 step 1 fastEncloseVolume 1000000
> volume #0-100 step 1 fastEncloseVolume 500000
> volume #0-100 step 1 fastEncloseVolume 400000
> volume #0-100 step 1 fastEncloseVolume 300000
> volume #0-100 step 1 fastEncloseVolume 200000
> volume #0-100 step 1 fastEncloseVolume 150000
> open /Users/navid/Downloads/cryosparc_P4_J1608_map.mrc
Opened cryosparc_P4_J1608_map.mrc as #1, grid size 240,240,240, pixel 0.93,
shown at level 0.00768, step 1, values float32
> open /Users/navid/Downloads/cryosparc_P4_J1610_map.mrc
Opened cryosparc_P4_J1610_map.mrc as #2, grid size 480,480,480, pixel 0.663,
shown at level 0.0458, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 150000
> volume #0-100 step 1 fastEncloseVolume 50000
> select #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,45.624,0,1,0,42.43,0,0,1,0.91972
> view matrix models #1,1,0,0,45.858,0,1,0,50.433,0,0,1,47.466
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.42352,0.89281,-0.15334,27.507,0.73844,-0.2422,0.62932,37.085,0.52473,-0.37977,-0.76187,226.05
> view matrix models
> #1,0.2591,0.94026,0.22086,-0.80315,0.96576,-0.24912,-0.072387,90.056,-0.013042,0.23205,-0.97262,241.08
> fitmap #1 inMap #2
Fit map cryosparc_P4_J1608_map.mrc in map cryosparc_P4_J1610_map.mrc using
62160 points
correlation = 0.6879, correlation about mean = 0.1059, overlap = 131
steps = 204, shift = 6.91, angle = 12.9 degrees
Position of cryosparc_P4_J1608_map.mrc (#1) relative to
cryosparc_P4_J1610_map.mrc (#2) coordinates:
Matrix rotation and translation
0.16103600 0.98572515 0.04912589 25.40710208
0.98589977 -0.16295955 0.03802427 62.60063168
0.04548701 0.04230993 -0.99806854 264.61475018
Axis 0.76191662 0.64693069 0.03104417
Axis point 0.00000000 20.27170290 131.80690150
Rotation angle (degrees) 179.83886000
Shift along axis 68.07110761
> show #!4 models
> hide #!4 models
> ui mousemode right "rotate selected models"
> select clear
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> turn x 90
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> turn y 90
> turn y 1
> turn y -1
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open /Users/navid/Downloads/cryosparc_P4_J1612_map.mrc
Opened cryosparc_P4_J1612_map.mrc as #3, grid size 480,480,480, pixel 0.663,
shown at level 0.0459, step 2, values float32
> volume #0-100 step 1 fastEncloseVolume 50000
===== Log before crash end =====
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro Vega 56 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac Pro
Model Identifier: iMacPro1,1
Processor Name: 8-Core Intel Xeon W
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 1 MB
L3 Cache: 11 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.12093.0.0,0)
OS Loader Version: 582~2898
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 1 hour
Graphics/Displays:
Radeon Pro Vega 56:
Chipset Model: Radeon Pro Vega 56
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x6867
Revision ID: 0x0000
ROM Revision: 113-D0500D-114
VBIOS Version: 113-D05001A1XL-018
Option ROM Version: 113-D05001A1XL-018
EFI Driver Version: 01.01.114
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 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 , 10 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 10 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 15.2, Radeon Pro Vega 56 |
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Apple AMD graphics driver crash.
Same reporter, same crash as #16560