![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16561 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff85e7134c0 (most recent call first):
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 250,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMacPro1,1",
"coalitionID" : 1063,
"osVersion" : {
"train" : "macOS 15.2",
"build" : "24C101",
"releaseType" : "User"
},
"captureTime" : "2025-01-06 11:28:01.0232 -0500",
"codeSigningMonitor" : 0,
"incident" : "5927D1B5-AE18-4A51-8550-22B19D4FA170",
"pid" : 2852,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-06 11:26:21.9818 -0500",
"procStartAbsTime" : 159449723431,
"procExitAbsTime" : 258402026234,
"procName" : "ChimeraX",
"procPath" : "\/programs\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E6FED3E7-1F19-5ABB-BB13-DA4560B015B7","thirdParty":true},
"parentProc" : "Exited process",
"parentPid" : 2851,
"coalitionName" : "com.googlecode.iterm2",
"crashReporterKey" : "555EFC51-FF05-FCB1-EF9E-2B937C6B784E",
"responsiblePid" : 1002,
"responsibleProc" : "iTerm2",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "23F4A1EF-9783-46A1-8415-5773685198EB",
"bridgeVersion" : {"build":"22P2093","train":"9.2"},
"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":2852},
"ktriageinfo" : "VM - (arg = 0x0) Waiting on busy page was interrupted\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000001\n"],
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"faultingThread" : 0,
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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: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
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: 4 minutes, 59 seconds
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: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
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