![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16997 closed defect (can't reproduce)
Crash in Side View swap_buffers
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | 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-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
Thread 0x000070000dc66000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007ff84e680b00 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 89 in draw_new_frame
File "/Applications/ChimeraX-1.6.1.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 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2025-03-01 22:39:59.00 +0100","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"AA6E1EBF-665F-4E4C-A9D7-E2450E88C182"}
{
"uptime" : 1600,
"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 582,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-03-01 22:39:56.5953 +0100",
"codeSigningMonitor" : 0,
"incident" : "AA6E1EBF-665F-4E4C-A9D7-E2450E88C182",
"pid" : 532,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-01 22:00:49.4805 +0100",
"procStartAbsTime" : 31616292667,
"procExitAbsTime" : 1697559016393,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9EEFCD16-95C9-5BE7-B080-8AB326ED8788","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BE130105-BC30-0506-F55C-C44420CE5CC6",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "4C588F66-1B40-4066-85B8-8DC862FBD108",
"wakeTime" : 923,
"bridgeVersion" : {"build":"22P3051","train":"9.3"},
"sleepWakeUUID" : "CED6E127-C8B6-42DF-9B9A-0342231559DE",
"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":532},
"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\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",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"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,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 348K 49 \nColorSync 256K 32 \nCoreAnimation 1068K 177 \nCoreGraphics 16K 3 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreServices 4K 1 \nCoreUI image data 5044K 56 \nFoundation 16K 1 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 3.1G 837 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 108K 27 \nStack 172.2M 28 \nStack Guard 56.0M 1 \nVM_ALLOCATE 379.0M 127 \n__CTF 824 1 \n__DATA 46.6M 1061 \n__DATA_CONST 93.6M 924 \n__DATA_DIRTY 2567K 338 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 214.7M 145 \n__OBJC_RO 76.9M 1 \n__OBJC_RW 2375K 2 \n__TEXT 1.3G 1083 \n__TPRO_CONST 272K 2 \ndyld private memory 20K 2 \nmapped file 276.3M 65 \nowned unmapped memory 266.5M 1 \nshared memory 3000K 28 \n=========== ======= ======= \nTOTAL 6.0G 5022 \nTOTAL, minus reserved VM space 6.0G 5022 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "5b5b023f092833a6fe1d221c9b483cc63baff9c5",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64c17a9925d75a7281053d4c",
"factorPackIds" : {
"SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
},
"deploymentId" : 240000002
},
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : {
},
"deploymentId" : 240000011
}
],
"experiments" : [
]
}
}
===== 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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/ekamsingh/Downloads/cryosparc_P445_J88_006_volume_map.mrc
> /Users/ekamsingh/Downloads/cryosparc_P445_J90_005_volume_map.mrc
> /Users/ekamsingh/Downloads/model_C2_homorefine-coot-0.pdb
> /Users/ekamsingh/Downloads/model_C2_homorefine.pdb
> /Users/ekamsingh/Downloads/cryosparc_P445_J53_007_volume_map(2).mrc
Opened cryosparc_P445_J88_006_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.919, shown at level 0.091, step 2, values float32
Opened cryosparc_P445_J90_005_volume_map.mrc as #2, grid size 384,384,384,
pixel 0.919, shown at level 0.0974, step 2, values float32
model_C2_homorefine-coot-0.pdb title:
Human proteasome 20S core particle [more info...]
Chain information for model_C2_homorefine-coot-0.pdb #3
---
Chain | Description | UniProt
A O | proteasome subunit α type-2 | PSA2_HUMAN 1-234
B P | proteasome subunit α type-4 | PSA4_HUMAN 1-261
C Q | proteasome subunit α type-7 | PSA7_HUMAN 1-248
D R | proteasome subunit α type-5 | PSA5_HUMAN 1-241
E S | proteasome subunit α type-1 | PSA1_HUMAN 1-263
F T | proteasome subunit α type-3 | PSA3_HUMAN 1-255
G U | proteasome subunit α type-6 | PSA6_HUMAN 1-246
H V | proteasome subunit β type-7 | PSB7_HUMAN 1-277
I W | proteasome subunit β type-3 | PSB3_HUMAN 1-205
J X | proteasome subunit β type-2 | PSB2_HUMAN 1-201
K Y | proteasome subunit β type-5 | PSB5_HUMAN 1-263
L Z | proteasome subunit β type-1 | PSB1_HUMAN 1-241
M a | proteasome subunit β type-4 | PSB4_HUMAN 1-264
N b | proteasome subunit β type-6 | PSB6_HUMAN 1-239
model_C2_homorefine.pdb title:
Human proteasome 20S core particle [more info...]
Chain information for model_C2_homorefine.pdb #4
---
Chain | Description | UniProt
A O | proteasome subunit α type-2 | PSA2_HUMAN 1-234
B P | proteasome subunit α type-4 | PSA4_HUMAN 1-261
C Q | proteasome subunit α type-7 | PSA7_HUMAN 1-248
D R | proteasome subunit α type-5 | PSA5_HUMAN 1-241
E S | proteasome subunit α type-1 | PSA1_HUMAN 1-263
F T | proteasome subunit α type-3 | PSA3_HUMAN 1-255
G U | proteasome subunit α type-6 | PSA6_HUMAN 1-246
H V | proteasome subunit β type-7 | PSB7_HUMAN 1-277
I W | proteasome subunit β type-3 | PSB3_HUMAN 1-205
J X | proteasome subunit β type-2 | PSB2_HUMAN 1-201
K Y | proteasome subunit β type-5 | PSB5_HUMAN 1-263
L Z | proteasome subunit β type-1 | PSB1_HUMAN 1-241
M a | proteasome subunit β type-4 | PSB4_HUMAN 1-264
N b | proteasome subunit β type-6 | PSB6_HUMAN 1-239
Opened cryosparc_P445_J53_007_volume_map(2).mrc as #5, grid size 384,384,384,
pixel 0.919, shown at level 0.0921, step 2, values float32
> close session
> open /Users/ekamsingh/Downloads/cryosparc_P445_J85_005_volume_map.mrc
> /Users/ekamsingh/Downloads/model_C2_homorefine-coot-0.pdb
> /Users/ekamsingh/Downloads/cryosparc_P445_J90_005_volume_map.mrc
> /Users/ekamsingh/Downloads/cryosparc_P445_J88_006_volume_map.mrc
> /Users/ekamsingh/Downloads/cryosparc_P445_J81_volume_map.mrc
Opened cryosparc_P445_J85_005_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.919, shown at level 0.104, step 2, values float32
model_C2_homorefine-coot-0.pdb title:
Human proteasome 20S core particle [more info...]
Chain information for model_C2_homorefine-coot-0.pdb #2
---
Chain | Description | UniProt
A O | proteasome subunit α type-2 | PSA2_HUMAN 1-234
B P | proteasome subunit α type-4 | PSA4_HUMAN 1-261
C Q | proteasome subunit α type-7 | PSA7_HUMAN 1-248
D R | proteasome subunit α type-5 | PSA5_HUMAN 1-241
E S | proteasome subunit α type-1 | PSA1_HUMAN 1-263
F T | proteasome subunit α type-3 | PSA3_HUMAN 1-255
G U | proteasome subunit α type-6 | PSA6_HUMAN 1-246
H V | proteasome subunit β type-7 | PSB7_HUMAN 1-277
I W | proteasome subunit β type-3 | PSB3_HUMAN 1-205
J X | proteasome subunit β type-2 | PSB2_HUMAN 1-201
K Y | proteasome subunit β type-5 | PSB5_HUMAN 1-263
L Z | proteasome subunit β type-1 | PSB1_HUMAN 1-241
M a | proteasome subunit β type-4 | PSB4_HUMAN 1-264
N b | proteasome subunit β type-6 | PSB6_HUMAN 1-239
Opened cryosparc_P445_J90_005_volume_map.mrc as #3, grid size 384,384,384,
pixel 0.919, shown at level 0.0974, step 2, values float32
Opened cryosparc_P445_J88_006_volume_map.mrc as #4, grid size 384,384,384,
pixel 0.919, shown at level 0.091, step 2, values float32
Opened cryosparc_P445_J81_volume_map.mrc as #5, grid size 384,384,384, pixel
0.919, shown at level 0.0979, step 2, values float32
> hide atoms
> show cartoons
> volume #1 step 1
> volume #4 step 1
> volume #5 step 1
> volume #3 step 1
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map
cryosparc_P445_J85_005_volume_map.mrc (#1) using 47753 atoms
average map value = 0.1303, steps = 48
shifted from previous position = 1.26
rotated from previous position = 0.0943 degrees
atoms outside contour = 18047, contour level = 0.1045
Position of model_C2_homorefine-coot-0.pdb (#2) relative to
cryosparc_P445_J85_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999920 -0.00100396 0.00077017 -0.11807453
0.00100315 0.99999894 0.00105239 -0.24410022
-0.00077122 -0.00105162 0.99999915 1.56388927
Axis -0.63930730 0.46835303 0.60986197
Axis point 0.00000000 956.02088776 640.07844797
Rotation angle (degrees) 0.09428272
Shift along axis 0.91491742
> fitmap #2 inMap #3
Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map
cryosparc_P445_J90_005_volume_map.mrc (#3) using 47753 atoms
average map value = 0.1217, steps = 40
shifted from previous position = 0.103
rotated from previous position = 0.0841 degrees
atoms outside contour = 18864, contour level = 0.097413
Position of model_C2_homorefine-coot-0.pdb (#2) relative to
cryosparc_P445_J90_005_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999992 -0.00010184 -0.00037400 -0.08767818
0.00010217 0.99999962 0.00086783 -0.06799888
0.00037391 -0.00086787 0.99999955 1.22849693
Axis -0.91306520 -0.39343872 0.10732154
Axis point 0.00000000 1386.03759175 -29.23093170
Rotation angle (degrees) 0.05445840
Shift along axis 0.23865347
> fitmap #2 inMap #3
Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map
cryosparc_P445_J90_005_volume_map.mrc (#3) using 47753 atoms
average map value = 0.1217, steps = 40
shifted from previous position = 0.00588
rotated from previous position = 0.00664 degrees
atoms outside contour = 18865, contour level = 0.097413
Position of model_C2_homorefine-coot-0.pdb (#2) relative to
cryosparc_P445_J90_005_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999996 -0.00010787 -0.00026018 -0.11034384
0.00010809 0.99999964 0.00084711 -0.06362204
0.00026009 -0.00084714 0.99999961 1.24065131
Axis -0.94892380 -0.29140079 0.12095125
Axis point 0.00000000 1425.50997669 -18.29715026
Rotation angle (degrees) 0.05114906
Shift along axis 0.27330574
> fitmap #2 inMap #4
Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map
cryosparc_P445_J88_006_volume_map.mrc (#4) using 47753 atoms
average map value = 0.1119, steps = 44
shifted from previous position = 0.124
rotated from previous position = 0.105 degrees
atoms outside contour = 19231, contour level = 0.091033
Position of model_C2_homorefine-coot-0.pdb (#2) relative to
cryosparc_P445_J88_006_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999813 -0.00193278 -0.00009307 0.19822207
0.00193285 0.99999789 0.00069965 -0.35874598
0.00009172 -0.00069983 0.99999975 1.12174842
Axis -0.34006760 -0.04490483 0.93932826
Axis point 162.62154486 278.76797020 0.00000000
Rotation angle (degrees) 0.11789518
Shift along axis 1.00239052
> fitmap #2 inMap #5
Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map
cryosparc_P445_J81_volume_map.mrc (#5) using 47753 atoms
average map value = 0.1169, steps = 48
shifted from previous position = 1.86
rotated from previous position = 0.113 degrees
atoms outside contour = 19413, contour level = 0.097901
Position of model_C2_homorefine-coot-0.pdb (#2) relative to
cryosparc_P445_J81_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999902 -0.00067324 -0.00122848 0.17466824
0.00067532 0.99999833 0.00169711 -0.31273652
0.00122734 -0.00169793 0.99999781 -0.75976155
Axis -0.77128275 -0.55791034 0.30636410
Axis point 0.00000000 -412.95756728 247.31866665
Rotation angle (degrees) 0.12610273
Shift along axis -0.19300333
> fitmap #2 inMap #5
Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map
cryosparc_P445_J81_volume_map.mrc (#5) using 47753 atoms
average map value = 0.1169, steps = 40
shifted from previous position = 0.0156
rotated from previous position = 0.00756 degrees
atoms outside contour = 19386, contour level = 0.097901
Position of model_C2_homorefine-coot-0.pdb (#2) relative to
cryosparc_P445_J81_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999884 -0.00069771 -0.00135614 0.20387953
0.00070004 0.99999828 0.00171924 -0.32214071
0.00135494 -0.00172019 0.99999760 -0.76292251
Axis -0.74817434 -0.58973610 0.30405014
Axis point 0.00000000 -409.48079695 253.68968434
Rotation angle (degrees) 0.13169739
Shift along axis -0.19452613
> set bgColor white
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select /K/Y
3106 atoms, 3168 bonds, 402 residues, 1 model selected
> color sel orange
> select add #2
47753 atoms, 48594 bonds, 8 pseudobonds, 6152 residues, 2 models selected
> select subtract #2
Nothing selected
> select /H/V
3300 atoms, 3354 bonds, 438 residues, 1 model selected
> color sel blue
> select add #2
47753 atoms, 48594 bonds, 8 pseudobonds, 6152 residues, 2 models selected
> select subtract #2
Nothing selected
> select /J/X
3122 atoms, 3186 bonds, 392 residues, 1 model selected
> color sel hot pink
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 3.5
> color zone #3 near #2 distance 3.5
> color zone #4 near #2 distance 3.5
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> color zone #5 near #2 distance 3.5
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> color #1 white models
===== 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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.0.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: 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: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
OS Loader Version: 582~3311
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 41 minutes, 9 seconds
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
MSI MP273A:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: PB4H944500109
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
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 , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in Side View swap_buffers |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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