![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17329 closed defect (nonchimerax)
Graphics hardware encountered an error and was reset
| 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: 1.6rc202305021906 (2023-05-02 19:06:00 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff85160b680 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 922 in _fill_lighting_parameter_buffer
File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 915 in update_lighting_parameters
File "/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 174 in draw
File "/Applications/ChimeraX-1.6-rc2023.05.02.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 "/Applications/ChimeraX-1.6-rc2023.05.02.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-rc2023.05.02.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-rc2023.05.02.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-rc2023.05.02.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-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.05.02.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" : 270000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 14448,
"osVersion" : {
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"build" : "22D68",
"releaseType" : "User"
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"captureTime" : "2025-04-08 17:59:00.0665 +0200",
"incident" : "1647BF7D-25A9-44EC-8C4D-FF3778860E51",
"pid" : 24789,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-08 17:20:56.9973 +0200",
"procStartAbsTime" : 274962665754733,
"procExitAbsTime" : 277245854946977,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.05.02.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3A79D504-E499-5692-B687-A33EF89D56DA","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "94FF881E-17F8-24BF-E3B0-161DB4B2EC81",
"throttleTimeout" : 2147483647,
"wakeTime" : 8456,
"bridgeVersion" : {"build":"20P3045","train":"7.2"},
"sleepWakeUUID" : "6047C1FA-06F9-4CC1-8CF5-B47C84A53C30",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"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,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
> format mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #1, grid size 220,220,220, pixel 3.94, shown at level 0.0861, step 1,
values float32
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open /Users/makubanska/motl_test_arrays_204_fix_clnd.em format motl
Summary of feedback from opening
/Users/makubanska/motl_test_arrays_204_fix_clnd.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_204_fix_clnd.em with 418 particles.
> artiax view xy
> open
> /Volumes/msdata/makubans/algae_light/mem_seg_bin8/204_px10_prediction_MemBrain_seg_v10_alpha_session.cxs
Opened 204_px10_MemBrain_seg_v10_alpha.ckpt_segmented.mrc as #1, grid size
808,808,434, pixel 10, shown at level 0.422, step 4, values int8
Opened 204_px10_MemBrain_seg_v10_alpha.ckpt_segmented.mrc copy as #3, grid
size 808,808,434, pixel 10, shown at level 0.422, step 1, values int8
opened ChimeraX session
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
> format mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #2, grid size 220,220,220, pixel 3.94, shown at level 0.0861, step 1,
values float32
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open /Users/makubanska/motl_test_arrays_204_fix_clnd.em format motl
Summary of feedback from opening
/Users/makubanska/motl_test_arrays_204_fix_clnd.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_204_fix_clnd.em with 418 particles.
> ui tool show "Map Coordinates"
> ui mousemode right select
> ui tool show "Map Coordinates"
> artiax view xy
> close session
> open /Users/makubanska/figures_thesis/204_stairs_segmentation_cleaned.mrc
Opened 204_stairs_segmentation_cleaned.mrc as #1, grid size 1020,827,550,
pixel 1, shown at step 1, values int8
> volume #1 region 0,0,0,1019,826,549 step 4
> volume #1 change image level 0,0 level 0.1,0.8 level 1,1
> volume #1 level 0.8435
> volume #1 step 1
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open /Users/makubanska/motl_test_arrays_204_fix_clnd.em format motl
Summary of feedback from opening
/Users/makubanska/motl_test_arrays_204_fix_clnd.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_204_fix_clnd.em with 418 particles.
> ui tool show "Map Coordinates"
> artiax view xy
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
> format mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #3, grid size 220,220,220, pixel 3.94, shown at level 0.0861, step 1,
values float32
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98958,0.1413,0.027572,1.0863,-0.1418,0.98975,0.016948,-3.7226,-0.024895,-0.020681,0.99948,-0.83431
> view matrix models
> #3,0.99052,-0.13528,-0.023812,-1.5373,0.13483,0.99067,-0.01965,3.3572,0.026248,0.016253,0.99952,0.82652
> view matrix models
> #3,0.96801,0.24591,0.049828,1.5363,-0.24744,0.96853,0.027056,-6.6261,-0.041606,-0.03852,0.99839,-1.4322
> view matrix models
> #3,0.99983,0.018187,0.0033934,0.16972,-0.018195,0.99983,0.0023873,-0.4667,-0.0033494,-0.0024486,0.99999,-0.10905
> view matrix models
> #3,0.99249,0.12008,0.023253,0.95757,-0.12044,0.99261,0.01464,-3.1494,-0.021324,-0.017331,0.99962,-0.71095
> view matrix models
> #3,-0.31346,0.88704,0.33898,-25.082,-0.9496,-0.29228,-0.11328,-36.643,-0.0014079,-0.3574,0.93395,-3.4572
set axis size 12.21515
12.21515
['.arrow', '0', '0', '0', '12.21515', '0', '0', '0.8143433333333333',
'3.2573733333333332']
set axis size 9.94356
9.94356
['.arrow', '0', '0', '0', '9.94356', '0', '0', '0.6629039999999999',
'2.6516159999999998']
set axis size 9.18636
9.18636
['.arrow', '0', '0', '0', '9.18636', '0', '0', '0.6124240000000001',
'2.4496960000000003']
set axis size 8.42917
8.42917
['.arrow', '0', '0', '0', '8.42917', '0', '0', '0.5619446666666666',
'2.2477786666666666']
set axis size 7.67197
7.67197
['.arrow', '0', '0', '0', '7.67197', '0', '0', '0.5114646666666667',
'2.0458586666666667']
set axis size 4.64318
4.64318
['.arrow', '0', '0', '0', '4.64318', '0', '0', '0.30954533333333334',
'1.2381813333333334']
set axis size 1.61439
1.61439
['.arrow', '0', '0', '0', '1.61439', '0', '0', '0.107626', '0.430504']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
set axis size 0.1
0.1
['.arrow', '0', '0', '0', '0.1', '0', '0', '0.006666666666666667',
'0.02666666666666667']
> artiax particles #2.2.1 axesSize 0.1
> artiax particles #2.2.1 radius 0.1
> artiax attach #3 toParticleList #2.2.1
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #2.2.1.1.1, grid size 220,220,220, pixel 1, shown at level 0.0861, step 1,
values float32
> volume #2.2.1.1.1 capFaces false
> hide #!2.2.1 models
> ui mousemode right select
> select #1
3 models selected
> ui mousemode right "translate selected models"
> show #!2.2.1 models
> view matrix models #1,1,0,0,118.8,0,1,0,-17.044,0,0,1,-10.122
> artiax view xz
> artiax view yz
> artiax view xz
> artiax view xy
> hide #!2.2.1 models
> ui mousemode right select
> select clear
> show #!2.2.1 models
> artiax particles #2.2.1 surfaceLevel 0.01
> hide #!2.2.1 models
> select #1
3 models selected
> ui mousemode right "translate selected models"
> show #!2.2.1 models
> view matrix models #1,1,0,0,126.63,0,1,0,22.084,0,0,1,-1.9573
> hide #!2.2.1 models
> artiax view xz
> show #!2.2.1 models
> hide #!2.2.1 models
> open /Users/makubanska/motl_test_arrays_204_fix_clnd.em format motl
Summary of feedback from opening
/Users/makubanska/motl_test_arrays_204_fix_clnd.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_204_fix_clnd.em with 418 particles.
> artiax view xy
> view matrix models #1,1,0,0,104.71,0,1,0,18.424,0,0,1,-1.9573
> view matrix models #1,1,0,0,116.5,0,1,0,17.412,0,0,1,-1.2459
> select add #1
3 models selected
> ui mousemode right select
> select clear
> hide #!2.2.2 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.2 models
> select #1
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,112.56,0,1,0,16.414,0,0,1,-1.1469
> ui mousemode right select
> select clear
> show #!2.2.1 models
> hide #!2.2.2 models
> artiax particles #2.2.2 color 0,46,86,100
> artiax particles #2.2.2 color 13,33,35,100
> artiax particles #2.2.1 color 94,64,100,100
> artiax particles #2.2.1 color 13,33,35,100
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> ui mousemode right "map eraser"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> volume copy #1 subregion 0,104,0,696,826,549
Opened 204_stairs_segmentation_cleaned.mrc copy as #4, grid size 697,723,550,
pixel 1.97, shown at step 1, values int8
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> show #!2.2.1 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6-rc2023.05.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models
self._populate()
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
Error processing trigger "remove models":
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted
File "/Users/makubanska/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate
self.combo.clear()
See log for complete Python traceback.
> ui mousemode right select
Drag select of axes, 220 of 418 instances, surfaces, 223 of 418 instances, 220
atoms, 4 204_stairs_segmentation_cleaned.mrc copy
> select clear
Drag select of axes, 185 of 418 instances, surfaces, 186 of 418 instances, 185
atoms
fine
> artiax particles #2.2.1 surfaceLevel 0.008
> artiax particles #2.2.1 surfaceLevel 0.006
> artiax particles #2.2.1 surfaceLevel 0.004
> artiax particles #2.2.1 surfaceLevel 0.008
> artiax particles #2.2.1 surfaceLevel 0.013
> artiax particles #2.2.1 surfaceLevel 0.016
> set bgColor white
> save /Users/makubanska/Desktop/image5.png supersample 3
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> save /Users/makubanska/Desktop/image6.png supersample 3
> save /Users/makubanska/Desktop/image7.png supersample 3
> lighting soft
> save /Users/makubanska/Desktop/image8.png supersample 3
> hide #!2.2.1 models
> ui tool show "Side View"
> lighting shadows true intensity 0.5
> lighting shadows false
> show #!2.2.1 models
> save /Users/makubanska/Desktop/image9.png supersample 3
> hide #!2.2.1 models
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> ui tool show "Side View"
> lighting flat
> lighting soft
> graphics silhouettes false
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> lighting soft
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open /Users/makubanska/figures_thesis/motl_only_1_in_radius_404.em
> /Users/makubanska/figures_thesis/motl_only_1_in_radius_204.em format motl
Summary of feedback from opening
/Users/makubanska/figures_thesis/motl_only_1_in_radius_404.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Summary of feedback from opening
/Users/makubanska/figures_thesis/motl_only_1_in_radius_204.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_only_1_in_radius_404.em with 1307 particles.
Opened Particle list motl_only_1_in_radius_204.em with 259 particles.
> hide #!1.2.1 models
Opened 204_bin8.rec as #1.1.1, grid size 512,512,275, pixel 1, shown at level
1.69e+15, step 1, values float32
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
Opened 404_bin8.rec as #1.1.2, grid size 512,512,275, pixel 1, shown at level
1.52e+15, step 1, values float32
> artiax tomo #1.1.2 sliceDirection 0,0,1
> artiax view xy
> volume #1.1.2 region 0,0,136,511,511,136 step 1 showOutlineBox true
> imageMode "full region"
> show #!1.2.1 models
> hide #!1.2.2 models
> artiax particles #1.2.1 radius 9.94356
set axis size 11.45795
11.45795
['.arrow', '0', '0', '0', '11.45795', '0', '0', '0.7638633333333333',
'3.0554533333333334']
set axis size 9.94356
9.94356
['.arrow', '0', '0', '0', '9.94356', '0', '0', '0.6629039999999999',
'2.6516159999999998']
set axis size 10.70076
10.70076
['.arrow', '0', '0', '0', '10.70076', '0', '0', '0.713384', '2.853536']
set axis size 11.45795
11.45795
['.arrow', '0', '0', '0', '11.45795', '0', '0', '0.7638633333333333',
'3.0554533333333334']
set axis size 12.97235
12.97235
['.arrow', '0', '0', '0', '12.97235', '0', '0', '0.8648233333333334',
'3.4592933333333336']
set axis size 13.72955
13.72955
['.arrow', '0', '0', '0', '13.72955', '0', '0', '0.9153033333333334',
'3.6612133333333334']
set axis size 14.48674
14.48674
['.arrow', '0', '0', '0', '14.48674', '0', '0', '0.9657826666666666',
'3.8631306666666663']
set axis size 15.24394
15.24394
['.arrow', '0', '0', '0', '15.24394', '0', '0', '1.0162626666666668',
'4.065050666666667']
set axis size 16.00114
16.00114
['.arrow', '0', '0', '0', '16.00114', '0', '0', '1.0667426666666666',
'4.2669706666666665']
set axis size 16.75833
16.75833
['.arrow', '0', '0', '0', '16.75833', '0', '0', '1.1172220000000002',
'4.468888000000001']
set axis size 17.51553
17.51553
['.arrow', '0', '0', '0', '17.51553', '0', '0', '1.1677019999999998',
'4.670807999999999']
set axis size 18.27273
18.27273
['.arrow', '0', '0', '0', '18.27273', '0', '0', '1.2181819999999999',
'4.8727279999999995']
set axis size 17.51553
17.51553
['.arrow', '0', '0', '0', '17.51553', '0', '0', '1.1677019999999998',
'4.670807999999999']
set axis size 16.75833
16.75833
['.arrow', '0', '0', '0', '16.75833', '0', '0', '1.1172220000000002',
'4.468888000000001']
set axis size 16.00114
16.00114
['.arrow', '0', '0', '0', '16.00114', '0', '0', '1.0667426666666666',
'4.2669706666666665']
set axis size 15.24394
15.24394
['.arrow', '0', '0', '0', '15.24394', '0', '0', '1.0162626666666668',
'4.065050666666667']
set axis size 14.48674
14.48674
['.arrow', '0', '0', '0', '14.48674', '0', '0', '0.9657826666666666',
'3.8631306666666663']
set axis size 14.48674
14.48674
['.arrow', '0', '0', '0', '14.48674', '0', '0', '0.9657826666666666',
'3.8631306666666663']
> artiax particles #1.2.1 axesSize 14.48674
> artiax view xy
> show #!1.2.2 models
> hide #!1.2.1 models
> artiax particles #1.2.2 radius 10.70076
> volume #1.1.1 region 0,0,136,511,511,136 step 1 showOutlineBox true
> imageMode "full region"
OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 564.40.4~66
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 5 days, 4 hours, 55 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
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: Yes
Connection Type: Internal
EV2795:
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: 50045042
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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-ArtiaX: 0.3
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: 1.6rc202305021906
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
geomdl: 5.3.1
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
pandas: 2.0.3
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
starfile: 0.4.12
superqt: 0.4.1
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 , 7 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 , 7 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
ChimeraX crashed in the Apple Intel graphics driver. Unfortunately Apple's graphics driver on Intel Macs is not very stable. There is nothing we can do to fix the graphics driver crash. All new Mac computers with Apple silicon GPUs have stable graphics drivers. It is unlikely Apple will ever fix their old Intel Mac graphics.
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Reported by Marta