![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17328 closed defect (nonchimerax)
Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics
| 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/chimerax/graphics/opengl.py", line 235 in swap_buffers
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 497 in swap_buffers
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 191 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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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
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"modelCode" : "MacBookPro16,2",
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"build" : "22D68",
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"captureTime" : "2025-04-08 17:14:35.2323 +0200",
"incident" : "9D72AF2A-3178-46D2-B556-70C43F243C3E",
"pid" : 19962,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-08 13:13:14.7918 +0200",
"procStartAbsTime" : 260970297441339,
"procExitAbsTime" : 274580891324484,
"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"},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "94FF881E-17F8-24BF-E3B0-161DB4B2EC81",
"throttleTimeout" : 2147483647,
"wakeTime" : 5791,
"bridgeVersion" : {"build":"20P3045","train":"7.2"},
"sleepWakeUUID" : "6047C1FA-06F9-4CC1-8CF5-B47C84A53C30",
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"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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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 /Volumes/msdata/makubans/algae_light/mem_seg_bin8/204_seg_bin4.mrc
Opened 204_seg_bin4.mrc as #1, grid size 1024,1024,550, pixel 1, shown at step
1, values int8
> volume #1 step 4
> volume #1 region 0,0,0,1023,1023,549 step 32
> volume #1 change image level 0,0 level 0.1,0.8 level 1,1
> volume #1 level 0.5727
> volume #1 step 8
> ui mousemode right "map eraser"
> volume erase #1 center 1201.3,85.867,755.22 radius 461.68
Opened 204_seg_bin4.mrc copy as #3, grid size 1024,1024,550, pixel 1, shown at
step 1, values int8
> artiax view xy
> volume copy #3 subregion 0,197,0,1019,1023,549
Opened 204_seg_bin4.mrc copy as #4, grid size 1020,827,550, pixel 1, shown at
step 1, values int8
> volume erase #4 center 1152,500.32,895.68 radius 512
> volume erase #4 center 1168.1,811.8,956.2 radius 512
> volume erase #4 center 675.13,236.35,891.69 radius 512
> volume erase #4 center 1241.7,855.42,-128.76 radius 512
> volume erase #4 center 1048.8,775.95,-254.53 radius 512
> volume erase #4 center 1093.6,312.86,-239.67 radius 512
> volume erase #4 center 1462.8,288.92,298.19 radius 512
> volume erase #4 center 1218.2,111.04,752.27 radius 512
> volume erase #4 center 779.7,234.04,394.88 radius 47.94
> volume erase #4 center 791.33,256.98,396.31 radius 47.94
> volume erase #4 center 792.77,193.19,391.93 radius 47.94
> volume erase #4 center 874.68,204.28,337.24 radius 47.94
> volume erase #4 center 874.96,249.94,347.53 radius 47.94
> volume erase #4 center 874.58,271.71,352.49 radius 47.94
> volume erase #4 center 879.1,235.56,334.47 radius 47.94
> save /Users/makubanska/204_stairs_segmentation_cleaned.mrc models #4
> volume erase #4 center 842.09,225.99,390.66 radius 47.94
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened 204_bin8.rec as #2.1.1, grid size 512,512,275, pixel 1, shown at level
1.69e+15, step 1, values float32
> artiax tomo #2.1.1 sliceDirection 0,0,1
> artiax view xy
> volume #2.1.1 region 0,0,136,511,511,136 step 1 showOutlineBox true
> imageMode "full region"
> open /Users/makubanska/motl_test_arrays_204_fix.em format motl
Summary of feedback from opening /Users/makubanska/motl_test_arrays_204_fix.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_204_fix.em with 438 particles.
> artiax view xy
> ui mousemode right select
Drag select of axes, 6 of 438 instances, 6 atoms
fine
Drag select of axes, 4 of 432 instances, 4 atoms
fine
Drag select of 1 atoms
fine
427 atoms, 427 residues, atom cross_correlation range 0.0163 to 0.128
> artiax colormap #2.2.1.3 cross_correlation palette redgreen minValue
> 0.016303179785609245 maxValue 0.12790599465370178 transparency 0.0
> artiax particles #2.2.1 radius 5.73099
set axis size 12.76972
12.76972
['.arrow', '0', '0', '0', '12.76972', '0', '0', '0.8513146666666667',
'3.4052586666666667']
set axis size 11.36197
11.36197
['.arrow', '0', '0', '0', '11.36197', '0', '0', '0.7574646666666667',
'3.0298586666666667']
set axis size 10.6581
10.6581
['.arrow', '0', '0', '0', '10.6581', '0', '0', '0.71054', '2.84216']
set axis size 9.95423
9.95423
['.arrow', '0', '0', '0', '9.95423', '0', '0', '0.6636153333333333',
'2.6544613333333333']
set axis size 9.25035
9.25035
['.arrow', '0', '0', '0', '9.25035', '0', '0', '0.61669', '2.46676']
set axis size 8.54648
8.54648
['.arrow', '0', '0', '0', '8.54648', '0', '0', '0.5697653333333333',
'2.2790613333333334']
set axis size 7.84261
7.84261
['.arrow', '0', '0', '0', '7.84261', '0', '0', '0.5228406666666666',
'2.0913626666666665']
set axis size 5.73099
5.73099
['.arrow', '0', '0', '0', '5.73099', '0', '0', '0.382066', '1.528264']
set axis size 5.02711
5.02711
['.arrow', '0', '0', '0', '5.02711', '0', '0', '0.3351406666666667',
'1.3405626666666668']
set axis size 4.32324
4.32324
['.arrow', '0', '0', '0', '4.32324', '0', '0', '0.288216', '1.152864']
set axis size 3.61937
3.61937
['.arrow', '0', '0', '0', '3.61937', '0', '0', '0.24129133333333333',
'0.9651653333333333']
set axis size 2.91549
2.91549
['.arrow', '0', '0', '0', '2.91549', '0', '0', '0.194366', '0.777464']
set axis size 2.21162
2.21162
['.arrow', '0', '0', '0', '2.21162', '0', '0', '0.14744133333333334',
'0.5897653333333334']
set axis size 0.80387
0.80387
['.arrow', '0', '0', '0', '0.80387', '0', '0', '0.05359133333333333',
'0.21436533333333332']
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
427 atoms, 427 residues, atom cross_correlation range 0.0163 to 0.128
> artiax colormap #2.2.1.3 cross_correlation palette redgreen minValue
> 0.07447191965625141 maxValue 0.12790599465370178 transparency 0.0
> open /Users/makubanska/motl_test_arrays_204_fix.em format motl
Summary of feedback from opening /Users/makubanska/motl_test_arrays_204_fix.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_204_fix.em with 438 particles.
438 atoms, 438 residues, atom cross_correlation range 0.0163 to 0.128
> artiax colormap #2.2.1.3 cross_correlation palette redgreen minValue
> 0.016303179785609245 maxValue 0.12790599465370178 transparency 0.0
438 atoms, 438 residues, atom class_number range 0 to 114
> artiax colormap #2.2.1.3 class_number palette redgreen minValue 0.0 maxValue
> 114.0 transparency 0.0
set axis size 16.28908
16.28908
['.arrow', '0', '0', '0', '16.28908', '0', '0', '1.0859386666666666',
'4.343754666666666']
set axis size 14.17746
14.17746
['.arrow', '0', '0', '0', '14.17746', '0', '0', '0.945164', '3.780656']
set axis size 13.47359
13.47359
['.arrow', '0', '0', '0', '13.47359', '0', '0', '0.8982393333333333',
'3.592957333333333']
set axis size 12.76972
12.76972
['.arrow', '0', '0', '0', '12.76972', '0', '0', '0.8513146666666667',
'3.4052586666666667']
set axis size 12.06585
12.06585
['.arrow', '0', '0', '0', '12.06585', '0', '0', '0.8043899999999999',
'3.2175599999999998']
set axis size 11.36197
11.36197
['.arrow', '0', '0', '0', '11.36197', '0', '0', '0.7574646666666667',
'3.0298586666666667']
set axis size 10.6581
10.6581
['.arrow', '0', '0', '0', '10.6581', '0', '0', '0.71054', '2.84216']
set axis size 9.95423
9.95423
['.arrow', '0', '0', '0', '9.95423', '0', '0', '0.6636153333333333',
'2.6544613333333333']
set axis size 9.25035
9.25035
['.arrow', '0', '0', '0', '9.25035', '0', '0', '0.61669', '2.46676']
set axis size 8.54648
8.54648
['.arrow', '0', '0', '0', '8.54648', '0', '0', '0.5697653333333333',
'2.2790613333333334']
set axis size 7.84261
7.84261
['.arrow', '0', '0', '0', '7.84261', '0', '0', '0.5228406666666666',
'2.0913626666666665']
set axis size 7.13873
7.13873
['.arrow', '0', '0', '0', '7.13873', '0', '0', '0.4759153333333333',
'1.9036613333333332']
set axis size 6.43486
6.43486
['.arrow', '0', '0', '0', '6.43486', '0', '0', '0.42899066666666663',
'1.7159626666666665']
set axis size 5.73099
5.73099
['.arrow', '0', '0', '0', '5.73099', '0', '0', '0.382066', '1.528264']
set axis size 5.02711
5.02711
['.arrow', '0', '0', '0', '5.02711', '0', '0', '0.3351406666666667',
'1.3405626666666668']
set axis size 4.32324
4.32324
['.arrow', '0', '0', '0', '4.32324', '0', '0', '0.288216', '1.152864']
set axis size 3.61937
3.61937
['.arrow', '0', '0', '0', '3.61937', '0', '0', '0.24129133333333333',
'0.9651653333333333']
set axis size 2.91549
2.91549
['.arrow', '0', '0', '0', '2.91549', '0', '0', '0.194366', '0.777464']
set axis size 2.21162
2.21162
['.arrow', '0', '0', '0', '2.21162', '0', '0', '0.14744133333333334',
'0.5897653333333334']
set axis size 1.50775
1.50775
['.arrow', '0', '0', '0', '1.50775', '0', '0', '0.10051666666666666',
'0.40206666666666663']
set axis size 0.80387
0.80387
['.arrow', '0', '0', '0', '0.80387', '0', '0', '0.05359133333333333',
'0.21436533333333332']
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
> select #2.1.1
3 models selected
Drag select of axes, 1 of 438 instances, 1 atoms
fine
> select #2.1.1
3 models selected
> select #2.1.1
3 models selected
> select clear
> select /M:351@M
1 atom, 1 residue, 1 model selected
> select #2.1.1
3 models selected
> select /M:350@M
1 atom, 1 residue, 1 model selected
fine
Drag select of axes, 2 of 436 instances, 2 atoms
fine
> select clear
Drag select of axes, 1 of 434 instances, 1 atoms
fine
Drag select of axes, 3 of 433 instances, 3 atoms
fine
Drag select of axes, 1 of 430 instances, 1 atoms
fine
Drag select of axes, 2 of 429 instances, 2 atoms
fine
> select /M:428@M
1 atom, 1 residue, 1 model selected
> select clear
> artiax view xy
Drag select of axes, 1 of 427 instances, 1 atoms
fine
> select clear
Drag select of axes, 2 of 426 instances, 2 atoms
fine
Drag select of axes, 1 of 424 instances, 1 atoms
fine
> select #2.1.1
3 models selected
Drag select of axes, 1 of 423 instances, 1 atoms
fine
> select /M:108@M
1 atom, 1 residue, 1 model selected
> select #2.1.1
3 models selected
> select /M:427@M
1 atom, 1 residue, 1 model selected
fine
Drag select of axes, 2 of 421 instances, 2 atoms
fine
Drag select of axes, 1 of 419 instances, 1 atoms
> select #2.1.1
3 models selected
> select clear
Drag select of axes, 1 of 419 instances, 1 atoms
fine
> select #2.1.1
3 models selected
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #5, grid size 220,220,220, pixel 3.94, shown at level 0.0861, step 1,
values float32
> volume #5 level -0.09289
> volume #5 level 0.04133
> artiax attach #5 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 2, shown at level 0.0861, step 1,
values float32
> volume #2.2.1.1.1 capFaces false
> close #2.2.1.1.1
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #5, grid size 220,220,220, pixel 3.94, shown at level 0.0861, step 1,
values float32
> artiax particles #2.2.1 surfaceLevel 0.1838
> artiax attach #5 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 1.97, shown at level 0.0861, step
1, values float32
> volume #2.2.1.1.1 capFaces false
> artiax particles #2.2.1 surfaceLevel 0.03738
> save /Users/makubanska/motl_test_arrays_204_fix_clnd.em partlist #2.2.1
> hide #!2.2.1.1 models
> hide #2.2.1.2 models
> hide #2.2.1.3 models
> show #2.2.1.2 models
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #5, grid size 220,220,220, pixel 1, shown at level 0.0861, step 1, values
float32
> close #2.2.1.1.1
> artiax attach #5 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
418 atoms, 418 residues, atom class_number range 0 to 114
> artiax colormap #2.2.1.3 class_number palette redgreen minValue 0.0 maxValue
> 114.0 transparency 0.0
> artiax particles #2.2.1 surfaceLevel 0.06216
> hide #!2.2.1 models
> hide #!2.1.1 models
Opened 404_bin8.rec as #2.1.2, grid size 512,512,275, pixel 1, shown at level
1.52e+15, step 1, values float32
> artiax tomo #2.1.2 sliceDirection 0,0,1
> artiax view xy
> open /Users/makubanska/motl_test_arrays_404_fix.em format motl
Summary of feedback from opening /Users/makubanska/motl_test_arrays_404_fix.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_404_fix.em with 2805 particles.
> artiax tomo #2.1.2 pixelSize 2.0
> artiax view xy
> artiax tomo #2.1.2 pixelSize 4.0
> artiax view xy
> artiax tomo #2.1.2 pixelSize 4.0
> artiax view xy
2805 atoms, 2805 residues, atom cross_correlation range 0.0108 to 0.117
> artiax colormap #2.2.2.3 cross_correlation palette redgreen minValue
> 0.010755396448075771 maxValue 0.11684773862361908 transparency 0.0
2805 atoms, 2805 residues, atom tomo_number range 404 to 404
> artiax colormap #2.2.2.3 tomo_number palette redgreen minValue 404.0
> maxValue 404.0 transparency 0.0
set axis size 15.58521
15.58521
['.arrow', '0', '0', '0', '15.58521', '0', '0', '1.039014', '4.156056']
set axis size 14.17746
14.17746
['.arrow', '0', '0', '0', '14.17746', '0', '0', '0.945164', '3.780656']
set axis size 13.47359
13.47359
['.arrow', '0', '0', '0', '13.47359', '0', '0', '0.8982393333333333',
'3.592957333333333']
set axis size 12.76972
12.76972
['.arrow', '0', '0', '0', '12.76972', '0', '0', '0.8513146666666667',
'3.4052586666666667']
set axis size 12.06585
12.06585
['.arrow', '0', '0', '0', '12.06585', '0', '0', '0.8043899999999999',
'3.2175599999999998']
set axis size 11.36197
11.36197
['.arrow', '0', '0', '0', '11.36197', '0', '0', '0.7574646666666667',
'3.0298586666666667']
set axis size 10.6581
10.6581
['.arrow', '0', '0', '0', '10.6581', '0', '0', '0.71054', '2.84216']
set axis size 9.25035
9.25035
['.arrow', '0', '0', '0', '9.25035', '0', '0', '0.61669', '2.46676']
set axis size 8.54648
8.54648
['.arrow', '0', '0', '0', '8.54648', '0', '0', '0.5697653333333333',
'2.2790613333333334']
set axis size 7.84261
7.84261
['.arrow', '0', '0', '0', '7.84261', '0', '0', '0.5228406666666666',
'2.0913626666666665']
set axis size 7.13873
7.13873
['.arrow', '0', '0', '0', '7.13873', '0', '0', '0.4759153333333333',
'1.9036613333333332']
set axis size 6.43486
6.43486
['.arrow', '0', '0', '0', '6.43486', '0', '0', '0.42899066666666663',
'1.7159626666666665']
set axis size 5.73099
5.73099
['.arrow', '0', '0', '0', '5.73099', '0', '0', '0.382066', '1.528264']
set axis size 5.02711
5.02711
['.arrow', '0', '0', '0', '5.02711', '0', '0', '0.3351406666666667',
'1.3405626666666668']
set axis size 3.61937
3.61937
['.arrow', '0', '0', '0', '3.61937', '0', '0', '0.24129133333333333',
'0.9651653333333333']
set axis size 2.91549
2.91549
['.arrow', '0', '0', '0', '2.91549', '0', '0', '0.194366', '0.777464']
set axis size 2.21162
2.21162
['.arrow', '0', '0', '0', '2.21162', '0', '0', '0.14744133333333334',
'0.5897653333333334']
set axis size 1.50775
1.50775
['.arrow', '0', '0', '0', '1.50775', '0', '0', '0.10051666666666666',
'0.40206666666666663']
set axis size 0.80387
0.80387
['.arrow', '0', '0', '0', '0.80387', '0', '0', '0.05359133333333333',
'0.21436533333333332']
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 #2.2.2 axesSize 0.1
> artiax particles #2.2.2 radius 7.13873
2805 atoms, 2805 residues, atom class_number range 0 to 973
> artiax colormap #2.2.2.3 class_number palette redgreen minValue 0.0 maxValue
> 973.0 transparency 0.0
> volume #2.1.2 region 0,0,136,511,511,136 step 1 showOutlineBox true
> imageMode "full region"
> volume #2.1.2 region 0,0,138,511,511,138
> volume #2.1.2 region 0,0,135,511,511,135
> ui mousemode right select
Drag select of axes, 1 of 2805 instances, 1 atoms
2805 atoms, 2805 residues, atom class_number range 0 to 973
> artiax colormap #2.2.2.3 class_number palette redgreen minValue
> 288.9515151515152 maxValue 973.0 transparency 0.0
> open /Users/makubanska/motl_test_arrays_404_fix.em format motl
Summary of feedback from opening /Users/makubanska/motl_test_arrays_404_fix.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_404_fix.em with 2805 particles.
set axis size 12.06585
12.06585
['.arrow', '0', '0', '0', '12.06585', '0', '0', '0.8043899999999999',
'3.2175599999999998']
set axis size 10.6581
10.6581
['.arrow', '0', '0', '0', '10.6581', '0', '0', '0.71054', '2.84216']
set axis size 9.95423
9.95423
['.arrow', '0', '0', '0', '9.95423', '0', '0', '0.6636153333333333',
'2.6544613333333333']
set axis size 9.25035
9.25035
['.arrow', '0', '0', '0', '9.25035', '0', '0', '0.61669', '2.46676']
set axis size 7.84261
7.84261
['.arrow', '0', '0', '0', '7.84261', '0', '0', '0.5228406666666666',
'2.0913626666666665']
set axis size 6.43486
6.43486
['.arrow', '0', '0', '0', '6.43486', '0', '0', '0.42899066666666663',
'1.7159626666666665']
set axis size 5.73099
5.73099
['.arrow', '0', '0', '0', '5.73099', '0', '0', '0.382066', '1.528264']
set axis size 4.32324
4.32324
['.arrow', '0', '0', '0', '4.32324', '0', '0', '0.288216', '1.152864']
set axis size 2.91549
2.91549
['.arrow', '0', '0', '0', '2.91549', '0', '0', '0.194366', '0.777464']
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 #2.2.2 axesSize 0.1
> artiax particles #2.2.2 radius 9.25035
2805 atoms, 2805 residues, atom cross_correlation range 0.0108 to 0.117
> artiax colormap #2.2.2.3 cross_correlation palette redgreen minValue
> 0.010755396448075771 maxValue 0.11684773862361908 transparency 0.0
2805 atoms, 2805 residues, atom class_number range 0 to 380
> artiax colormap #2.2.2.3 class_number palette redgreen minValue 0.0 maxValue
> 380.0 transparency 0.0
> artiax view xy
> select #2.2.2.3/M:1146@M
1 atom, 1 residue, 1 model selected
fine
> select #2.2.2.3/M:324@M
1 atom, 1 residue, 1 model selected
fine
> select #2.2.2.3/M:910@M
1 atom, 1 residue, 1 model selected
fine
Drag select of axes, 1 of 2802 instances, 1 atoms
fine
> hide #!2.2.2 models
> open /Users/makubanska/figures_thesis/ref_b2_PS_v2_4_inv.mrc
Opened ref_b2_PS_v2_4_inv.mrc as #5, grid size 84,84,84, pixel 3.94, shown at
level 0.169, step 1, values float32
> show #!2.2.2 models
> volume #5 level 0.1364
> volume #5 level 0.1161
> artiax view xy
> hide #!2.2.2 models
Drag select of 5 ref_b2_PS_v2_4_inv.mrc
> select clear
> volume #5 level 0.03527
> close #5
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #5, grid size 220,220,220, pixel 1, shown at level 0.0861, step 1, values
float32
> artiax view xy
> close #5
> open
> /Users/makubanska/figures_thesis/tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #5, grid size 220,220,220, pixel 1, shown at level 0.0861, step 1, values
float32
> artiax attach #5 toParticleList #2.2.2
Opened tomsa_reali_wangles_all_bin2_r4_tightmask_ref_b2_all_3_trimmed_inv.mrc
as #2.2.2.1.1, grid size 220,220,220, pixel 1, shown at level 0.0861, step 1,
values float32
> volume #2.2.2.1.1 capFaces false
> show #!2.2.2 models
> artiax particles #2.2.2 surfaceLevel 0.00133
> artiax view xy
> artiax view xz
> artiax view yz
> artiax view xy
2801 atoms, 2801 residues, atom class_number range 0 to 380
> artiax colormap #2.2.2.3 class_number palette redgreen minValue
> 96.72727272727272 maxValue 380.0 transparency 0.0
2801 atoms, 2801 residues, atom class_number range 0 to 380
> artiax colormap #2.2.2.3 class_number palette redgreen minValue 0.0 maxValue
> 380.0 transparency 0.0
2801 atoms, 2801 residues, atom class_number range 0 to 380
> artiax colormap #2.2.2.3 class_number palette redgreen minValue 40.0
> maxValue 380.0 transparency 0.0
2801 atoms, 2801 residues, atom class_number range 0 to 380
> artiax colormap #2.2.2.3 class_number palette redgreen minValue 40.0
> maxValue 380.0 transparency 0.0
2801 atoms, 2801 residues, atom class_number range 0 to 380
> artiax colormap #2.2.2.3 class_number palette redgreen minValue 80.0
> maxValue 380.0 transparency 0.0
> hide #!2.2.2 models
> open /Users/makubanska/motl_test_arrays_404_fix.em format motl
Summary of feedback from opening /Users/makubanska/motl_test_arrays_404_fix.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list motl_test_arrays_404_fix.em with 2805 particles.
> volume #4 level 0.5438
> view #3 clip false
No displayed objects specified.
> show #!3 models
> show #!4 target m
> view #4 clip false
> artiax view xy
> hide #!2.2.3 models
> 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.
> select add #4
2 models selected
> select clear
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,103.22,0,1,0,11.054,0,0,1,-5.731
> view matrix models #4,1,0,0,107.13,0,1,0,16.632,0,0,1,-6.2433
> artiax view xy
> view matrix models #4,1,0,0,106.33,0,1,0,16.632,0,0,1,-6.2433
> ui mousemode right select
> select clear
> show #!2.2.1 models
> hide #!2.2.1 models
> hide #!2.2.4 models
> set bgColor white
> show #!2.2.1 models
Drag select of axes, 3 of 418 instances, surfaces, 3 of 418 instances
fine
> hide #!2.2.1 models
> lighting simple
> show #!2.2.1 models
> save /Users/makubanska/Desktop/image1.png supersample 3
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> volume #4 level 0.6758
> show #!2.2.1 models
> save /Users/makubanska/Desktop/image1.png supersample 3
> save /Users/makubanska/Desktop/image2.png supersample 3
> artiax particles #2.2.1 surfaceLevel 0.00809
> artiax particles #2.2.1 surfaceLevel 0.01
> save /Users/makubanska/Desktop/image3.png supersample 3
> artiax particles #2.2.1 color 0,46,86,100
> artiax particles #2.2.1 color 13,33,35,100
> artiax particles #2.2.1 radius 0.1
> save /Users/makubanska/Desktop/image2.png supersample 3
> hide #!2.2.1 models
> show #!2.2.1 models
> save /Users/makubanska/Desktop/image3.png supersample 3
> save /Users/makubanska/Desktop/image4.png supersample 3
> hide #!2.2.1 models
> lighting soft
> lighting simple
> show #!2.2.1 models
> hide #!2.2.1 models
> lighting soft
> show #!2.2.1 models
> hide #!2.2.1 models
> lighting simple
> show #!2.2.1 models
> hide #!2.2.1 models
===== 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
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, 3 hours, 59 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 |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.