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#10239 closed defect (fixed)
Crash in GL.glDeleteBuffers() while updating tomogram surfaces
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Greg Couch, chimerax-programmers | |
| 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: Segmentation fault
Current thread 0x000000030f0af000 (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 2643 in release_buffer
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 2634 in delete_buffer
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1721 in delete
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1712 in __del__
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 364 in notify
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 381 in notify_all
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 544 in set
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 962 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
Thread 0x0000000200578240 (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 312 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 897 in start
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/logger.py", line 232 in status
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/logger.py", line 459 in status
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 111 in message
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 2092 in update_surface
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 808 in _update_surfaces
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 785 in update_drawings
File "/Users/jenny/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/artiax/volume/Tomogram.py", line 34 in __init__
File "/Users/jenny/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/artiax/volume/VolumePlus.py", line 28 in from_volume
File "/Users/jenny/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/artiax/ArtiaX.py", line 351 in open_tomogram
File "/Users/jenny/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/artiax/tool.py", line 393 in _open_volume
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
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"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000001420","rawCodes":[1,5152],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000001420"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":64985},
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{
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},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8989D2A78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/jenny/Desktop/231128_TemplateComparison.cxs
Opened NR_mask_ellipsoid_112px_25x_35y_18z_G2_0,0,0shifts.em as #1, grid size
112,112,112, pixel 1, shown at level 1, step 1, values float32
Opened NRmask_ellipsoid_112px_sx25sy35sz18_dx-2dy-5dz5_G1.em as #2, grid size
112,112,112, pixel 1, shown at level 1, step 1, values float32
Opened NRtmpl_tomsa_r2_b4_NR_center_ref_11.em as #3, grid size 112,112,112,
pixel 1, shown at level -0.125, step 1, values float32
Opened EMD14330_NRpublished_CRposition.em as #4, grid size 112,112,112, pixel
1, shown at level -2.45, step 1, values float32
Opened Ver1 as #5, grid size 112,112,112, pixel 1, shown at level -0.145, step
1, values float32
Opened Template as #6, grid size 112,112,112, pixel 1, shown at level -0.73,
step 1, values float32
Opened Ver2 as #7, grid size 112,112,112, pixel 1, shown at level -2.36, step
1, values float32
Opened Ver3 as #8, grid size 112,112,112, pixel 1, shown at level -2.45, step
1, values float32
Log from Tue Nov 28 09:43:26 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 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
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em
Opened 420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em as #2, grid size
20,65,1, pixel 1, shown at step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 420TEST_CRpublished_5deg_STD8_dist25_thresh0.0634.em with
65 particles.
> close #2
> hide #!1.2.1 models
> show #!1.2.1 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/420_CRpublished_5deg_STD8_dist25_thresh0.0634.em
Opened 420_CRpublished_5deg_STD8_dist25_thresh0.0634.em as #2, grid size
20,65,1, pixel 1, shown at step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/420_CRpublished_5deg_STD8_dist25_thresh0.0634.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/420_CRpublished_5deg_STD8_dist25_thresh0.0634.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 420_CRpublished_5deg_STD8_dist25_thresh0.0634.em with 65
particles.
> close #2
> hide #!1.2.1 models
> show #!1.2.1 models
> view all
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.1 models
> show #!1.2.1 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0053.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/CRpublished_5deg/peak_extraction/test_trimming/420TEST_CRpublished_5deg_STD8_dist25_thresh0.0053.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 420TEST_CRpublished_5deg_STD8_dist25_thresh0.0053.em with
73 particles.
> hide #!1.2.1 models
> hide #!1.2.2 models
> show #!1.2.2 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.023.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.023.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.023.em with 1324
particles.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0515.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0515.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0515.em with 656
particles.
> hide #!1.2.4 models
> hide #!1.2.3 models
> hide #!1.2.2 models
> show #!1.2.4 models
> show #!1.2.3 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0359.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0359.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0359.em with
1742 particles.
> hide #!1.2.4 models
> hide #!1.2.3 models
> hide #!1.2.5 models
> hide #!1.2.6 models
> show #!1.2.6 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0524.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0524.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0524.em with 641
particles.
> view all
> hide #!1.2.7 models
> hide #!1.2.6 models
> show #!1.2.6 models
> show #!1.2.5 models
> hide #!1.2.6 models
> show #!1.2.4 models
> hide #!1.2.5 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0417.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0417.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0417.em with
1802 particles.
> hide #!1.2.4 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0405.em with
1917 particles.
> hide #!1.2.8 models
> show #!1.2.8 models
> hide #!1.2.8 models
> show #!1.2.8 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0405.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0405.em with
1917 particles.
> hide #!1.2.9 models
> hide #!1.2.8 models
> hide #!1.2.10 models
> show #!1.2.10 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0379.em with
2095 particles.
> hide #!1.2.10 models
> show #!1.2.10 models
> close #1.2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0379.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0379.em with
2095 particles.
Opened 251_dose-filt_rec.mrc as #1.1.1, grid size 1024,1024,500, pixel 4,
shown at level 39.7, step 1, values float32
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> artiax tomo #1.1.1 pixelSize 1.0
> artiax view xy
> artiax tomo #1.1.1 pixelSize 1.0
> artiax view xy
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0697.em with 344
particles.
344 atoms, 344 residues, atom cross_correlation range 0.0697 to 0.135
[Repeated 1 time(s)]
> artiax colormap #1.2.2.3 cross_correlation palette redgreen minValue
> 0.06972353905439377 maxValue 0.13522033393383026 transparency 0.0
> artiax particles #1.2.2 radius 10.0
set axis size 25.0
25.0
['.arrow', '0', '0', '0', '25.0', '0', '0', '1.6666666666666667',
'6.666666666666667']
set axis size 25.0
25.0
['.arrow', '0', '0', '0', '25.0', '0', '0', '1.6666666666666667',
'6.666666666666667']
> artiax particles #1.2.2 axesSize 25.0
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD8_dist25_thresh0.0697.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD8_dist25_thresh0.0697.em with 344
particles.
> artiax tomo #1.1.1 slice 344
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0853.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0853.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD10_dist25_thresh0.0853.em with
101 particles.
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> artiax particles #1.2.1 radius 10.0
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD15_dist25_thresh0.1241.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD15_dist25_thresh0.1241.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD15_dist25_thresh0.1241.em with 2
particles.
> hide #!1.2.1 models
> hide #!1.2.2 models
> artiax tomo #1.1.1 slice 261
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD12_dist25_thresh0.1008.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD12_dist25_thresh0.1008.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD12_dist25_thresh0.1008.em with 29
particles.
> artiax tomo #1.1.1 slice 177
> show #!1.2.2 models
> hide #!1.2.3 models
> artiax tomo #1.1.1 slice 154
> show #!1.2.3 models
> show #!1.2.1 models
> hide #!1.2.1 models
> hide #!1.2.3 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> hide #!1.2.2 models
> show #!1.2.2 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.093.em with 55
particles.
> hide #!1.2.2 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> artiax particles #1.2.5 color 88,100,40,100
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> hide #!1.2.4 models
> show #!1.2.4 models
> close #1.1
> close #1.2
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.0992.em with 33
particles.
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.093.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.093.em with 55
particles.
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.1 models
> show #!1.1.1 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1286.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1286.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.1286.em with
343 particles.
> hide #!1.1.3 models
> show #!1.1.3 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.1 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1283.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.1283.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.1283.em with
346 particles.
> hide #!1.1.4 models
> hide #!1.1.3 models
> show #!1.1.4 models
> hide #!1.1.4 models
> show #!1.1.4 models
> hide #!1.1.4 models
> show #!1.1.4 models
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD11_dist25_thresh0.0992.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD11_dist25_thresh0.0992.em with 33
particles.
> view all
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0909.em
> format motl
Summary of feedback from opening
/Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_new_5deg/peak_extraction/251_NRpublished_5deg_STD10_dist25_thresh0.0909.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 251_NRpublished_5deg_STD10_dist25_thresh0.0909.em with 67
particles.
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.1 models
> show #!1.1.1 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.2 models
Opened 251_dose-filt_full_rec.mrc as #1.2.1, grid size 1024,500,1024, pixel 4,
shown at level 39.7, step 1, values float32
> artiax tomo #1.2.1 sliceDirection 0,0,1
> artiax view xy
> close all
> set bgColor white
> set bgColor #ffffff00
> open
> /Volumes/msdata/jesachwe/EM_Projects/Mot2KO_cryo/IntranuclearNPCs/SA_IntranuclearNPC/IntranuclearNPCs_bin4/CompositeMap/oldscripts/wholemount_IR.m
Unrecognized file suffix '.m'
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/NR_mask_ellipsoid_112px_25x_35y_18z_G2_0,0,0shifts.em
Opened NR_mask_ellipsoid_112px_25x_35y_18z_G2_0,0,0shifts.em as #1, grid size
112,112,112, pixel 1, shown at level 1, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/NRmask_ellipsoid_112px_sx25sy35sz18_dx-2dy-5dz5_G1.em
Opened NRmask_ellipsoid_112px_sx25sy35sz18_dx-2dy-5dz5_G1.em as #2, grid size
112,112,112, pixel 1, shown at level 1, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/NRtmpl_tomsa_r2_b4_NR_center_ref_11.em
Opened NRtmpl_tomsa_r2_b4_NR_center_ref_11.em as #3, grid size 112,112,112,
pixel 1, shown at level 0.101, step 1, values float32
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/base/inputs/EMD14330_NRpublished_CRposition.em
Opened EMD14330_NRpublished_CRposition.em as #4, grid size 112,112,112, pixel
1, shown at level 2.32, step 1, values float32
> view all
> volume #4 level -2.451
> volume #3 level -0.1251
> volume all capFaces false
Unsupported scale factor (0.000000) detected on Display1
[Repeated 4 time(s)]
> vop multiply #3 #1
Opened volume product as #5, grid size 112,112,112, pixel 1, shown at step 1,
values float32
> rename #5 version 1
Expected a keyword
> rename #5 Ver1
> open
> /Volumes/msdata/jesachwe/EM_Projects/Flies358VNVC/CytoplasmicNPCs/TemplateMatching_FlyNPCs_GPU/NRpublished_5deg/inputs/EMD14330_NRtemplate.em
Opened EMD14330_NRtemplate.em as #6, grid size 112,112,112, pixel 1, shown at
level 2.39, step 1, values float32
> vop multiply #6 #1
Opened volume product as #7, grid size 112,112,112, pixel 1, shown at step 1,
values float32
> rename #6 Ver1
> vop multiply #4 #2
Opened volume product as #8, grid size 112,112,112, pixel 1, shown at step 1,
values float32
> rename #7 Ver3
> rename #6 Ver2
> ui tool show "Volume Viewer"
> volume #7 level -3.09
> volume all capFaces false
> rename #7 Ver2
> rename #8 Ver3
> volume #6 level -0.7298
> rename #6 Template
> ui tool show "Volume Viewer"
> volume #5 color #ffd479
> volume #6 color #7a81ff
> volume #7 color #ff85ff
> volume #7 color #ff2f92
> tile
3 models tiled
> tile off
> volume #5 color #ff9300
> graphics silhouettes true
> lighting soft
> volume #7 level -2.357
> volume #5 level -0.1453
> volume #8 color #00fa92
> volume #8 color #00f900
> volume #8 color #73fcd6
> volume #8 color #7a81ff
> volume #8 color #0433ff
> ui mousemode right select
> select clear
> select #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.9506,-0.048013,-0.30669,22.435,0.14231,-0.81065,0.56798,56.984,-0.27589,-0.58356,-0.76377,139.59
> ui mousemode right "move picked models"
> view matrix models
> #8,0.9506,-0.048013,-0.30669,24.969,0.14231,-0.81065,0.56798,63.242,-0.27589,-0.58356,-0.76377,143.74
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.87326,0.049417,0.48474,-19.474,-0.25494,-0.80146,0.54098,85.878,0.41524,-0.596,-0.68729,102.55
> ui mousemode right "move picked models"
> view matrix models
> #8,0.87326,0.049417,0.48474,-20.973,-0.25494,-0.80146,0.54098,87.285,0.41524,-0.596,-0.68729,103.24
> fitmap #8 inMap #7 metric correlation
Fit map Ver3 in map Ver2 using 1399302 points
correlation = 0.5283, correlation about mean = 0.5294, overlap = 4.362e+04
steps = 116, shift = 2.24, angle = 10 degrees
Position of Ver3 (#8) relative to Ver2 (#7) coordinates:
Matrix rotation and translation
0.98348560 0.15935560 0.08580126 -10.81601839
0.15850813 -0.98721736 0.01664497 103.20266885
0.08735696 -0.00276989 -0.99617322 106.44537391
Axis -0.99586274 -0.07979802 -0.04347039
Axis point 0.00000000 52.29493812 53.20661068
Rotation angle (degrees) 179.44148558
Shift along axis -2.09132105
> ui mousemode right select
> select clear
> ui mousemode right select
> save /Users/jenny/Desktop/231128_TemplateComparison.cxs
——— End of log from Tue Nov 28 09:43:26 2023 ———
opened ChimeraX session
> show #!4 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> rename #6 EMD14330_NRtemplate.em
> save /Users/jenny/Desktop/231128_HumanNR_TemplateComparison.cxs includeMaps
> true
> close all
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened 251_dose-filt_rec.mrc as #1.1.1, grid size 1024,1024,500, pixel 4,
shown at level 39.7, step 1, values float32
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
Opened 265_dose-filt_rec.mrc as #1.1.2, grid size 1024,1024,500, pixel 4,
shown at level 80.4, step 1, values float32
> artiax tomo #1.1.2 sliceDirection 0,0,1
> artiax view xy
> hide #!1.1.1 models
> hide #!1.1.2 models
> show #!1.1.2 models
> hide #!1.1.2 models
> show #!1.1.1 models
> show #!1.1.2 models
> hide #!1.1.1 models
===== Log before crash end =====
Log:
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 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
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: MacBookPro18,3
Model Number: MKGP3D/A
Chip: Unknown
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 1 day, 2 hours, 12 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2721DE:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
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: 1.6.1
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
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
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: 0.5.3
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 (7)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash while updating tomogram surfaces |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash while updating tomogram surfaces → Crash in GL.glDeleteBuffers() while updating tomogram surfaces |
Mac M1 graphics driver crash in ChimeraX code
GL.glDeleteBuffers(1, [self.opengl_buffer])
ChimeraX had malloc'ed 9.5 GBytes of memory, and probably the graphics crash was related to high memory use.
comment:3 by , 2 years ago
This crash was reported again as #10240.
I see now that the OpenGL crash calling glDeleteBuffers() was not in the main thread. That was probably the cause of the crash. The OpenGL buffer was created in the main thread and must be deleted in the main thread. The main thread was showing a status message and called
QTimer.start()
which blocked and another thread started and a Drawing del method was called.
Current thread 0x000000030f0af000 (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 2643 in release_buffer
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 2634 in delete_buffer
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1721 in delete
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1712 in del
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 364 in notify
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 381 in notify_all
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 544 in set
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 962 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
What code started a separate Python thread?
It is a bug that a Drawing del() method was called without the code that created the Drawing deleting it. I suspect that mistake is done by ArtiaX which makes special Drawings to show subtomogram surfaces.
If ChimeraX is allowing separate Python to run where arbitrary destructors can get called then we need to protect against this in the graphics that uses OpenGL in the Drawing destructor. Qt can also not be used except in the main thread and some destructors using Qt could also cause crashes.
Maybe the separate thread is related to Toolshed or check for updates.
comment:4 by , 2 years ago
| Cc: | added |
|---|---|
| Resolution: | nonchimerax |
| Status: | closed → reopened |
Hi Greg,
Maybe you know or can find this Python esoterica -- can a Python object finalizer (del) method be called in a thread other than the main thread?
In this bug report a Drawing was made, probably by ArtiaX in the main thread and was not properly deleted by calling its delete method. Then its finalizer __del__() was called in a different thread and it tried to free OpenGL resources and crashed.
I think the Python allows the finalizers to be called in any thread. But the only mention of that I could find was in PEP 556 (https://peps.python.org/pep-0556/):
"One may wonder whether the default mode should simply be changed to “threaded”. For multi-threaded applications, it would probably not be a problem: those applications must already be prepared for finalization handlers to be run in arbitrary threads. In single-thread applications, however, it is currently guaranteed that finalizers will always be called in the main thread."
and also in that PEP 556:
"The author believes that the overwhelming majority of painful reentrancy issues occur with finalizers."
But I'd like to see a more definitive statement in the Python documentation. This could be the cause of other ChimeraX crashes because Qt is not thread-safe and so any Qt in a finalizer (even calling to delete some Qt objects is off limits).
In general we of course don't rely on finalizers (__del__) and it is a bug in Toolshed ArtiaX that it did not properly delete its Drawing. But still if it causes a crash that is hard to debug that is a disaster. I have the finalizer code for Drawing because otherwise the OpenGL resources (many buffers and textures will simply never be released).
I have seen a surprising number of unsolved ChimeraX crash reports that had Toolshed or update checking running in another thread. So that may be the other thread that triggers these finalizer in wrong thread problems.
comment:5 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | reopened → closed |
Fixed in daily build and 1.7.
Removed unnecessary _DrawShape.__del__() since deletion is guaranteed by the Drawing which creates the _DrawShape instances.
Still would like to know if we should survey the ChimeraX code for non-thread-safe __del__() methods
comment:6 by , 2 years ago
Yes, I the del could be done in a different thread. Because it happens when garbage collection takes place, and that might not be on the main thread. See https://github.com/napari/napari/issues/1029, it's solution is to disable Python's garbage collector, and then periodically run the garbage collector on the GUI thread.
comment:7 by , 2 years ago
I think our main solution to this problem has been to not use finalizer __del__ methods. They seem much despised in Python and I think for good reason. Context managers sometimes help, but not for long-lived objects like our Drawing class. Using a finalizer and making PyQt calls or OpenGL calls in it would be a big no-no since those are not thread safe. I think because we rarely use finalizers it is not necessary to go to running garbage collection ourselves as Napari has done.
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Hard to say if this is a ChimeraX problem, an ArtiaX problem, or what