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Opened 3 years ago
Closed 3 years ago
#8882 closed defect (nonchimerax)
Crash while rendering sequence alignment
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | 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: 1.5 (2022-11-24 00:03:27 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 0x00007ff853655340 (most recent call first):
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 2386 in make_item
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 2292 in _layout_line
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 2315 in layout_lines
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1619 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/398820E7-3CF5-4BF6-96A6-0ACF2931C9CF/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq_view/seq_canvas.py", line 1624 in __init__
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===== Log before crash start =====
Startup Messages
---
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'
1 messages similar to the above omitted
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jamisonlaw/Downloads/DEEPMSA1129_results/finalMSAs/final.fa
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'
1 messages similar to the above omitted
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.10.12
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 509.0.0.0.0
OS Loader Version: 577~129
SMC Version (system): 2.45f5
Software:
System Software Overview:
System Version: macOS 13.3.1 (22E261)
Kernel Version: Darwin 22.4.0
Time since boot: 1 hour, 54 minutes
Graphics/Displays:
Intel HD Graphics 630:
Chipset Model: Intel HD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x591b
Revision ID: 0x0004
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Support: Metal 3
Radeon Pro 555:
Chipset Model: Radeon Pro 555
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c7
ROM Revision: 113-C980AJ-927
VBIOS Version: 113-C9801AP-A02
EFI Driver Version: 01.A0.927
Automatic Graphics Switching: Supported
gMux Version: 4.0.29 [3.2.8]
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
argcomplete: 3.0.5
asttokens: 2.1.0
attrs: 22.2.0
Babel: 2.11.0
backcall: 0.2.0
basis-set-exchange: 0.9
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-DevelExtras: 0.4.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-GenomeTools: 0.9
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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-ISOLDE: 1.5
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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-NIHPresets: 1.1.9
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-OpenCommands: 1.0
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBImages: 1.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.1.7
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RIBFIND: 0.2
ChimeraX-RMF: 0.13
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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-StarMap: 1.1.70
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-StrudelScore: 0.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-TestManager: 0.3
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jsonschema: 4.17.3
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
propka: 3.5.0
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyrsistent: 0.19.3
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
regex: 2023.3.23
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.6.4
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Attachments (1)
Change History (9)
comment:1 by , 3 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash while rendering sequence alignment |
comment:2 by , 3 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 3 years ago
Hello Eric,
Yes, it happens every time but the file is quite large. It is a multiple sequence alignment file generated by DeepMSA2. See attached.
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, April 21, 2023 at 11:40 AM
To:
Cc: Law, Jamison D. <law.199@osu.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8882: Crash while rendering sequence alignment
#8882: Crash while rendering sequence alignment
--------------------------------+----------------------
Reporter: law.199@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------
Changes (by pett):
* status: accepted => feedback
Comment:
Hi Jamison,
Thanks for reporting this problem. Does it happen every time you
open that final.fa file? If so, is there any chance you could share the
file?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8882*comment:2__;Iw!!KGKeukY!z3Fc_a1AmAW7uh_XA-ooJCO_9MyMdgu_uAHtfPf8pVDBG7dJW2uR8qLuK9J3Ud9goLhulAeQDyzt08-kuKZSEBI7b6Z3LppYcQ$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!KGKeukY!z3Fc_a1AmAW7uh_XA-ooJCO_9MyMdgu_uAHtfPf8pVDBG7dJW2uR8qLuK9J3Ud9goLhulAeQDyzt08-kuKZSEBI7b6akuh80Gg$ >
ChimeraX Issue Tracker
comment:4 by , 3 years ago
It's not a sequence alignment. It's a single sequence that's 1.6 million characters long. Is that what you expected/wanted?
comment:5 by , 3 years ago
Hmm, no. I have an MSA .aln file as well but chimera will not import it. The error message “Cannot open files: Syntax error in ALN file 'final.aln': First non-blank line does not start with 'CLUSTAL'” comes up. Do you know how I fix this?
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, April 21, 2023 at 12:04 PM
To:
Cc: Law, Jamison D. <law.199@osu.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8882: Crash while rendering sequence alignment
#8882: Crash while rendering sequence alignment
--------------------------------+----------------------
Reporter: law.199@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------
Comment (by pett):
It's not a sequence alignment. It's a single sequence that's 1.6 million
characters long. Is that what you expected/wanted?
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8882*comment:4__;Iw!!KGKeukY!zu4D6ZEKmyN-Frhj3rPCzqBLf8FLg4ny4At4i-4xqw3ziRo1RD0TJBf1pov9Fx3xI_8PVO3IA7_ohtYOf7DAm-ieakRb4Bf2uA$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!KGKeukY!zu4D6ZEKmyN-Frhj3rPCzqBLf8FLg4ny4At4i-4xqw3ziRo1RD0TJBf1pov9Fx3xI_8PVO3IA7_ohtYOf7DAm-ieakTh8pxyUg$ >
ChimeraX Issue Tracker
follow-up: 5 comment:6 by , 3 years ago
Looking at the DeepMSA2 example output, its "aln" output is clearly not ClustalW ALN Format (described here: https://meme-suite.org/meme/doc/clustalw-format.html). In fact, it's no sequence alignment format I recognize -- where are the sequence names? DeepMSA2's "a3m" format is *almost* FASTA format, but there are lower case letters inserted into the sequences for some reason, which make them unequal in length to one another. If you remove the lower case letters from the sequences then you can in fact open the file in ChimeraX as FASTA format (suffix .fa or .afa).
comment:7 by , 3 years ago
Ok then this appears to be an issue with formatting and not with Chimera. I will contact Wei Zheng about the formatting issue with the DeepMSA2 files. Thank you for your assistance!
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, April 21, 2023 at 2:13 PM
To:
Cc: Law, Jamison D. <law.199@osu.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8882: Crash while rendering sequence alignment
#8882: Crash while rendering sequence alignment
--------------------------------+----------------------
Reporter: law.199@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------
Comment (by pett):
Looking at the DeepMSA2 example output, its "aln" output is clearly not
ClustalW ALN Format (described here: https://urldefense.com/v3/__https://meme-suite.org/meme/doc__;!!KGKeukY!1vNd-NmsNqVbpZUEC54C5EJDyuHzBG4pebY0BO4IxTyNq6g6_X_glqG_ZkWUyV-j3z6ayiXhJutbOQ4kKtOwbdynmBGT7d7McQ$<https://urldefense.com/v3/__https:/meme-suite.org/meme/doc__;!!KGKeukY!1vNd-NmsNqVbpZUEC54C5EJDyuHzBG4pebY0BO4IxTyNq6g6_X_glqG_ZkWUyV-j3z6ayiXhJutbOQ4kKtOwbdynmBGT7d7McQ$>
/clustalw-format.html). In fact, it's no sequence alignment format I
recognize -- where are the sequence names? DeepMSA2's "a3m" format is
*almost* FASTA format, but there are lower case letters inserted into the
sequences for some reason, which make them unequal in length to one
another. If you remove the lower case letters from the sequences then you
can in fact open the file in ChimeraX as FASTA format (suffix .fa or
.afa).
--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8882*comment:6__;Iw!!KGKeukY!1vNd-NmsNqVbpZUEC54C5EJDyuHzBG4pebY0BO4IxTyNq6g6_X_glqG_ZkWUyV-j3z6ayiXhJutbOQ4kKtOwbdynmBEn4m_YLA$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!KGKeukY!1vNd-NmsNqVbpZUEC54C5EJDyuHzBG4pebY0BO4IxTyNq6g6_X_glqG_ZkWUyV-j3z6ayiXhJutbOQ4kKtOwbdynmBGObv3e-g$ >
ChimeraX Issue Tracker
follow-up: 7 comment:8 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | feedback → closed |
Note:
See TracTickets
for help on using tickets.
Hi Jamison,
--Eric