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Opened 7 months ago
Closed 7 months ago
#17326 closed defect (duplicate)
Crash accessing StructureSeq.structure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 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 0x00000001ec214f40 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91 in get_prop
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1254 in _changes_cb
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1069 in proxy_handler
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 54 in check_for_changes
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3318 in command_trigger
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3203 in run
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 225 in delete
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 308 in _key_closed
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py", line 105 in delete
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 1010 in close
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/close.py", line 43 in close
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 53)
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===== Log before crash start =====
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_4.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_3.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_2.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_1.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif
Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_4.cif #1
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_3.cif #2
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_1.cif #4
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
> ui tool show "AlphaFold Error Plot"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #5 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_0.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "AlphaFold Error Plot"
> alphafold pae #5 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_0.json
> color bfactor #5 palette alphafold
6989 atoms, 886 residues, atom bfactor range 13.2 to 97
> color bfactor #5 palette alphafold
6989 atoms, 886 residues, atom bfactor range 13.2 to 97
> alphafold pae #5 colorDomains true
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> save /Users/vincent/Desktop/image5.png supersample 3
> color #5/A:1-98 lime
> save /Users/vincent/Desktop/image6.png supersample 3
> color #5/B:65-429 lime
> save /Users/vincent/Desktop/image7.png supersample 3
> color #5/C:7-339 lime
> save /Users/vincent/Desktop/image8.png supersample 3
> color #5/B:4-428 lime
> color #5/C:6-71 lime
> color #5/A:4-97 magenta
> save /Users/vincent/Desktop/image9.png supersample 3
> save /Users/vincent/Desktop/image10.png supersample 3
> color #5/A:1-98 lime
> color #5/C:3-57 magenta
> color #5/C:46-121 lime
> color #5/B:68-432 magenta
> save /Users/vincent/Desktop/image11.png supersample 3
> color #5/C:169 lime
> color #5/B:181 magenta
> color #5/C:182-245 lime
> color #5/B:68-421 magenta
> save /Users/vincent/Desktop/image12.png supersample 3
> color bfactor #5 palette alphafold
6989 atoms, 886 residues, atom bfactor range 13.2 to 97
> color bfactor #5 palette alphafold
6989 atoms, 886 residues, atom bfactor range 13.2 to 97
> help help:user/tools/alphafold.html#pae
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #5/C:186 lime
> color #5/C:322 magenta
> color #5/B:18 lime
> color #5/B:5 magenta
> color #5/A:5-98 lime
> color #5/B:60-438/C:1-3 lime
> color #5/C:4-341 lime
> color #5/C:4-105 lime
> color #5/A:6-88 magenta
> color #5/C:17-152 lime
> color #5/B:72-414 magenta
> color #5/C:189-244 lime
> color #5/B:75-407 magenta
> view name fixed_view
> rainbow chains palette silver:orchid:cornflower
> 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95
> 2dlabels create #2 text USP27X color orchid size 24 xpos 0.8 ypos 0.90
> 2dlabels create #3 text ATXN7L3 color orchid size 24 xpos 0.8 ypos 0.85
> 2dlabels create #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos
> 0.85
Label "#3" already exists
> 2dlabels #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos 0.85
> save /Users/vincent/Desktop/image13.png supersample 3
> 2dlabels delete
> hide #5 models
> show #1 models
> show #5 models
> hide #5 models
> view name fixed_view
> 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95
> 2dlabels create #2 text USP27X color orchid size 24 xpos 0.8 ypos 0.90
> 2dlabels create #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos
> 0.85
> save /Users/vincent/Desktop/image5.png supersample 3
> alphafold pae #4 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_1.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #4 colorDomains true
> color bfactor #4 palette alphafold
6989 atoms, 886 residues, atom bfactor range 13.7 to 97
> color bfactor #4 palette alphafold
6989 atoms, 886 residues, atom bfactor range 13.7 to 97
> alphafold pae #4 colorDomains true
> show #4 models
> hide #1 models
> show #1 models
> hide #4 models
> show #4 models
> hide #4 models
> alphafold pae #1 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_4.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #1 colorDomains true
> hide #!7 models
> save /Users/vincent/Desktop/image6.png supersample 3
> color #1/A:1 lime
> color #1/A:2 magenta
> color #1/A:1-99 lime
> save /Users/vincent/Desktop/image7.png supersample 3
> save /Users/vincent/Desktop/image8.png supersample 3
> color #1/B:57-431 lime
> save /Users/vincent/Desktop/image9.png supersample 3
> color #1/C:4-346 lime
> save /Users/vincent/Desktop/image10.png supersample 3
> color #1/C:4-109 lime
> color #1/A:4-97 magenta
> save /Users/vincent/Desktop/image11.png supersample 3
> color #1/C:11-120 lime
> color #1/B:68-425 magenta
> save /Users/vincent/Desktop/image12.png supersample 3
> color #1/C:183-250 lime
> color #1/B:68-416 magenta
> save /Users/vincent/Desktop/image13.png supersample 3
> hide #1 models
> show #4 models
> rainbow chains palette silver:orchid:cornflower
> show #!7 models
> hide #!7 models
> show #!7 models
> save /Users/vincent/Desktop/image14.png supersample 3
> alphafold pae #4 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_full_data_1.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #4 colorDomains true
> save /Users/vincent/Desktop/image15.png supersample 3
> save /Users/vincent/Desktop/image16.png supersample 3
> color #4/C:208 lime
> color #4/C:303 magenta
> color #4/A:30 lime
> color #4/A:26 magenta
> color #4/A:1-97 lime
> save /Users/vincent/Desktop/image17.png supersample 3
> hide #!7 models
> save /Users/vincent/Desktop/image18.png supersample 3
> color #4/B:57-430 lime
> save /Users/vincent/Desktop/image19.png supersample 3
> color #4/C:3-346 lime
> save /Users/vincent/Desktop/image20.png supersample 3
> color #4/B:438/C:1-110 lime
> color #4/A magenta
> save /Users/vincent/Desktop/image21.png supersample 3
> color #4/C:8-126 lime
> color #4/B:70-427 magenta
> save /Users/vincent/Desktop/image22.png supersample 3
> color #4/C:188-255 lime
> color #4/B:73-425 magenta
> save /Users/vincent/Desktop/image23.png supersample 3
> color #4/B:12-436 lime
> color #4/A:4-97 magenta
> save /Users/vincent/Desktop/image24.png supersample 3
> color #4/C:188-248 lime
> color #4/C:64-109 magenta
> color #4/B:62-182 lime
> color #4/B:258-344 magenta
> color #4/B:65-431 lime
> close
> open
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_4.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_3.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_2.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_1.cif
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif
Chain information for
fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_4.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
Chain information for
fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_3.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
Chain information for
fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
Chain information for
fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_1.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
Chain information for
fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> select add #5
8502 atoms, 8688 bonds, 1071 residues, 1 model selected
> select subtract #5
Nothing selected
> rainbow chains palette silver:orchid:cornflower
> rainbow chains palette silver:orchid:cornflower:green
> rainbow chains palette silver:orchid:cornflower:greenyellow
> view name fixed_view
> 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95
> 2dlabels create #2 text USP22 color orchid size 24 xpos 0.8 ypos 0.90
> 2dlabels create #3 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos
> 0.85
> 2dlabels create #3 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8
Label "#3" already exists
> 2dlabels create #4 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8
> save /Users/vincent/Desktop/image25.png supersample 3
> alphafold pae #5 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_full_data_0.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #5 colorDomains true
> save /Users/vincent/Desktop/image26.png supersample 3
> hide #!6 models
> save /Users/vincent/Desktop/image27.png supersample 3
> color #5/C:267 lime
> color #5/D:70 magenta
> color #5/A:2-95 lime
> save /Users/vincent/Desktop/image28.png supersample 3
> color #5/B:13-519 lime
> save /Users/vincent/Desktop/image29.png supersample 3
> color #5/C:8-341 lime
> save /Users/vincent/Desktop/image30.png supersample 3
> color #5/C:346-347/D lime
> save /Users/vincent/Desktop/image31.png supersample 3
> color #5/B:15-519 lime
> color #5/A:5-94 magenta
> save /Users/vincent/Desktop/image32.png supersample 3
> color #5/C:3-342 lime
> color #5/A:1-94 magenta
> color #5/C:285 lime
> color #5/A:76 magenta
> color #5/C:10-120 lime
> color #5/A:7-85 magenta
> color #5/C:190-246 lime
> color #5/A:16-87 magenta
> color #5/C:5-120 lime
> color #5/A:7-100 magenta
> save /Users/vincent/Desktop/image33.png supersample 3
> color #5/C:190-255 lime
> color #5/A:7-94 magenta
> save /Users/vincent/Desktop/image34.png supersample 3
> color #5/D:1-97 lime
> color #5/A:3-92 magenta
> save /Users/vincent/Desktop/image35.png supersample 3
> save /Users/vincent/Desktop/image36.png supersample 3
> color #5/C:10-118 lime
> color #5/B:21-513 magenta
> save /Users/vincent/Desktop/image37.png supersample 3
> color #5/C:180-255 lime
> color #5/A:7-87 magenta
> color #5/D lime
> color #5/A:1-87 magenta
> color #5/C:6-125 lime
> color #5/B:17-509 magenta
> color #5/C:185-251 lime
> color #5/B:23-513 magenta
> save /Users/vincent/Desktop/image38.png supersample 3
> color #5/D:4-97 lime
> color #5/B:25-513 magenta
> save /Users/vincent/Desktop/image39.png supersample 3
> color #5/D:8-98 lime
> color #5/C:194-253 magenta
> save /Users/vincent/Desktop/image40.png supersample 3
> close
> open
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_UBTF2L3_ATXN7short/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17_model_0.cif
Chain information for
fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
> rainbow chains palette silver:orchid:cornflower:greenyellow
> select /d
786 atoms, 807 bonds, 98 residues, 1 model selected
> select /c
7669 atoms, 7823 bonds, 945 residues, 1 model selected
> /c
Unknown command: sequence /c
> sequence chain /c
Alignment identifier is 1/C
> select /C:598-599
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /C:374-599
1887 atoms, 1922 bonds, 226 residues, 1 model selected
> select /C:598-599
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /C:1-599
4973 atoms, 5077 bonds, 599 residues, 1 model selected
> sequence chain /c 1:600
Expected a keyword
> select :1-600.c
Expected an objects specifier or a keyword
> select /c 1-600
Expected a keyword
> select /1-600.c
Expected an objects specifier or a keyword
> select /c.1-600
Expected an objects specifier or a keyword
> select /c#1-600
13467 atoms, 13758 bonds, 1669 residues, 1 model selected
> select subtract #1
Nothing selected
> select /C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:1-598
4965 atoms, 5069 bonds, 598 residues, 1 model selected
> color sel orange
> color sel gray
> select add #1
13467 atoms, 13758 bonds, 1669 residues, 1 model selected
> select subtract #1
Nothing selected
> view name fixed_view
> 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95
> 2dlabels create #3 text UBTF2::ATXN7L3 color cornflowerblue size 24 xpos 0.8
> ypos 0.85
> 2dlabels create #2 text USP22 color cornflowerblue size 24 xpos 0.8 ypos
> 0.90
> 2dlabels #2 text USP22 color orchid size 24 xpos 0.8 ypos 0.90
> 2dlabels create #4 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.80
> save /Users/vincent/Desktop/image5.png supersample 3
> alphafold pae #1 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_UBTF2L3_ATXN7short/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_ubtf2l3_atxn7short_2025_04_07_11_17_full_data_0.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #1 colorDomains true
> hide #!2 models
> save /Users/vincent/Desktop/image6.png supersample 3
> color bfactor #1 palette alphafold
13467 atoms, 1669 residues, atom bfactor range 14.1 to 97.2
> h-key true
Unknown command: h-key true
> h-key truekey true
Unknown command: h-key truekey true
Fetching url
https://www.colourlovers.com/api/palettes?keywords=true&format=json&numResults=100
failed:
HTTP Error 522:
> color bfactor palette
> 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff
> key true
> key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90
> #106dff:90 #106dff:100 showTool true
> ui mousemode right "color key"
13467 atoms, 1669 residues, atom bfactor range 14.1 to 97.2
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/vincent/Desktop/image7.png supersample 3
> key delete
> ui mousemode right translate
> color /C:435 lime
> color /B:82 magenta
> color /A:8-101/B:1-4 lime
> color /A:3-97 lime
> color /A/B:1 lime
> save /Users/vincent/Desktop/image8.png supersample 3
> color /B:165 lime
> color /C:3 magenta
> color /B:14-523 lime
> save /Users/vincent/Desktop/image9.png supersample 3
> color /C:22 lime
> color /C:43 magenta
> color /C:19-349 lime
> color /C:329 lime
> color /C:361 magenta
> color /C:222-347 lime
> color /C:435-513 magenta
> color /C:6-854 lime
> color /C:16-182 lime
> color /C:206-339 lime
> color /C:365-429 lime
> color /C:212-329 lime
> color /C:445-506 magenta
> color /C:440-513 lime
> color /C:513-602 lime
> color /C:591-711 lime
> color /C:617-721 lime
> color /C:790-837 magenta
> color /C:768-843 lime
> color /C:17-856 lime
> color /C:206-349 lime
> color /C:368-432 lime
> color /C:445-513 lime
> color /C:521-601 lime
> color /C:596-716 lime
> color /C:768-861 lime
> color /C:6-861 lime
> save /Users/vincent/Desktop/image10.png supersample 3
> color /D lime
> save /Users/vincent/Desktop/image11.png supersample 3
> color /C:22 lime
> color /C:270-273 magenta
> color /C:16-188 lime
> save /Users/vincent/Desktop/image12.png supersample 3
> color /C:240 lime
> color /C:300 magenta
> color /C:222-347 lime
> save /Users/vincent/Desktop/image13.png supersample 3
> color /C:362-433 lime
> save /Users/vincent/Desktop/image14.png supersample 3
> color /C:594 lime
> color /C:327-331 magenta
> color /C:440-511 lime
> save /Users/vincent/Desktop/image15.png supersample 3
> color /C:404 lime
> color /C:648 magenta
> color /C:518-608 lime
> save /Users/vincent/Desktop/image16.png supersample 3
> color /C:732 lime
> color /C:449 magenta
> color /C:604-713 lime
> save /Users/vincent/Desktop/image17.png supersample 3
> color /C:778 lime
> color /C:746 magenta
> color /C:773-854 lime
> save /Users/vincent/Desktop/image18.png supersample 3
> color /C:438-518 lime
> color /C:223-341 magenta
> save /Users/vincent/Desktop/image19.png supersample 3
> color /C:791 lime
> color /C:560 magenta
> color /C:833 lime
> color /C:537 magenta
> color /C:781-859 lime
> color /C:611-709 magenta
> color /C:602-734 lime
> color /C:777-834 magenta
> color /C:773-846 lime
> color /C:608-712 magenta
> save /Users/vincent/Desktop/image20.png supersample 3
> color /D:10-98 lime
> color /C:783-837 magenta
> color /C:513-531 lime
> color /A:1-88 magenta
> color /C:583-721 lime
> color /A:1-85 magenta
> save /Users/vincent/Desktop/image21.png supersample 3
> color /C:776-849 lime
> color /A:4-88 magenta
> save /Users/vincent/Desktop/image22.png supersample 3
> color /D:2-98 lime
> color /A:4-85 magenta
> save /Users/vincent/Desktop/image23.png supersample 3
> color /C:425 lime
> color /B:379 magenta
> color /C:589-719 lime
> color /B:25-511 magenta
> save /Users/vincent/Desktop/image24.png supersample 3
> color /C:810 lime
> color /B:68 magenta
> color /C:781-851 lime
> color /B:21-521 magenta
> save /Users/vincent/Desktop/image25.png supersample 3
> save /Users/vincent/Desktop/image26.png supersample 3
> color /D:2-91 lime
> color /B:18-518 magenta
> color /D:91 lime
> color /B:518 magenta
> color /C:942-945/D lime
> color /B:14-525/C:1-6 magenta
> save /Users/vincent/Desktop/image27.png supersample 3
> color /D:2-91 lime
> color /A/B:1-521 magenta
> view fixed_view
> color /D:5-93 lime
> color /C:601-692 magenta
> color /A-D lime
> color /C:308 lime
> color /B:109 magenta
> color /C:9-498 lime
> color /A:11-88 magenta
> color /C:446 lime
> color /B:89 magenta
> close
> open
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP22_L3_ATXN7short/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17/fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif
Chain information for
fold_eny2_usp22_l3_atxn7short_2025_04_07_11_17_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
> rainbow chains palette silver:orchid:cornflower:greenyellow
> color bfactor palette
> 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff
> key true
> key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90
> #106dff:90 #106dff:100 showTool true
> ui mousemode right "color key"
8502 atoms, 1071 residues, atom bfactor range 10.8 to 97.2
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/vincent/Desktop/image28.png supersample 3
> close
> ui mousemode right translate
> open
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/ENY2_USP27X_L3/fold_eny2_usp27x_l3_2025_04_07_11_17/fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif
Chain information for fold_eny2_usp27x_l3_2025_04_07_11_17_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
> rainbow chains palette silver:orchid:cornflower
> color bfactor palette
> 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff
> key true
> key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90
> #106dff:90 #106dff:100 showTool true
> ui mousemode right "color key"
6989 atoms, 886 residues, atom bfactor range 13.2 to 97
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/vincent/Desktop/image29.png supersample 3
> close
> ui mousemode right translate
> open
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/EN2_USP22_UBTF1L3_ATXN7short/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08_model_0.cif
Chain information for
fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
> rainbow chains palette silver:orchid:cornflower:greenyellow
> 2dlabels create #1 text ENY2 color silver size 24 xpos 0.8 ypos 0.95
> 2dlabels create #2 text USP22 color orchid size 24 xpos 0.8 ypos 0.90
> 2dlabels create #3 text UBTF1::ATXN7L3 color cornflowerblue size 24 xpos 0.8
> ypos 0.85
> 2dlabels create #3 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8
Label "#3" already exists
> 2dlabels create #4 text ATXN7 color greenyellow size 24 xpos 0.8 ypos 0.8
> save /Users/vincent/Desktop/image30.png supersample 3
> select /c
7985 atoms, 8145 bonds, 982 residues, 1 model selected
> sequence chain /C:1-600
Alignment identifier is 1/C
> select /C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:1-635
5281 atoms, 5391 bonds, 635 residues, 1 model selected
> color sel gray
> 2dlabels create #5 text UBTF1 color gray size 24 xpos 0.8 ypos 0.8
> 2dlabels #5 text UBTF1 color gray size 24 xpos 0.8 ypos 0.75
> 2dlabels create #6 text ATXN7L3 color cornflowerblue size 24 xpos 0.8 ypos
> 0.70
> save /Users/vincent/Desktop/image31.png supersample 3
> select add #1
13783 atoms, 14080 bonds, 1706 residues, 1 model selected
> select subtract #1
Nothing selected
> save /Users/vincent/Desktop/image32.png supersample 3
> color bfactor palette
> 0,#ef821e:49.99,#ef821e:50,#f6ed12:69.99,#f6ed12:70,#10cff1:89.99,#10cff1:90,#106dff:100,#106dff
> key true
> key #ef821e:0 #ef821e:50 #f6ed12:50 #f6ed12:70 #10cff1:70 #10cff1:90
> #106dff:90 #106dff:100 showTool true
> ui mousemode right "color key"
13783 atoms, 1706 residues, atom bfactor range 15.7 to 96.7
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!2 models
> save /Users/vincent/Desktop/image33.png supersample 3
> alphafold pae #1 file
> /Users/vincent/Seafile/Administrative/InCA_PLBIO24-261-19488/Alphafold3/EN2_USP22_UBTF1L3_ATXN7short/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08/fold_eny2_usp22_ubtf1l3_atxn7short_2025_04_08_full_data_0.json
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> alphafold pae #1 colorDomains true
> hide #3 models
> save /Users/vincent/Desktop/image34.png supersample 3
> color /A:1-97 lime
> save /Users/vincent/Desktop/image35.png supersample 3
> color /B:10-521 lime
> save /Users/vincent/Desktop/image36.png supersample 3
> color /B:234 lime
> color /C:321 magenta
> color /C:20-896 lime
> save /Users/vincent/Desktop/image37.png supersample 3
> color /C:978-982/D lime
> save /Users/vincent/Desktop/image38.png supersample 3
> color /C:623-751 lime
> color /A:1-83 magenta
> color /C:558-572 lime
> color /A:1-76 magenta
> color /C:626-748 lime
> color /A:1-80 magenta
> save /Users/vincent/Desktop/image39.png supersample 3
> color /C:243 lime
> color /B:245 magenta
> color /C:819-887 lime
> color /A:1-90 magenta
> save /Users/vincent/Desktop/image40.png supersample 3
> color /D:2-96 lime
> color /A:1-87 magenta
> save /Users/vincent/Desktop/image41.png supersample 3
> color /C:629-751 lime
> color /B:20-521 magenta
> save /Users/vincent/Desktop/image42.png supersample 3
> color /C:819-890 lime
> color /B:20-507 magenta
> save /Users/vincent/Desktop/image43.png supersample 3
> color /C:981-982/D lime
> color /B:13-525 magenta
> save /Users/vincent/Desktop/image44.png supersample 3
> color /D:11 lime
> color /C:728 magenta
> color /D:2-98 lime
> color /C:638-742 magenta
> save /Users/vincent/Desktop/image45.png supersample 3
> color /C:357 lime
> color /C:228 magenta
> color /D:11-93 lime
> color /C:821-873 magenta
> save /Users/vincent/Desktop/image46.png supersample 3
> color /C:16-98 lime
> save /Users/vincent/Desktop/image47.png supersample 3
> color /C:98-179 lime
> save /Users/vincent/Desktop/image48.png supersample 3
> color /C:404-479 lime
> save /Users/vincent/Desktop/image49.png supersample 3
> color /C:646 lime
> color /C:580 magenta
> color /C:482-558 lime
> save /Users/vincent/Desktop/image50.png supersample 3
> color /C:555-646 lime
> save /Users/vincent/Desktop/image51.png supersample 3
> color /C:638-754 lime
> save /Users/vincent/Desktop/image52.png supersample 3
> color /C:811-894 lime
> save /Users/vincent/Desktop/image53.png supersample 3
> color /C:107-195 lime
> color /C:17-103 magenta
> save /Users/vincent/Desktop/image54.png supersample 3
> color /C:544 lime
> color /C:269 magenta
> color /C:817-890 lime
> color /C:649-735 magenta
> save /Users/vincent/Desktop/image55.png supersample 3
> close
> ui mousemode right translate
===== Log before crash end =====
Log:
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AU001VTFN/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 6 heures et 57 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 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 P2719H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2719H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405202242
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.3
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash accessing StructureSeq.structure |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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