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Opened 7 months ago
Closed 7 months ago
#17181 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-15.3-arm64-arm-64bit
ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000030b8a7000 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f6750840 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 576 in __init__
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1616 in remove_deleted_pointers
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1190 in __init__
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2246 in process_changes
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2251 in changes
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.8-rc2024.05.28.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-rc2024.05.28.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-rc2024.05.28.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-rc2024.05.28.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-rc2024.05.28.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-rc2024.05.28.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-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
File "/Applications/ChimeraX-1.8-rc2024.05.28.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-rc2024.05.28.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-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 535 in run
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 592 in run_expanded_command
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 338 in run
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 419 in run_shortcut
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 401 in try_shortcut
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1386 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1306 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)
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===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lassa_wt_endo_5j1n_2copies/fold_lassa_wt_endo_5j1n_2copies_model_0.cif"
Chain information for fold_lassa_wt_endo_5j1n_2copies_model_0.cif #1
---
Chain | Description
A B | .
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lassa_pross_des3_2copies/fold_lassa_pross_des3_2copies_model_0.cif"
Chain information for fold_lassa_pross_des3_2copies_model_0.cif #2
---
Chain | Description
A B | .
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lassa_pross_des3_2copies_model_0.cif, chain A (#2) with
fold_lassa_wt_endo_5j1n_2copies_model_0.cif, chain A (#1), sequence alignment
score = 860
RMSD between 170 pruned atom pairs is 0.507 angstroms; (across all 171 pairs:
0.562)
> set bgColor white
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lassa_wt_endo_5j1n/fold_lassa_wt_endo_5j1n_model_0.cif"
Chain information for fold_lassa_wt_endo_5j1n_model_0.cif #3
---
Chain | Description
A | .
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lassa_pross_des3/fold_lassa_pross_des3_model_0.cif"
Chain information for fold_lassa_pross_des3_model_0.cif #4
---
Chain | Description
A | .
> hide #2 models
> hide #1 models
> matchmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lassa_pross_des3_model_0.cif, chain A (#4) with
fold_lassa_wt_endo_5j1n_model_0.cif, chain A (#3), sequence alignment score =
854.2
RMSD between 155 pruned atom pairs is 0.947 angstroms; (across all 171 pairs:
1.493)
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #4/A
Alignment identifier is 1
> sequence chain #1/A #1/B #3/A
Alignment identifier is 2
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lasv_pross3_s107n/fold_lasv_pross3_s107n_model_0.cif"
Chain information for fold_lasv_pross3_s107n_model_0.cif #5
---
Chain | Description
A | .
> matchmaker #5 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lassa_pross_des3_model_0.cif, chain A (#4) with
fold_lasv_pross3_s107n_model_0.cif, chain A (#5), sequence alignment score =
913
RMSD between 173 pruned atom pairs is 0.555 angstroms; (across all 176 pairs:
0.800)
> hide #3 models
> ui mousemode right select
> select #5/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:109
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:108
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:108
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:109
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lasv_pross3_s107n_2copies/fold_lasv_pross3_s107n_2copies_model_0.cif"
Chain information for fold_lasv_pross3_s107n_2copies_model_0.cif #6
---
Chain | Description
A B | .
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lassa_wt_endo_5j1n_2copies_model_0.cif, chain A (#1) with
fold_lasv_pross3_s107n_2copies_model_0.cif, chain A (#6), sequence alignment
score = 857.9
RMSD between 171 pruned atom pairs is 0.454 angstroms; (across all 171 pairs:
0.454)
> hide #4 models
> hide #5 models
> hide #6 models
> show #1 models
> show #2 models
> show #6 models
> hide #2 models
> show #3 models
> show #4 models
> hide #6 models
> hide #1 models
> select clear
> open /Users/simeonbabarinde/Desktop/March_25_SSRL/ref9/B5_P61_210_009.pdb
> format pdb
Chain information for B5_P61_210_009.pdb #7
---
Chain | Description
A | No description available
B | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> sequence chain #1/A #1/B #3/A
Alignment identifier is 1
> sequence chain #2/A #2/B #4/A
Alignment identifier is 2
> close
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lassa_wt_endo_5j1n/fold_lassa_wt_endo_5j1n_model_0.cif"
Chain information for fold_lassa_wt_endo_5j1n_model_0.cif #1
---
Chain | Description
A | .
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lassa_pross_des3/fold_lassa_pross_des3_model_0.cif"
Chain information for fold_lassa_pross_des3_model_0.cif #2
---
Chain | Description
A | .
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lassa_wt_endo_5j1n_model_0.cif, chain A (#1) with
fold_lassa_pross_des3_model_0.cif, chain A (#2), sequence alignment score =
854.2
RMSD between 155 pruned atom pairs is 0.947 angstroms; (across all 171 pairs:
1.493)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:171
13 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A
1375 atoms, 1397 bonds, 171 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A
1416 atoms, 1438 bonds, 176 residues, 1 model selected
> open 5J1N
5j1n title:
Lassa virus L protein cap-snatching endonuclease. Bound to one manganese ion
[more info...]
Chain information for 5j1n #3
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase L | Q6GWS6_9VIRU 1-174
Non-standard residues in 5j1n #3
---
MN3 — manganese (III) ion
MPD — (4S)-2-methyl-2,4-pentanediol
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lassa_wt_endo_5j1n_model_0.cif, chain A (#1) with 5j1n, chain
A (#3), sequence alignment score = 877.5
RMSD between 155 pruned atom pairs is 0.957 angstroms; (across all 171 pairs:
1.346)
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:61-62,90-94,97-105,136-144
199 atoms, 199 bonds, 25 residues, 1 model selected
> select clear
> select #3/A:0-170
1373 atoms, 1395 bonds, 171 residues, 1 model selected
> close #1
> select #2/A:58-59
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:58-59
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> color sel byhetero
> select #2/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> open "/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease
> project/fold_lasv_wt_5j1n/fold_lasv_wt_5j1n_model_0.cif"
Chain information for fold_lasv_wt_5j1n_model_0.cif #1
---
Chain | Description
A | .
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lasv_wt_5j1n_model_0.cif, chain A (#1) with 5j1n, chain A
(#3), sequence alignment score = 908.3
RMSD between 162 pruned atom pairs is 0.922 angstroms; (across all 171 pairs:
1.074)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_lasv_wt_5j1n_model_0.cif, chain A (#1) with
fold_lassa_pross_des3_model_0.cif, chain A (#2), sequence alignment score =
891.6
RMSD between 164 pruned atom pairs is 0.808 angstroms; (across all 175 pairs:
1.261)
> select #1/A:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:2-17,22-32,37-60,71-78,111-135,156-175
867 atoms, 874 bonds, 104 residues, 1 model selected
> select #2/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/A:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #3/A:166
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:167
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/A:167
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> select #3/A:166
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> select #2/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> select clear
> select #1/A:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 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: MacBookPro18,3
Model Number: Z15G001WGLL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.2
OS Loader Version: 11881.81.2
Software:
System Software Overview:
System Version: macOS 15.3 (24D60)
Kernel Version: Darwin 24.3.0
Time since boot: 5 days, 11 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 U2419H:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
LG ULTRAFINE:
Resolution: 4096 x 2304
UI Looks like: 2048 x 1152 @ 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: 1.2.7
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-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
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: 1.8rc202405282004
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: 1.2.4
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: 2.7.1
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: 3.0.13
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: 1.16.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.2
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: 4.52.4
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: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
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
MolecularDynamicsViewer: 1.4
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: 3.0.45
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: 4.12.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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 in garbage collection |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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