![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16227 closed defect (duplicate)
Crash in garbage collection
| 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-14.7-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x00000001fe2d4f40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/matrix.py", line 467 in length
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/geometry/matrix.py", line 440 in normalize_vector
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/common_geom.py", line 19 in test_phi
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/acceptor_geom.py", line 80 in test_phi_psi
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/acceptor_geom.py", line 48 in acc_syn_anti
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 614 in find_hbonds
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/cmd.py", line 94 in cmd_hbonds
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 59)
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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/dwheeler/Downloads/relaxed_model_1_multimer_v3_pred_0-2.pdb
> format pdb
Chain information for relaxed_model_1_multimer_v3_pred_0-2.pdb #1
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E F | No description available
> close session
> open
> /Users/dwheeler/Downloads/fold_phpnuc_2024_10_31_14_11/fold_phpnuc_2024_10_31_14_11_model_4.cif
Chain information for fold_phpnuc_2024_10_31_14_11_model_4.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
> hide atoms
> show cartoons
> open
> /Users/dwheeler/Downloads/fold_php_nuc_moc3_2024_10_31_14_32/fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif
Chain information for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif #2
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
> hide atoms
> show cartoons
> name end /B:100-114
> color end red
> ui tool show Matchmaker
> matchmaker #2/I#2/J to #1/I#1/J pairing ss
Reference chain (fold_phpnuc_2024_10_31_14_11_model_4.cif (#1) chain I) not
compatible with BLOSUM-62 similarity matrix
> matchmaker #2/A#2/B to #1/A#1/B pairing ss
Parameters
---
Chain pairing | ss
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_phpnuc_2024_10_31_14_11_model_4.cif, chain A (#1) with
fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif, chain A (#2), sequence
alignment score = 176.2
Matchmaker fold_phpnuc_2024_10_31_14_11_model_4.cif, chain B (#1) with
fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif, chain B (#2), sequence
alignment score = 176.2
RMSD between 54 pruned atom pairs is 0.964 angstroms; (across all 202 pairs:
10.594)
> hide #2 models
> show #2 models
> hide #1 models
> hide #2 models
> show #1 models
> hide #1 models
> show #2 models
> name php3 #1/B |#2/B
> hide ~ php3 arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~php3 arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1 models
> hide arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 models
> hide #2 models
> show php3 arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show php3 cartoons
> show #1 models
> show #2 models
> hide ~php3 cartoons
> hide #1 models
> show all
> hide #2 atoms
> show #2 cartoons
> view #2
> hide #2 models
> show #1 models
> hide #1 atoms
> show #1 cartoons
> color #1 bychain
> color #1 bypolymer
> coulombic #1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_A SES surface
#1.1: minimum, -18.52, mean -1.45, maximum 13.65
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_B SES surface
#1.2: minimum, -17.57, mean -1.45, maximum 10.66
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_C SES surface
#1.3: minimum, -27.23, mean -0.78, maximum 15.27
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_D SES surface
#1.4: minimum, -22.94, mean -0.79, maximum 15.72
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_E SES surface
#1.5: minimum, -8.30, mean 4.17, maximum 16.00
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_F SES surface
#1.6: minimum, -8.28, mean 4.19, maximum 15.78
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_G SES surface
#1.7: minimum, -12.88, mean 2.54, maximum 13.94
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_H SES surface
#1.8: minimum, -12.93, mean 2.56, maximum 13.73
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_I SES surface
#1.9: minimum, -32.07, mean -14.98, maximum -4.06
Coulombic values for fold_phpnuc_2024_10_31_14_11_model_4.cif_J SES surface
#1.10: minimum, -34.01, mean -14.99, maximum -3.96
To also show corresponding color key, enter the above coulombic command and
add key true
> hide @ca & @@bfactor surface style dot
> surface style mesh
> hide /J | /I arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /J | /I surfaces
> show #2 models
> hide #!1 models
> coulombic #2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_A SES
surface #2.1: minimum, -13.44, mean 2.92, maximum 14.80
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_B SES
surface #2.2: minimum, -10.85, mean 2.94, maximum 16.29
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_C SES
surface #2.3: minimum, -16.77, mean 3.02, maximum 17.32
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_D SES
surface #2.4: minimum, -16.87, mean 3.01, maximum 17.14
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_E SES
surface #2.5: minimum, -8.24, mean 4.21, maximum 16.09
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_F SES
surface #2.6: minimum, -8.15, mean 4.21, maximum 16.48
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_G SES
surface #2.7: minimum, -16.46, mean 2.76, maximum 13.76
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_H SES
surface #2.8: minimum, -21.34, mean 2.73, maximum 13.49
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_I SES
surface #2.9: minimum, -12.11, mean -0.01, maximum 16.56
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_J SES
surface #2.10: minimum, -12.96, mean -0.06, maximum 15.27
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_K SES
surface #2.11: minimum, -27.89, mean -15.25, maximum -4.13
Coulombic values for fold_php_nuc_moc3_2024_10_31_14_32_model_4.cif_L SES
surface #2.12: minimum, -29.44, mean -15.25, maximum -4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> hide @ca & @@bfactor surface style #2 mesh
> hide /J | /I surfaces
> hide /K | /L surfaces
> show/J | /I s
Unknown command: show/J | /I s
> show #2/J | #2/I surfaces
> close session
> open
> /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
> hide surfaces
> hide cartoons
> show cartoons
> hide atoms
> open
> /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_3.cif
> /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_2.cif
> /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_1.cif
> /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_0.cif
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_3.cif #2
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_2.cif #3
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_1.cif #4
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_0.cif #5
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
> hide #1 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #2 cartoons
> hide #2 atoms
> show #3 models
> hide #2 models
> show #3 cartoons
> hide #3 atoms
> show #4 models
> hide #3 models
> show #4 cartoons
> hide #4 atoms
> hide #4 models
> show #5 models
> show #5 cartoons
> hide #5 atoms
> hide #5 models
> show #1 models
> hide arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide all arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 models
> show #1/C | #1/I
> show #1/C | #1/I cartoons
> show #1 models
> name X #1/C | #1/I
> hide #1/ arcs
> hide #1/
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/ c
> hide #1/
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/ arcs
> hide #1/* arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/A arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1/B arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 target m
> show X cartoons
> view X
No displayed objects specified.
> view X c
Expected keyword "clip" or "cofr"
> show #1/C | #1/I cartoons
> show #1 models
> hide ~( #1/C | #1/I) arcs
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~( #1/C | #1/I) cartoons
> show #1/C | #1/I surfaces
> show #!1 cartoons
> hide #!1 cartoons
> select #1/C | #1/I
7248 atoms, 7425 bonds, 923 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> ~select
Nothing selected
> ui tool show Matchmaker
> split #1/C #1/I
Split fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif (#1) into 12 models
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif A #1.1
---
Chain | Description
A | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif B #1.2
---
Chain | Description
B | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif C #1.3
---
Chain | Description
C | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif D #1.4
---
Chain | Description
D | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif E #1.5
---
Chain | Description
E | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif F #1.6
---
Chain | Description
F | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif G #1.7
---
Chain | Description
G | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif H #1.8
---
Chain | Description
H | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif I #1.9
---
Chain | Description
I | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif J #1.10
---
Chain | Description
J | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif K #1.11
---
Chain | Description
K | No description available
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif L #1.12
---
Chain | Description
L | No description available
> ui tool show Matchmaker
> matchmaker #1.9/I to #1.3/C pairing ss
Parameters
---
Chain pairing | ss
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_php_moc3_nuc_2024_10_31_15_45_model_4.cif C, chain C (#1.3)
with fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif I, chain I (#1.9),
sequence alignment score = 254.4
RMSD between 10 pruned atom pairs is 1.377 angstroms; (across all 382 pairs:
35.313)
No model chosen to save relative to
> save /Users/dwheeler/HistoneFold/php3.pdb models #1.3 relModel #1
> save /Users/dwheeler/HistoneFold/moc3.pdb models #1.9 relModel #1
> close session
> open /Users/dwheeler/HistoneFold/moc3.pdb
> /Users/dwheeler/HistoneFold/php3.pdb
Chain information for moc3.pdb #1
---
Chain | Description
I | No description available
Chain information for php3.pdb #2
---
Chain | Description
C | No description available
> ui mousemode right "rotate selected models"
> select add #1
3979 atoms, 4078 bonds, 508 residues, 1 model selected
> view matrix models
> #1,0.13985,-0.92395,0.35604,43.851,0.29152,0.38206,0.87695,52.684,-0.94629,-0.018847,0.32278,-24.131
> view matrix models
> #1,0.70382,0.1283,0.69869,24.144,0.58392,-0.66463,-0.46616,31.186,0.40456,0.73607,-0.5427,-83.841
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.70382,0.1283,0.69869,25.322,0.58392,-0.66463,-0.46616,-2.7728,0.40456,0.73607,-0.5427,-84.034
> view matrix models
> #1,0.70382,0.1283,0.69869,39.245,0.58392,-0.66463,-0.46616,-3.662,0.40456,0.73607,-0.5427,-79.015
> view matrix models
> #1,0.70382,0.1283,0.69869,66.172,0.58392,-0.66463,-0.46616,36.109,0.40456,0.73607,-0.5427,-95.642
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.95808,-0.1982,0.2069,60.134,-0.050642,-0.59362,-0.80315,21.983,0.282,-0.77996,0.5587,-5.9639
> view matrix models
> #1,-0.87077,0.27489,-0.40766,21.407,0.35379,-0.22546,-0.90774,5.8507,-0.34144,-0.93467,0.099069,-18.059
> view matrix models
> #1,0.58085,0.75728,0.29856,31.548,0.80387,-0.59135,-0.064025,49.236,0.12807,0.2772,-0.95224,-97.208
> view matrix models
> #1,0.83357,0.45652,0.31103,40.686,0.54809,-0.75373,-0.3626,42.963,0.068899,0.47273,-0.87851,-100.14
> view matrix models
> #1,0.69687,0.42718,0.5761,52.27,0.53452,-0.84492,-0.020061,59.226,0.47819,0.32192,-0.81713,-93.965
> view matrix models
> #1,-0.027276,-0.22564,0.97383,89.23,-0.49022,-0.84599,-0.20975,53.868,0.87117,-0.48311,-0.087539,-41.58
> view matrix models
> #1,-0.31034,-0.76726,0.56124,90.078,-0.94979,0.22544,-0.21699,21.889,0.039968,-0.6004,-0.7987,-64.279
> view matrix models
> #1,-0.73319,-0.50487,-0.45556,42.988,-0.56802,0.82301,0.0020898,11.537,0.37388,0.2603,-0.8902,-94.751
> view matrix models
> #1,-0.3413,0.33608,-0.87782,0.0045776,-0.45646,0.75712,0.46735,31.6,0.82168,0.5602,-0.105,-73.929
> view matrix models
> #1,-0.33347,0.32636,-0.88447,0.023446,-0.46869,0.75663,0.4559,31.189,0.818,0.56658,-0.099354,-73.894
> view matrix models
> #1,-0.70688,-0.59615,-0.38068,48.656,-0.64919,0.33311,0.68381,53.402,-0.28085,0.7305,-0.62248,-97.228
> view matrix models
> #1,-0.96012,-0.091031,-0.26437,38.358,-0.27594,0.461,0.84341,55.027,0.045098,0.88272,-0.46774,-96.438
> view matrix models
> #1,-0.70215,0.37485,-0.60537,10.256,-0.28625,0.62987,0.72203,45.138,0.65195,0.68026,-0.33496,-86.279
> view matrix models
> #1,-0.29396,0.10539,-0.94999,4.0965,-0.82864,0.46727,0.30825,34.921,0.47639,0.87781,-0.050028,-80.744
> select subtract #1
Nothing selected
> select add #2
3269 atoms, 3347 bonds, 415 residues, 1 model selected
> view matrix models
> #2,0.95759,-0.00091914,-0.28813,-8.1163,0.054012,0.98284,0.17637,5.1774,0.28302,-0.18446,0.94121,0.51819
> view matrix models
> #2,0.90767,-0.04481,-0.41728,-11.727,0.11586,0.9824,0.14653,4.6604,0.40337,-0.18135,0.89689,-0.1263
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.90767,-0.04481,-0.41728,13.617,0.11586,0.9824,0.14653,21.486,0.40337,-0.18135,0.89689,-35.523
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.075416,-0.97513,-0.2084,19.117,-0.60952,0.12032,-0.78359,-4.0578,0.78917,0.18612,-0.58529,-75.861
> view matrix models
> #2,-0.93282,-0.35841,0.037275,18.432,-0.062934,0.06019,-0.9962,-6.9915,0.3548,-0.93162,-0.078702,-59.48
> view matrix models
> #2,-0.14692,0.58192,-0.79986,-4.5904,-0.067812,-0.81266,-0.57878,8.0263,-0.98682,-0.030794,0.15886,-63.175
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.14692,0.58192,-0.79986,11.702,-0.067812,-0.81266,-0.57878,26.584,-0.98682,-0.030794,0.15886,-47.126
> view matrix models
> #2,-0.14692,0.58192,-0.79986,6.392,-0.067812,-0.81266,-0.57878,26.371,-0.98682,-0.030794,0.15886,-36.505
> view matrix models
> #2,-0.14692,0.58192,-0.79986,4.9394,-0.067812,-0.81266,-0.57878,28.537,-0.98682,-0.030794,0.15886,-36.826
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.33348,0.75098,-0.56993,9.6544,-0.094421,-0.6281,-0.77239,22.333,-0.93802,-0.20376,0.28036,-32.543
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.33348,0.75098,-0.56993,15.52,-0.094421,-0.6281,-0.77239,14.302,-0.93802,-0.20376,0.28036,-27.177
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.65405,-0.21568,-0.72505,20.026,0.1543,-0.9003,0.407,49.021,-0.74054,-0.37808,-0.55557,-48.461
> view matrix models
> #2,0.51036,-0.20644,0.83481,62.132,-0.85995,-0.11685,0.49683,43.343,-0.0050187,-0.97146,-0.23716,-33.706
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.51036,-0.20644,0.83481,51.226,-0.85995,-0.11685,0.49683,48.217,-0.0050187,-0.97146,-0.23716,-47.535
> view matrix models
> #2,0.51036,-0.20644,0.83481,45.356,-0.85995,-0.11685,0.49683,57.171,-0.0050187,-0.97146,-0.23716,-43.33
> view matrix models
> #2,0.51036,-0.20644,0.83481,45.741,-0.85995,-0.11685,0.49683,80,-0.0050187,-0.97146,-0.23716,-81.988
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.38546,-0.11094,0.91603,46.973,-0.90575,-0.23502,0.35267,76.302,0.17617,-0.96564,-0.19108,-79.865
> view matrix models
> #2,0.33217,-0.081273,0.93971,47.242,-0.91209,-0.28151,0.29806,74.962,0.24032,-0.95611,-0.16764,-78.948
> view matrix models
> #2,-0.75921,0.63559,-0.14011,9.3358,0.061788,-0.14392,-0.98766,43.823,-0.64791,-0.75849,0.069996,-77.552
> view matrix models
> #2,0.1864,0.26047,-0.94732,-6.6967,0.57678,-0.80958,-0.10911,73.187,-0.79535,-0.52606,-0.30114,-89.416
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.1864,0.26047,-0.94732,17.912,0.57678,-0.80958,-0.10911,26.511,-0.79535,-0.52606,-0.30114,-60.044
> view matrix models
> #2,0.1864,0.26047,-0.94732,23.31,0.57678,-0.80958,-0.10911,27.888,-0.79535,-0.52606,-0.30114,-58.782
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99302,0.02984,0.11413,57.334,-0.065443,-0.66558,0.74345,47.589,0.098145,-0.74573,-0.65898,-63.363
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99302,0.02984,0.11413,33.505,-0.065443,-0.66558,0.74345,60.109,0.098145,-0.74573,-0.65898,-82.662
> view matrix models
> #2,0.99302,0.02984,0.11413,33.222,-0.065443,-0.66558,0.74345,66.901,0.098145,-0.74573,-0.65898,-89.124
> view matrix models
> #2,0.99302,0.02984,0.11413,40.052,-0.065443,-0.66558,0.74345,69.944,0.098145,-0.74573,-0.65898,-86.123
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.98601,0.060639,-0.15528,22.896,0.023287,-0.87226,-0.48849,37.386,-0.16507,-0.48528,0.85864,-46.788
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.98601,0.060639,-0.15528,40.461,0.023287,-0.87226,-0.48849,17.575,-0.16507,-0.48528,0.85864,-21.844
> view matrix models
> #2,-0.98601,0.060639,-0.15528,45.767,0.023287,-0.87226,-0.48849,23.89,-0.16507,-0.48528,0.85864,-32.016
> view matrix models
> #2,-0.98601,0.060639,-0.15528,52.851,0.023287,-0.87226,-0.48849,20.401,-0.16507,-0.48528,0.85864,-26.655
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.64524,0.73287,0.21579,61.947,-0.75875,-0.64772,-0.06898,27.198,0.089219,-0.20824,0.974,-23.384
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.64524,0.73287,0.21579,80.044,-0.75875,-0.64772,-0.06898,48.609,0.089219,-0.20824,0.974,-22.318
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.67821,-0.0941,-0.72882,63.928,0.39114,-0.79339,0.46642,69.506,-0.62213,-0.6014,-0.50128,-64.689
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.67821,-0.0941,-0.72882,60.458,0.39114,-0.79339,0.46642,51.812,-0.62213,-0.6014,-0.50128,-49.519
> view matrix models
> #2,0.67821,-0.0941,-0.72882,32.765,0.39114,-0.79339,0.46642,33.052,-0.62213,-0.6014,-0.50128,-37.372
> view matrix models
> #2,0.67821,-0.0941,-0.72882,41.104,0.39114,-0.79339,0.46642,41.945,-0.62213,-0.6014,-0.50128,-63.429
> view matrix models
> #2,0.67821,-0.0941,-0.72882,14.66,0.39114,-0.79339,0.46642,38.742,-0.62213,-0.6014,-0.50128,-62.891
> view matrix models
> #2,0.67821,-0.0941,-0.72882,16.857,0.39114,-0.79339,0.46642,47.285,-0.62213,-0.6014,-0.50128,-68.603
> view matrix models
> #2,0.67821,-0.0941,-0.72882,12.866,0.39114,-0.79339,0.46642,49.243,-0.62213,-0.6014,-0.50128,-69.754
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.89835,-0.014926,-0.43904,21.572,0.24386,-0.81435,0.52666,50.267,-0.36539,-0.58018,-0.72793,-74.817
> view matrix models
> #2,0.84878,0.12961,-0.51261,18.718,0.3155,-0.90214,0.2943,44.593,-0.4243,-0.41152,-0.80661,-77.956
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.84878,0.12961,-0.51261,24.953,0.3155,-0.90214,0.2943,43.157,-0.4243,-0.41152,-0.80661,-74.725
> close session
> open
> /Users/dwheeler/Downloads/fold_php_moc3_nuc_2024_10_31_15_45/fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif
> format mmcif
Chain information for fold_php_moc3_nuc_2024_10_31_15_45_model_4.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I J | .
K L | .
> show cartoons
> hide atoms
> show atoms
> style stick
Changed 26058 atom styles
> hide cartoons
> select zone /J:54 10
Selected 258 atoms
> hide ~sel
> view sel
> style sel stick
Changed 258 atom styles
> color sel byhetero
> select zone /J:54 15
Selected 608 atoms
> show sel
> hbonds sel reveal true
===== 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
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.2
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: Mac14,9
Model Number: Z17G002HSLL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.1.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7 (23H124)
Kernel Version: Darwin 23.6.0
Time since boot: 14 days, 3 hours, 1 minute
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
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
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-GenomeTools: 0.9
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
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
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 12 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 , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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