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Opened 6 weeks ago
Closed 6 weeks ago
#18874 closed defect (can't reproduce)
Crash in swap_buffers
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.0-arm64-arm-64bit
ChimeraX Version: 1.11.dev202507041857 (2025-07-04 18:57:15 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x0000000203990800 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 143 in render
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1058 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1223 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.surface._surface, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, 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 (total: 46)
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"codeSigningMonitor" : 2,
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"procLaunch" : "2025-09-24 09:04:21.3452 -0400",
"procStartAbsTime" : 1710929846855,
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"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":99085},
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"faultingThread" : 0,
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"name" : "libqmacjp2.dylib"
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"uuid" : "5200c6a0-ccdb-3607-9947-1defdd6fb647",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/unicodedata.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202507041857 (2025-07-04)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 8eW6
8ew6 title:
Anti-human CD8 VHH complex with CD8 α [more info...]
Chain information for 8ew6 #1
---
Chain | Description | UniProt
V | Anti-CD8 alpha VHH |
W | T-cell surface glycoprotein CD8 alpha chain | CD8A_HUMAN 1-120
8ew6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1768 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show "Show Sequence Viewer"
> sequence chain /V
Alignment identifier is 1/V
> lighting soft
> set bgColor white
> select clear
> select /V:1-123
913 atoms, 937 bonds, 123 residues, 1 model selected
> color sel cornflower blue
> select /V:1-2
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /V:1-3
21 atoms, 20 bonds, 3 residues, 1 model selected
> select /V:8-9
8 atoms, 7 bonds, 2 residues, 1 model selected
> select /V:8-11
20 atoms, 19 bonds, 4 residues, 1 model selected
> select /V:15
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /V:15-23
58 atoms, 57 bonds, 9 residues, 1 model selected
> select /V:27
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /V:26
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /V:26
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /V:23
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:23-29
49 atoms, 50 bonds, 7 residues, 1 model selected
> select /V:23-29
49 atoms, 50 bonds, 7 residues, 1 model selected
> select /V:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /V:25-32
67 atoms, 69 bonds, 8 residues, 1 model selected
> color sel forest green
> select /V:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:53-56
38 atoms, 38 bonds, 4 residues, 1 model selected
> color sel forest green
> select /V:102
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /V:100-101
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /V:100-105
49 atoms, 51 bonds, 6 residues, 1 model selected
> color sel forest green
> surface sel
> select clear
> select /V:1-123
913 atoms, 937 bonds, 123 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> surface (#!1 & sel)
> select /V:52@CD
1 atom, 1 residue, 1 model selected
> select /V:49-50
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /V:49-56
71 atoms, 71 bonds, 8 residues, 1 model selected
> select /V:50-51
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /V:50-56
63 atoms, 63 bonds, 7 residues, 1 model selected
> select /V:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:52-56
49 atoms, 49 bonds, 5 residues, 1 model selected
> select /V:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:52-55
38 atoms, 38 bonds, 4 residues, 1 model selected
> color (#!1 & sel) forest green
> select /V:99@O
1 atom, 1 residue, 1 model selected
> select /V:96
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /V:96-99
20 atoms, 19 bonds, 4 residues, 1 model selected
> select /V:33@N
1 atom, 1 residue, 1 model selected
> select /V:28
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /V:28-33
51 atoms, 52 bonds, 6 residues, 1 model selected
> color (#!1 & sel) forest green
> select /V:28-31,62-65,87-91,100-105
145 atoms, 146 bonds, 19 residues, 1 model selected
> select /V:100-101
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /V:100-101
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /V:96
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /V:96-101
37 atoms, 37 bonds, 6 residues, 1 model selected
> select /V:55@OD2
1 atom, 1 residue, 1 model selected
> select /V:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:51-56
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /V:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:49-56
71 atoms, 71 bonds, 8 residues, 1 model selected
> select /V:52-53
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /V:52-60
84 atoms, 86 bonds, 9 residues, 1 model selected
> select /V:54-55
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /V:54-57
40 atoms, 41 bonds, 4 residues, 1 model selected
> select /V:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:54-55
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /V:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:52-55
38 atoms, 38 bonds, 4 residues, 1 model selected
> select /V:50
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /V:50-51
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /V:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /V:48-55
67 atoms, 67 bonds, 8 residues, 1 model selected
> select /V:52-53
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /V:52-55
38 atoms, 38 bonds, 4 residues, 1 model selected
> select /V:28
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /V:28-33
51 atoms, 52 bonds, 6 residues, 1 model selected
> select /V:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:52-55
38 atoms, 38 bonds, 4 residues, 1 model selected
> select /V:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:52-55
38 atoms, 38 bonds, 4 residues, 1 model selected
> select /V:28-29
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /V:28-32
46 atoms, 47 bonds, 5 residues, 1 model selected
> select /V:100@CB
1 atom, 1 residue, 1 model selected
> select /V:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /V:100-105
49 atoms, 51 bonds, 6 residues, 1 model selected
> select /V:104
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /V:100-104
42 atoms, 44 bonds, 5 residues, 1 model selected
> color (#!1 & sel) forest green
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:103-104
11 atoms, 10 bonds, 2 residues, 1 model selected
> color (#!1 & sel) red
> select /V:99@O
1 atom, 1 residue, 1 model selected
> select /V:97-98
10 atoms, 9 bonds, 2 residues, 1 model selected
> select /V:97-99
14 atoms, 13 bonds, 3 residues, 1 model selected
> select /V:95
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /V:95-99
32 atoms, 32 bonds, 5 residues, 1 model selected
> select /V:98-99
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /V:98-99
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /V:28-31,62-65,87-91,100-105
145 atoms, 146 bonds, 19 residues, 1 model selected
> select /V:98
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:98-99
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /V:97
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:97-98
10 atoms, 9 bonds, 2 residues, 1 model selected
> select /V:99
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /V:99
4 atoms, 3 bonds, 1 residue, 1 model selected
> color (#!1 & sel) forest green
> select /V:110@O
1 atom, 1 residue, 1 model selected
> select /V:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:110-113
33 atoms, 33 bonds, 4 residues, 1 model selected
> color (#!1 & sel) forest green
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select /V:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /V:110
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select /V:110@CB
1 atom, 1 residue, 1 model selected
> select /W:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /V
946 atoms, 937 bonds, 156 residues, 1 model selected
> select /W
903 atoms, 879 bonds, 1 pseudobond, 155 residues, 2 models selected
> surface (#!1 & sel)
> select /W:55@ND2
1 atom, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /W
Alignment identifier is 1/W
> select /W:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /W:53-56
32 atoms, 31 bonds, 4 residues, 1 model selected
> select /W:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /W:55-56
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /W:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /W:53-54
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /W:53-54
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /W:53-55
23 atoms, 22 bonds, 3 residues, 1 model selected
> color (#!1 & sel) lime
> color (#!1 & sel) purple
> show (#!1 & sel-residues & sidechain) target ab
> surface hidePatches (#!1 & sel)
> select /V:110@CB
1 atom, 1 residue, 1 model selected
> select /V:103@CB
1 atom, 1 residue, 1 model selected
> surface hidePatches (#!1 & sel)
> select /V:110@CB
1 atom, 1 residue, 1 model selected
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> select /V:110@CB
1 atom, 1 residue, 1 model selected
> show (#!1 & sel-residues & sidechain) target ab
> surface hidePatches (#!1 & sel)
> select /W:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /W
903 atoms, 879 bonds, 1 pseudobond, 155 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select /V:103@CB
1 atom, 1 residue, 1 model selected
> measure sasa
Solvent accessible area for all atoms (1849 atoms) = 11644
> select /V:28
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /V:28-32
46 atoms, 47 bonds, 5 residues, 1 model selected
> select /V:52
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /V:52-55
38 atoms, 38 bonds, 4 residues, 1 model selected
> select /V
946 atoms, 937 bonds, 156 residues, 1 model selected
> surface (#!1 & sel)
fromIccProfile: Failed to parse description
> stop
fromIccProfile: Failed to parse description
> surface hidePatches (#!1 & sel)
fromIccProfile: Failed to parse description
> select clear
fromIccProfile: Failed to parse description
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> select /V:99
4 atoms, 3 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> select /V:99-113
113 atoms, 117 bonds, 15 residues, 1 model selected
fromIccProfile: Failed to parse description
> color (#!1 & sel) magenta
fromIccProfile: Failed to parse description
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> select /V:104
6 atoms, 5 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> select /V:104
6 atoms, 5 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> undo
fromIccProfile: Failed to parse description
> select /V:103
5 atoms, 4 bonds, 1 residue, 1 model selected
fromIccProfile: Failed to parse description
> select /V
946 atoms, 937 bonds, 156 residues, 1 model selected
fromIccProfile: Failed to parse description
> surface (#!1 & sel)
fromIccProfile: Failed to parse description
> select /W
903 atoms, 879 bonds, 1 pseudobond, 155 residues, 2 models selected
fromIccProfile: Failed to parse description
> surface (#!1 & sel)
fromIccProfile: Failed to parse description
> ui tool show "Side View"
fromIccProfile: Failed to parse description
> cartoon hide (#!1 & sel)
fromIccProfile: Failed to parse description
Desktop color scheme is dark
Desktop color scheme is light
===== Log before crash end =====
Log:
Startup Messages
---
warnings | fromIccProfile: Failed to parse description
fromIccProfile: Failed to parse description
fromIccProfile: Failed to parse description
UCSF ChimeraX version: 1.11.dev202507041857 (2025-07-04)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
fromIccProfile: Failed to parse description
[Repeated 227 time(s)]
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHE3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0 (25A354)
Kernel Version: Darwin 25.0.0
Time since boot: 3 days, 6 hours, 51 minutes
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 4
Displays:
Display:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.1
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.10
ChimeraX-AtomicLibrary: 14.1.20
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202507041857
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.2
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.12.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.0
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.21
ChimeraX-ModelPanel: 1.5.1
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: 1.0.1
ChimeraX-MutationScores: 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: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.4
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.46.3
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 0.3
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.2
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.5
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 6 weeks ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers |
comment:2 by , 6 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
A lot going on in the crash stack trace. It appears a display was added or removed
[NSWindow _displayChangedSoAdjustWindows:]
and it is in Qt opengl makeCurrent() and it is in an expose event for the status line and it is trying to call swapBuffers(). Not sure how you can be in makeCurrent() and end up calling swapBuffers() before makeCurrent() completes is a mystery.
I'd categorize this as a Mac multi-display crash. It is using Qt 6.8.2 where these crashes were common. Have not seen them in Qt 6.9 in more recent daily builds.
Note:
See TracTickets
for help on using tickets.
The "fromIccProfile: Failed to parse description" messages later in the log seem to relate to International Color Consortium profiles. AI sez:
The error message "fromIccProfile: Failed to parse description" indicates an issue with parsing an ICC (International Color Consortium) profile, specifically within its description field. This error is often encountered in applications that handle image processing and color management, such as those built with Qt or PyQt5.