![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17663 closed defect (nonchimerax)
Graphics hardware encountered an error and was reset:
| 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-15.4.1-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
Fatal Python error: Aborted
Current thread 0x00007ff84995cbc0 (most recent call first):
File "/Applications/ChimeraX-1.9.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-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath (total: 54)
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"procLaunch" : "2025-05-13 18:06:00.0956 -0700",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> set bgColor white
> graphics silhouettes true
> lighting soft
> ui mousemode right "translate selected models"
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone all; sel; close #10000; marker #10000
> position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone all; sel; close #10000; marker #10000 position
> cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel distance 0; close
> #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add VolView command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add ModelPanel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add DefaultDisp command default_mol_display
> buttonpanel Shortcuts add MapSphere command map_sphere_15
> buttonpanel Shortcuts add MapUnSphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/glander/Scripps Research Dropbox/Gabriel Lander/Manuscripts-
> InProg/2025-ACB manuscript shared folder/0. DensitiesAndModels/Maps/0. final
> models/2. IKZF1_with_DEG_and_ACB_FINAL.pdb"
Chain information for 2. IKZF1_with_DEG_and_ACB_FINAL.pdb #1
---
Chain | Description
A | No description available
C | No description available
> open "/Users/glander/Scripps Research Dropbox/Gabriel Lander/Manuscripts-
> InProg/2025-ACB manuscript shared folder/0. DensitiesAndModels/Maps/0. final
> models/2a. Ikzf1_with_DEG_and_ACB.mrc"
Opened 2a. Ikzf1_with_DEG_and_ACB.mrc as #2, grid size 443,443,443, pixel 0.5,
shown at level 2.59, step 1, values float32
> volume #2 level 4.258
> volume #2 level 2.157
> volume #2 level 11.21
> open "/Users/glander/Scripps Research Dropbox/Gabriel Lander/Manuscripts-
> InProg/2025-ACB manuscript shared folder/0. DensitiesAndModels/Maps/0. final
> models/1a. Ikzf1_with_DEG.mrc"
Opened 1a. Ikzf1_with_DEG.mrc as #3, grid size 443,443,443, pixel 0.5, shown
at level 2.31, step 1, values float32
> volume #3 level 6.579
> tool show Models
> molmap #1 5
Opened 2. IKZF1_with_DEG_and_ACB_FINAL.pdb map 5 as #4, grid size 68,82,70,
pixel 1.67, shown at level 0.0973, step 1, values float32
> close #4
> molmap #1/B 5
Opened 2. IKZF1_with_DEG_and_ACB_FINAL.pdb map 5 as #4, grid size 23,24,26,
pixel 1.67, shown at level 0.0383, step 1, values float32
> close #4
> molmap #1/C 5
Opened 2. IKZF1_with_DEG_and_ACB_FINAL.pdb map 5 as #4, grid size 55,61,50,
pixel 1.67, shown at level 0.091, step 1, values float32
> fitmap #3 inMap #4
Fit map 1a. Ikzf1_with_DEG.mrc in map 2. IKZF1_with_DEG_and_ACB_FINAL.pdb map
5 using 452939 points
correlation = 0.5646, correlation about mean = 0.1282, overlap = 9.987e+05
steps = 96, shift = 0.562, angle = 3.7 degrees
Position of 1a. Ikzf1_with_DEG.mrc (#3) relative to 2.
IKZF1_with_DEG_and_ACB_FINAL.pdb map 5 (#4) coordinates:
Matrix rotation and translation
0.99937151 0.02653510 0.02350467 -6.38973169
-0.02522867 0.99820944 -0.05423499 9.55132667
-0.02490172 0.05360791 0.99825152 -3.80352518
Axis 0.83569631 0.37511083 -0.40112785
Axis point 0.00000000 78.39386343 175.12211962
Rotation angle (degrees) 3.69945317
Shift along axis -0.23136926
> close #4
> volume #3 level 21.51
> volume #2 level 2.447
> volume #3 level 7.788
> volume #3 color #ffffb223
> volume #2 level 1.577
> volume #3 level 2.952
> fitmap #3 inMap #2
Fit map 1a. Ikzf1_with_DEG.mrc in map 2a. Ikzf1_with_DEG_and_ACB.mrc using
770205 points
correlation = 0.9171, correlation about mean = 0.7099, overlap = 8.443e+07
steps = 76, shift = 0.693, angle = 2.84 degrees
Position of 1a. Ikzf1_with_DEG.mrc (#3) relative to 2a.
Ikzf1_with_DEG_and_ACB.mrc (#2) coordinates:
Matrix rotation and translation
0.99992306 0.00968774 0.00774772 -2.41723639
-0.00960868 0.99990204 -0.01017753 2.26818786
-0.00784556 0.01010231 0.99991819 -0.62905482
Axis 0.63288843 0.48663123 -0.60219788
Axis point 0.00000000 66.90308407 224.47771142
Rotation angle (degrees) 0.91801248
Shift along axis -0.04725441
> molmap #1/C 5
Opened 2. IKZF1_with_DEG_and_ACB_FINAL.pdb map 5 as #4, grid size 55,61,50,
pixel 1.67, shown at level 0.091, step 1, values float32
> fitmap #3 inMap #4
Fit map 1a. Ikzf1_with_DEG.mrc in map 2. IKZF1_with_DEG_and_ACB_FINAL.pdb map
5 using 770205 points
correlation = 0.5425, correlation about mean = 0.1587, overlap = 1.16e+06
steps = 464, shift = 0.673, angle = 2.8 degrees
Position of 1a. Ikzf1_with_DEG.mrc (#3) relative to 2.
IKZF1_with_DEG_and_ACB_FINAL.pdb map 5 (#4) coordinates:
Matrix rotation and translation
0.99937787 0.02592850 0.02390794 -6.37647211
-0.02461722 0.99825903 -0.05359954 9.38938752
-0.02525607 0.05297764 0.99827626 -3.69204670
Axis 0.83399280 0.38472049 -0.39553274
Axis point 0.00000000 77.19763306 174.42999488
Rotation angle (degrees) 3.66345206
Shift along axis -0.24531671
> hide #!4 models
> volume #3 level 7.582
> color #2 #b2b2b276 models
> color #2 #b2b2b275 models
> open "/Users/glander/Scripps Research Dropbox/Gabriel Lander/Manuscripts-
> InProg/2025-ACB manuscript shared folder/0. DensitiesAndModels/Maps/0. final
> models/1. IKZF1_with_DEG_FINAL.pdb"
Chain information for 1. IKZF1_with_DEG_FINAL.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> tool show Models
> fitmap #5 inMap #3
Fit molecule 1. IKZF1_with_DEG_FINAL.pdb (#5) to map 1a. Ikzf1_with_DEG.mrc
(#3) using 9639 atoms
average map value = 16.83, steps = 92
shifted from previous position = 0.602
rotated from previous position = 3.66 degrees
atoms outside contour = 1042, contour level = 7.5818
Position of 1. IKZF1_with_DEG_FINAL.pdb (#5) relative to 1a.
Ikzf1_with_DEG.mrc (#3) coordinates:
Matrix rotation and translation
1.00000000 -0.00007152 0.00004940 0.00597490
0.00007152 1.00000000 -0.00000604 -0.00856355
-0.00004940 0.00000604 1.00000000 -0.00132494
Axis 0.06929196 0.56694589 0.82083554
Axis point 75.91516038 88.89600540 0.00000000
Rotation angle (degrees) 0.00499213
Shift along axis -0.00552861
> hide #!2 models
> hide #!1 models
> hide #!3 models
> hide #!5 models
> close #4
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!3 models
> volume #2 level 5.49
> volume #2 level 4.403
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> set bgColor white
> graphics silhouettes true
> lighting soft
> ui mousemode right "translate selected models"
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone all; sel; close #10000; marker #10000
> position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone all; sel; close #10000; marker #10000 position
> cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel distance 0; close
> #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add VolView command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add ModelPanel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add DefaultDisp command default_mol_display
> buttonpanel Shortcuts add MapSphere command map_sphere_15
> buttonpanel Shortcuts add MapUnSphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/glander/Scripps Research Dropbox/Gabriel Lander/Manuscripts-
> InProg/2025-ACB manuscript shared folder/0. DensitiesAndModels/Maps/0. final
> models/1. IKZF1_with_DEG_FINAL.pdb"
Chain information for 1. IKZF1_with_DEG_FINAL.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/glander/Scripps Research Dropbox/Gabriel Lander/Manuscripts-
> InProg/2025-ACB manuscript shared folder/0. DensitiesAndModels/Maps/0. final
> models/1a. Ikzf1_with_DEG.mrc"
Opened 1a. Ikzf1_with_DEG.mrc as #2, grid size 443,443,443, pixel 0.5, shown
at level 2.31, step 1, values float32
OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro Vega 64X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac Pro
Model Identifier: iMacPro1,1
Processor Name: 18-Core Intel Xeon W
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 18
L2 Cache (per Core): 1 MB
L3 Cache: 24.8 MB
Hyper-Threading Technology: Enabled
Memory: 256 GB
System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0)
OS Loader Version: 583~900
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 12 days, 9 hours, 17 minutes
Graphics/Displays:
Radeon Pro Vega 64X:
Chipset Model: Radeon Pro Vega 64X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 16 GB
Vendor: AMD (0x1002)
Device ID: 0x686b
Revision ID: 0x0000
ROM Revision: 113-D0500D-114
VBIOS Version: 113-D05001A1XX-021
Option ROM Version: 113-D05001A1XX-021
EFI Driver Version: 01.01.114
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL U3219Q:
Resolution: 6720 x 3780
UI Looks like: 3360 x 1890 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 3QXS413
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset: |
comment:2 by , 6 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
This is a known ChimeraX crash. The bug report panel now tells you about such crashes in red font, for instance this one said:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics."
I am sad to see you are still using a 2017 Intel/AMD Mac. We've seen hundreds of these reports crashing in the Mac Intel or AMD OpenGL driver but I don't have anything more specific to tell you to avoid them. Sometimes they happen with very little data opened. Apple deprecated the community standard OpenGL graphics about 10 years ago when the developed their proprietary Mac-only Metal graphics. Fortunately the Mac M1,M2... machines have a very stable OpenGL driver. They probably had to reimplement OpenGL for the Apple Silicon GPUs and they did a good job.
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Reported by Gabe Lander