![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 26 hours ago
Closed 5 hours ago
#20485 closed defect (nonchimerax)
Crash in glBufferSubData
| 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-13.7.8-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x00007ff85f891a00 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1769 in set_multishadow_view
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 251 in _draw_scene
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imaging, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, pyarrow.lib, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, chimerax.atomic._ribbons, chimerax.graphics._graphics (total: 90)
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"incident" : "CAD5C161-88AE-4BAF-80F1-D4B3DE959C89",
"pid" : 1283,
"cpuType" : "X86-64",
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"bug_type" : "309",
"procLaunch" : "2026-06-11 23:17:39.6780 +0200",
"procStartAbsTime" : 348277299424,
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"crashReporterKey" : "94FF881E-17F8-24BF-E3B0-161DB4B2EC81",
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"codeSigningTeamID" : "LWV8X224YF",
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"asi" : {"libsystem_c.dylib":["abort() called"]},
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open
> /Users/makubanska/figures_thesis/thesis_results/sta_core63/lists/motl_core_v63_6_8_somemissalignedremoved.em
> format motl
Opened Particle list motl_core_v63_6_8_somemissalignedremoved.em with 12088
particles.
> ui mousemode right "delete selected particles"
> save
> /Users/makubanska/figures_thesis/thesis_results/sta_core63/lists/motl_core_v63_6_8_somemissalignedremoved_502.em
> partlist #1.2.1
> open
> /Users/makubanska/thesis_viva_presentation/ref_composite_thesis_forbackprojections_correctlyrotated.mrc
Opened ref_composite_thesis_forbackprojections_correctlyrotated.mrc as #2,
grid size 220,220,220, pixel 1, shown at level 0.945, step 1, values float32
1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652
> artiax colormap #1.2.1.3 cross_correlation palette crest minValue
> 0.10220000147819519 maxValue 0.6520000100135803 transparency 0.0
1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652
> artiax colormap #1.2.1.3 cross_correlation palette crest minValue
> 0.3640095293521881 maxValue 0.6520000100135803 transparency 0.0
1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652
> artiax colormap #1.2.1.3 cross_correlation palette crest minValue
> 0.3640095293521881 maxValue 0.4462925238268716 transparency 0.0
> artiax particles #1.2.1 radius 0.1
> artiax particles #1.2.1 axesSize 0.1
> artiax attach #2 toParticleList #1.2.1
Opened ref_composite_thesis_forbackprojections_correctlyrotated.mrc as
#1.2.1.1.1, grid size 220,220,220, pixel 1, shown at level 0.945, step 1,
values float32
> volume #1.2.1.1.1 capFaces false
1832 atoms, 1832 residues, atom cross_correlation range 0.102 to 0.652
> artiax colormap #1.2.1.3 cross_correlation palette crest minValue
> 0.33408844045230324 maxValue 0.4462925238268716 transparency 0.0
1832 atoms, 1832 residues, atom legacy_x range 0 to 0
> artiax colormap #1.2.1.3 legacy_x palette crest minValue 0.0 maxValue 0.0
> transparency 0.0
1832 atoms, 1832 residues, atom tomo_number range 502 to 502
> artiax colormap #1.2.1.3 tomo_number palette crest minValue 502.0 maxValue
> 502.0 transparency 0.0
1832 atoms, 1832 residues, atom psi range -86.7 to 245
> artiax colormap #1.2.1.3 psi palette crest minValue -86.6886978149414
> maxValue 244.8070068359375 transparency 0.0
1832 atoms, 1832 residues, atom psi range -86.7 to 245
> artiax colormap #1.2.1.3 psi palette crest minValue 55.380889892578125
> maxValue 244.8070068359375 transparency 0.0
1832 atoms, 1832 residues, atom psi range -86.7 to 245
> artiax colormap #1.2.1.3 psi palette crest minValue 55.380889892578125
> maxValue 114.01278323218935 transparency 0.0
> ui mousemode right select
Drag select of axes, 1 of 1832 instances, 1 atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
Drag select of axes, 1 of 1831 instances, surfaces, 1 of 1831 instances, 1
atoms
Drag select of axes, 1 of 1831 instances, surfaces, 2 of 1831 instances, 1
atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
Drag select of axes, 1 of 1829 instances, 1 atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
> artiax view xy
Drag select of surfaces, 1 of 1828 instances
Drag select of axes, 1 of 1828 instances, 1 atoms
Drag select of axes, 1 of 1828 instances, surfaces, 3 of 1828 instances, 1
atoms
> select add #1.2.1.2
3 atoms, 3 residues, 2 models selected
> select clear
Drag select of axes, 1 of 1828 instances, surfaces, 3 of 1828 instances, 1
atoms
> select #1.2.1.2
1 model selected
Drag select of axes, 2 of 1828 instances, surfaces, 2 of 1828 instances, 2
atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
Drag select of axes, 2 of 1826 instances, surfaces, 2 of 1826 instances, 2
atoms
> ui mousemode right "delete selected particles"
> artiax view xy
> artiax view xz
> artiax view yz
> artiax view xy
> ui mousemode right select
Drag select of axes, 2 of 1824 instances, surfaces, 1 of 1824 instances, 2
atoms
> select add #1.2.1.2
2 atoms, 2 residues, 2 models selected
Drag select of axes, 1 of 1824 instances, surfaces, 1 of 1824 instances, 1
atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
Drag select of axes, 1 of 1823 instances, surfaces, 1 of 1823 instances, 1
atoms
Drag select of axes, 1 of 1823 instances, 1 atoms
> select clear
Drag select of axes, 1 of 1823 instances, surfaces, 1 of 1823 instances, 1
atoms
> select clear
Drag select of surfaces, 1 of 1823 instances
Drag select of axes, 3 of 1823 instances, surfaces, 2 of 1823 instances, 3
atoms
> select clear
Drag select of axes, 2 of 1823 instances, surfaces, 1 of 1823 instances, 2
atoms
> select clear
Drag select of axes, 2 of 1823 instances, surfaces, 1 of 1823 instances, 2
atoms
> select add #1.2.1.2
2 atoms, 2 residues, 2 models selected
Drag select of axes, 1 of 1823 instances, surfaces, 1 of 1823 instances, 1
atoms
Drag select of surfaces, 1 of 1823 instances
> ui mousemode right "delete selected particles"
> ui mousemode right select
Drag select of axes, 1 of 1822 instances, surfaces, 1 of 1822 instances, 1
atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
Drag select of axes, 1 of 1821 instances, surfaces, 1 of 1821 instances, 1
atoms
> ui mousemode right "delete selected particles"
> ui mousemode right select
> artiax view xy
Drag select of axes, 3 of 1820 instances, surfaces, 4 of 1820 instances, 3
atoms
> select #1.2.1.2
1 model selected
Drag select of axes, 1 of 1820 instances, surfaces, 1 of 1820 instances, 1
atoms
> ui mousemode right "delete selected particles"
> artiax particles #1.2.1 surfaceLevel 0.45492
> artiax view xy
> save
> /Users/makubanska/figures_thesis/thesis_results/sta_core63/lists/motl_core_v63_6_8_somemissalignedremoved_502.em
> partlist #1.2.1
> open
> /Users/makubanska/thesis_viva_presentation/PBS_reprojected_502/502_bin4_MemBrain_seg_v10_alpha.mrc
Opened 502_bin4_MemBrain_seg_v10_alpha.mrc as #2, grid size 1024,1024,550,
pixel 7.88,7.88,7.88, shown at step 1, values int8
> volume #2 color #cfd3db color #ffffb3 color #ffffb3
> volume #2 region 0,0,0,1023,1023,549 step 4
> hide #!1.2.1 models
> close #2
> open
> /Users/makubanska/thesis_viva_presentation/PBS_reprojected_502/502_bin4_MemBrain_seg_v10_alpha.mrc
Opened 502_bin4_MemBrain_seg_v10_alpha.mrc as #2, grid size 1024,1024,550,
pixel 7.88,7.88,7.88, shown at step 1, values int8
> volume #2 region 0,0,0,1023,1023,549 step 4
> volume #2 change image level 0,0 level 0.1,0.8 level 1,1
> volume #2 level 0.9838
> volume #2 step 8
> volume #2 level 0.2262
> show #!1.2.1 models
> hide #!1.2.1 models
> volume #2 step 4
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> volume #2 color #cfd3db
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> lighting soft
> set bgColor white
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: 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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2075.140.4.0.0 (iBridge: 22.16.16083.0.0,0)
OS Loader Version: 577.140.2~30
Software:
System Software Overview:
System Version: macOS 13.7.8 (22H730)
Kernel Version: Darwin 22.6.0
Time since boot: 43 minutes, 20 seconds
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PA302W:
Resolution: 2560 x 1600
UI Looks like: 2560 x 1600 @ 30.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 66105741TW
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: ff.c8
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
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: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.5.1
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
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: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
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
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: 1.14.1
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: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
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: 4.3.2
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
pandas: 2.3.1
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
pyarrow: 21.0.0
pycollada: 0.8
pydicom: 2.4.4
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
starfile: 0.5.13
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 , 7 hours ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in glBufferSubData |
comment:2 by , 5 hours ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
ChimeraX crashed in the Mac Intel graphics driver. Unfortunately Intel Macs have unstable OpenGL graphics. This is not a problem on newer Apple Silicon Macs. There is nothing we can do to fix this. The crash is more common when large maps are being shown, and probably relates to the Intel graphics running out of memory.
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Reported by Marta