"graphics quality" → out of memory

[saverio.lemme@…]

The following bug report has been submitted:
Platform:        Linux-6.11.0-24-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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 7n0b format mmcif fromDatabase pdb

7n0b title:  
Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)-RNA complex [more info...]  
  
Chain information for 7n0b #1  
---  
Chain | Description | UniProt  
A | Non-structural protein 10 | R1AB_SARS2 1-139  
B | Proofreading exoribonuclease | R1AB_SARS2 1-527  
D | RNA (5'-R(*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |   
T | RNA (5'-R(*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*U)-3') |   
  
Non-standard residues in 7n0b #1  
---  
CA — calcium ion  
ZN — zinc ion  
  

> save /media/xxxx/DATAOCEAN/7N0B_dsRNA_interactions/7N0B.pdb

> graphics quality atomTriangles 500 bondTriangles 500 totalAtomTriangles
> 5000000 totalBondTriangles 5000000 bondSides 500 ribbonSides 500
> ribbonDivisions 500 colorDepth 16

> set bgColor white

> close session

> open /media/xxxx/DATAOCEAN/7N0B_dsRNA_interactions/7N0B_CAs2MGs.pdb

Summary of feedback from opening
/media/xxxx/DATAOCEAN/7N0B_dsRNA_interactions/7N0B_CAs2MGs.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CA (601 )  
Cannot find LINK/SSBOND residue CA (602 )  
Cannot find LINK/SSBOND residue CA (601 )  
Cannot find LINK/SSBOND residue CA (602 )  
Cannot find LINK/SSBOND residue CA (601 )  
5 messages similar to the above omitted  
  
Chain information for 7N0B_CAs2MGs.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
T | No description available  
  

> nucleotides atoms

> style nucleic stick

Changed 823 atom styles  

> ~cartoon /D-T

> windowsize 1024 1024

> graphics quality

Quality 1, atom triangles 500, bond triangles 2000, pseudobond sides 10,
ribbon divisions 500  

> graphics quality atomTriangles 750 bondTriangles 750 totalAtomTriangles
> 5000000 totalBondTriangles 5000000 bondSides 750 ribbonSides 750
> ribbonDivisions 750 colorDepth 16

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glBufferData,  
pyArgs = (  
34963,  
7647677232,  
array([[ 1, 0, 376],  
[ 1, 376, 377],  
[ 2, 1, ...,  
GL_STATIC_DRAW,  
),  
cArgs = (  
34963,  
7647677232,  
array([[ 1, 0, 376],  
[ 1, 376, 377],  
[ 2, 1, ...,  
GL_STATIC_DRAW,  
),  
cArguments = (  
34963,  
7647677232,  
array([[ 1, 0, 376],  
[ 1, 376, 377],  
[ 2, 1, ...,  
GL_STATIC_DRAW,  
)  
)  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 259, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1554, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 787, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1924, in activate_bindings  
self.update_buffers()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1912, in update_buffers  
b.update_buffer_data(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2829, in update_buffer_data  
GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW)  
File "src/latebind.pyx", line 51, in OpenGL_accelerate.latebind.Curry.__call__  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/OpenGL/GL/VERSION/GL_1_5.py", line 89, in glBufferData  
return baseOperation( target, size, data, usage )  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glBufferData,  
pyArgs = (  
34963,  
7647677232,  
array([[ 1, 0, 376],  
[ 1, 376, 377],  
[ 2, 1, ...,  
GL_STATIC_DRAW,  
),  
cArgs = (  
34963,  
7647677232,  
array([[ 1, 0, 376],  
[ 1, 376, 377],  
[ 2, 1, ...,  
GL_STATIC_DRAW,  
),  
cArguments = (  
34963,  
7647677232,  
array([[ 1, 0, 376],  
[ 1, 376, 377],  
[ 2, 1, ...,  
GL_STATIC_DRAW,  
)  
)  
  




OpenGL version: 4.6 (Core Profile) Mesa 24.3.0-devel
OpenGL renderer: AMD Radeon Graphics (radeonsi, raphael_mendocino, LLVM 19.1.2, DRM 3.59, 6.11.0-24-generic)
OpenGL vendor: AMD

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: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7E16
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 7950X3D 16-Core Processor
Cache Size: 1024 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            93Gi        29Gi        54Gi        72Mi        10Gi        64Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	15:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Raphael [1002:164e] (rev c9)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Raphael [1462:7e16]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    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-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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    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
    distro: 1.9.0
    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
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    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
    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
    packaging: 23.2
    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
    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
    tornado: 6.4.2
    traitlets: 5.14.3
    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-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Tom Goddard]

Your graphics quality command requests 750 bond triangles, ribbon sides, ribbon divisions which are absurdly high values resulting in the graphics trying to allocate 7 Gbytes for your ribbons or bond depictions which your graphics card cannot handle.

graphics quality atomTriangles 750 bondTriangles 750 totalAtomTriangles 5000000 totalBondTriangles 5000000 bondSides 750 ribbonSides 750 ribbonDivisions 750 colorDepth 16

Make sure you read the ChimeraX documentation so you know what these parameters mean and set them to sensible values.