Opened 9 months ago

Closed 9 months ago

#16875 closed defect (nonchimerax)

Nothing shown in graphics window

Reported by: michael.r.rufrano@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I am loading into ChimeraX and I cannot see anything displayed. The screen is black and I cannot see the displayed protein I load into the program. I cannot even change the background color from black to white. I have Windows 11 and graphics driver AMD Radeon RX 6950 XT updated to the latest version. Please advise.

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 "C:\Users\Public\Desktop\hemeglobin alpha helix.cxs" format session

No such file/path: C:\Users\Public\Desktop\hemeglobin alpha helix.cxs  

> open "C:\Users\Public\Desktop\hemeglobin alpha helix.cxs" format session

No such file/path: C:\Users\Public\Desktop\hemeglobin alpha helix.cxs  

> open C:/Users/mikey/Downloads/4wgk.pdb

4wgk.pdb title:  
Crystal structure of human neutral ceramidase with Zn-bound phosphate [more
info...]  
  
Chain information for 4wgk.pdb #1  
---  
Chain | Description | UniProt  
A B | neutral ceramidase | ASAH2_HUMAN 99-780  
  
Non-standard residues in 4wgk.pdb #1  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
CA — calcium ion  
CIT — citric acid  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
PO4 — phosphate ion  
ZN — zinc ion  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> show cartoons

> select all

11135 atoms, 10895 bonds, 27 pseudobonds, 1861 residues, 4 models selected  

> show sel cartoons

> show sel atoms

> set bgColor white

> open C:/Users/mikey/Downloads/rcsb_pdb_4WGK.fasta

Summary of feedback from opening C:/Users/mikey/Downloads/rcsb_pdb_4WGK.fasta  
---  
notes | Alignment identifier is rcsb_pdb_4WGK.fasta  
Associated 4wgk.pdb chain A to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  
Associated 4wgk.pdb chain B to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  
  
Opened 1 sequence from rcsb_pdb_4WGK.fasta  

> open C:/Users/mikey/Downloads/4wgk.cif

Summary of feedback from opening C:/Users/mikey/Downloads/4wgk.cif  
---  
notes | Fetching CCD BMA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
Fetching CCD CIT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/CIT/CIT.cif  
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
4wgk.cif title:  
Crystal structure of human neutral ceramidase with Zn-bound phosphate [more
info...]  
  
Chain information for 4wgk.cif #2  
---  
Chain | Description | UniProt  
A B | Neutral ceramidase | ASAH2_HUMAN 99-780  
  
Non-standard residues in 4wgk.cif #2  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CA — calcium ion  
CIT — citric acid  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PO4 — phosphate ion  
ZN — zinc ion  
  
4wgk.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Associated 4wgk.cif chain A to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  
Associated 4wgk.cif chain B to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  

> open C:/Users/mikey/Downloads/4wgk.cif

4wgk.cif title:  
Crystal structure of human neutral ceramidase with Zn-bound phosphate [more
info...]  
  
Chain information for 4wgk.cif #3  
---  
Chain | Description | UniProt  
A B | Neutral ceramidase | ASAH2_HUMAN 99-780  
  
Non-standard residues in 4wgk.cif #3  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CA — calcium ion  
CIT — citric acid  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PO4 — phosphate ion  
ZN — zinc ion  
  
4wgk.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Associated 4wgk.cif chain A to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  
Associated 4wgk.cif chain B to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> open C:/Users/mikey/Downloads/4wgk-assembly1.cif.gz

File reader requires uncompressed file; 'C:/Users/mikey/Downloads/4wgk-
assembly1.cif.gz' is compressed  

> open C:/Users/mikey/Downloads/4wgk.pdb

4wgk.pdb title:  
Crystal structure of human neutral ceramidase with Zn-bound phosphate [more
info...]  
  
Chain information for 4wgk.pdb #4  
---  
Chain | Description | UniProt  
A B | neutral ceramidase | ASAH2_HUMAN 99-780  
  
Non-standard residues in 4wgk.pdb #4  
---  
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)  
CA — calcium ion  
CIT — citric acid  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
PO4 — phosphate ion  
ZN — zinc ion  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Associated 4wgk.pdb chain A to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  
Associated 4wgk.pdb chain B to 4WGK_1|Chains A, B|Neutral ceramidase|Homo
sapiens (9606) with 0 mismatches  

> hide #!3 models

> hide #!4 models

> hide #!2 models

> set bgColor white

[Repeated 2 time(s)]

> set bgColor black

> set bgColor transparent

> set bgColor black

> set bgColor white

> set bgColor #ffffff00

> set bgColor white

[Repeated 2 time(s)]

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor white

[Repeated 4 time(s)]

> ui mousemode right rotate

> ui mousemode right select

> select clear

[Repeated 5 time(s)]

> set bgColor white

[Repeated 3 time(s)]

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> set bgColor white

[Repeated 5 time(s)]

> interfaces #!1 & ~solvent

1 buried areas: B A 698  

> hbonds #!1 reveal true

21567 hydrogen bonds found  




OpenGL version: 3.3.0 Core Profile Context 24.10.27.02.241120
OpenGL renderer: AMD Radeon RX 6950 XT
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: MicroElectronics
Model: G715
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 17,101,881,344
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800X3D 8-Core Processor           
OSLanguage: en-US

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-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
    comtypes: 1.4.5
    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
    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
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    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
    pywin32: 306
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 9 months ago

Cc: Greg Couch added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Nothing shown in graphics window

comment:2 by Tom Goddard, 9 months ago

Resolution: → nonchimerax
Status: assigned → closed

You are right that the black screen is because of a problem with your graphics driver. ChimeraX reports your graphics driver version in this bug report is 24.10.27.02.241120 which is not the current AMD driver for AMD Radeon RX 6950 XT according to the AMD driver web site

​https://www.amd.com/en/support/downloads/drivers.html/graphics/radeon-rx/radeon-rx-6000-series/amd-radeon-rx-6950-xt.html

Updating to a working driver is the only solution to your problem.

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