Opened 2 years ago

Closed 2 years ago

#9895 closed defect (duplicate)

MemoryError opening mmCIF files

Reported by: lubiosan.uah@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8OX0

Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319,
in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> volume dataCacheSize 10000

> open tpmt

'tpmt' has no suffix  

> open TPMT

'TPMT' has no suffix  

> open C:/Users/lucyp/Downloads/AF-P51580-F1-model_v4.pdb

AF-P51580-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for thiopurine S-methyltransferase (P51580)
[more info...]  
  
Chain information for AF-P51580-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | thiopurine S-methyltransferase | TPMT_HUMAN 1-245  
  

> open 2BZG

Summary of feedback from opening 2BZG fetched from pdb  
---  
note | Fetching compressed mmCIF 2bzg from
http://files.rcsb.org/download/2bzg.cif  
  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319,
in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: es_ES.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HUAWEI
Model: BOD-WXX9
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 8,379,490,304
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: es-ES

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MemoryError opening mmCIF files

comment:2 by Eric Pettersen, 2 years ago

Status: assigned → feedback

Hi Lucía,

Thanks for reporting this problem. We haven't been able to reproduce ourselves, but nonetheless we have put in what we believe to be fix in the daily build. If you could try the daily build and let us know if it solves the problem for you, we would really appreciate it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Greg Couch, 2 years ago

Resolution: → duplicate
Status: feedback → closed

Duplicated of #8815.

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