Opened 4 weeks ago
Closed 4 weeks ago
#18839 closed defect (duplicate)
MemoryError opening mmCIF files
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields 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 D:/Desktop/mGIPR- > mGIP/fold_mgipr_mgip2025_09_12_15_03/fold_mgipr_mgip2025_09_12_15_03_model_0.cif Traceback (most recent call last): File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 563, in dropEvent _open_dropped_file(self.session, p) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 1918, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line 464, in collated_open return remember_data_format() File "D:\soft\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:\soft\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. > open D:/Desktop/mGIPR- > mGIP/fold_mgipr_mgip2025_09_12_15_03/fold_mgipr_mgip2025_09_12_15_03_model_0.cif Traceback (most recent call last): File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 563, in dropEvent _open_dropped_file(self.session, p) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 1918, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line 464, in collated_open return remember_data_format() File "D:\soft\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:\soft\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. > open D:\Desktop\mGIPR- > mGIP\fold_mgipr_mgip2025_09_12_15_03\fold_mgipr_mgip2025_09_12_15_03_model_0.cif > format mmcif Traceback (most recent call last): File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in thread_safe func(*args, **kw) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line 464, in collated_open return remember_data_format() File "D:\soft\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:\soft\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. > open D:\Desktop\mGIPR- > mGIP\fold_mgipr_mgip2025_09_12_15_03\fold_mgipr_mgip2025_09_12_15_03_model_0.cif > format mmcif Traceback (most recent call last): File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in thread_safe func(*args, **kw) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "D:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "D:\soft\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:\soft\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line 464, in collated_open return remember_data_format() File "D:\soft\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:\soft\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: 3.3.13560 Core Profile Forward-Compatible Context 26.20.11030.22001 OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: zh_CN.cp936 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: HUAWEI Model: HN-WX9X OS: Microsoft Windows 11 家庭中文版 (Build 26100) Memory: 16,040,079,360 MaxProcessMemory: 137,438,953,344 CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx OSLanguage: zh-CN 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 (2)
comment:1 by , 4 weeks ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → MemoryError opening mmCIF files |
comment:2 by , 4 weeks ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
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