Opened 17 months ago

Last modified 17 months ago

#15378 feedback defect

MemoryError running coulombic

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/wayne/Downloads/site.maegz

Chain information for site.maegz  
---  
Chain | Description  
1.6/A | No description available  
  
Opened site.maegz containing 6 structures (10240 atoms, 9230 bonds)  

> rainbow

> set bgColor white

> color #1.1 #aa5500ff

> hide #1.6 models

> show #1.6 models

> color #1.1 white

> style sphere

Changed 10240 atom styles  

> style sphere

Changed 10240 atom styles  

> select add #1.1

111 atoms, 1 residue, 1 model selected  

> style sel ball

Changed 111 atom styles  

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting simple

> show sel cartoons

[Repeated 1 time(s)]

> set bgColor white

> style sel stick

Changed 111 atom styles  

> style sel sphere

Changed 111 atom styles  

> style sel ball

Changed 111 atom styles  

> style sel sphere

Changed 111 atom styles  

> select add #1.2

478 atoms, 2 residues, 2 models selected  

> select subtract #1.1

367 atoms, 1 residue, 1 model selected  

> select subtract #1.2

Nothing selected  

> style sphere

Changed 10240 atom styles  

> color #1.1 #00aa00ff

> color #1.1 blue

> rename #1.1 "site E.maegz"

> color #1.2 #55ff00ff

> rename #1.2 "site A.maegz"

> color #1.3 #ffaaffff

> rename #1.3 "site B.maegz"

> color #1.4 #aa5500ff

> color #1.4 yellow

> rename #1.4 "site C.maegz"

> color #1.5 #00aa00ff

> color #1.5 red

> color #1.4 #55ff7fff

> color #1.4 springgreen

> color #1.4 magenta

> color #1.3 yellow

> rename #1.5 "site D.maegz"

> lighting soft

> lighting full

> lighting simple

> lighting full

> ui tool show "Selection Inspector"

> select add #1.1

111 atoms, 1 residue, 1 model selected  

> style sel stick

Changed 111 atom styles  

> style sel stick

Changed 111 atom styles  

> style sel sphere

Changed 111 atom styles  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> volume showOutlineBox true

No volumes specified  

> ui mousemode right "tape measure"

> volume step 2

No volumes specified  

> volume step 1

No volumes specified  

> transparency 50

> volume style image

No volumes specified  

> volume style mesh

No volumes specified  

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 205,
in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line
397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\\__init__.py",
line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\\__init__.py", line
66, in run_provider  
shortcuts.run_provider(session, name)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
1376, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
402, in try_shortcut  
self.run_shortcut(keys)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
339, in run  
f(s)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
72, in func_plus_tip  
func(cmd + " %s")(session)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
582, in run_expanded_command  
run(session, cmd)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line
525, in run  
run_command(session, command, **kw)  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py", line
49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py", line
2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 99,
in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line
110, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\add_charge\charge.py", line
34, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\add_charge\charge.py", line
204, in add_standard_charges  
br_type = "%s[non-%s]" % (br_type, a.name)  
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~  
MemoryError  
  
MemoryError  
  
File "D:\ChimeraX\bin\Lib\site-packages\chimerax\add_charge\charge.py", line
204, in add_standard_charges  
br_type = "%s[non-%s]" % (br_type, a.name)  
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  

> mlp sel

mlp: no amino acids specified  

> style sel stick

Changed 111 atom styles  

> show sel surfaces




OpenGL version: 3.3.0 NVIDIA 512.77
OpenGL renderer: NVIDIA GeForce RTX 3050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: zh_TW.cp950
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 專業版 (Build 22631)
Memory: 34,088,136,704
MaxProcessMemory: 137,438,953,344
CPU: 24 13th Gen Intel(R) Core(TM) i7-13700
OSLanguage: zh-TW

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 17 months ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MemoryError running coulombic

comment:2 by pett, 17 months ago

Status: accepted → feedback

Hi Criss,

It seems weird that you would run out memory running coulombic on not-that-big of a structure. I don't think I would be able to reproduce this behavior without access to your site.maegz file. Would you be willing to provide it? You could send it directly to pett@… if it needs to remain confidential.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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