Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#6779 closed defect (limitation)

MemoryError running coulombic

Reported by: liuhao193@… 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-10-10.0.22000
ChimeraX Version: 1.4.dev202203080653 (2022-03-08 06:53:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00002f5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open "C:\Users\10492\Desktop\toctic20220407phenix refine-10-coot-150
> qdayu1.pdb" format pdb

Chain information for toctic20220407phenix refine-10-coot-150 qdayu1.pdb #1  
---  
Chain | Description  
3 | No description available  
4 | No description available  
5 | No description available  
7 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
U | No description available  
X | No description available  
  

> set bgColor white

> lighting full

> graphics silhouettes true

> hide atoms

> show cartoons

> color /A #83CBAC atoms,cartoons,surfaces

> color /B #FF8CC5 atoms,cartoons,surfaces

> color /C #482BCC atoms,cartoons,surfaces

> color /D #CCC37A atoms,cartoons,surfaces

> color /E #CC7E70 atoms,cartoons,surfaces

> color /F #1a5d66 atoms,cartoons,surfaces

> color /G #D25454 atoms,cartoons,surfaces

> color /U #8CF1FF atoms,cartoons,surfaces

> color /3 #B066CC atoms,cartoons,surfaces

> color /4 #CBD194 atoms,cartoons,surfaces

> color /5 #805F46 atoms,cartoons,surfaces

> color /7 #CCAF70 atoms,cartoons,surfaces

> color /9 #99A3CC atoms,cartoons,surfaces

> color /X #C85AAE atoms,cartoons,surfaces

> graphics silhouettes false

> graphics silhouettes true

> hide cartoons

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/3 LEU 269  
/3 HIS 270  
/3 ARG 271  
/3 LYS 274  
/3 ARG 280  
/3 GLN 281  
/3 TYR 284  
/3 ARG 285  
/3 GLU 300  
/3 LYS 305  
/4 GLN 5  
/4 GLU 6  
/4 ASP 10  
/4 PHE 11  
/4 VAL 12  
/4 TRP 22  
/4 ARG 23  
/4 ILE 25  
/4 PHE 29  
/4 LEU 31  
/4 LYS 32  
/4 ARG 42  
/4 VAL 47  
/4 ASP 64  
/4 GLN 66  
/4 SER 72  
/4 LEU 73  
/4 LYS 74  
/4 LEU 75  
/4 ASN 76  
/4 THR 77  
/4 LEU 78  
/4 ILE 80  
/4 VAL 82  
/4 SER 83  
/4 ALA 84  
/4 ASN 86  
/4 ILE 87  
/4 THR 88  
/4 LEU 106  
/4 ILE 107  
/4 LEU 110  
/4 LYS 111  
/4 LEU 112  
/4 THR 113  
/4 LYS 116  
/4 GLN 117  
/4 PHE 118  
/4 LYS 119  
/4 ASN 122  
/4 ILE 124  
/4 ASP 129  
/4 LYS 131  
/4 HIS 132  
/4 GLN 133  
/4 LYS 134  
/4 GLU 144  
/4 ARG 149  
/4 THR 151  
/4 LEU 152  
/4 ARG 197  
/4 HIS 198  
/4 TYR 201  
/4 GLU 205  
/4 ARG 209  
/4 ASP 210  
/4 LEU 211  
/4 THR 215  
/4 CYS 219  
/4 GLU 276  
/4 ASP 282  
/4 PHE 283  
/4 SER 286  
/4 LYS 299  
/4 LYS 300  
/4 LEU 302  
/4 TYR 311  
/4 ARG 316  
/4 GLU 317  
/4 ARG 332  
/4 ARG 349  
/4 VAL 354  
/5 GLU 135  
/5 GLU 197  
/7 LYS 272  
/7 GLN 273  
/7 GLU 411  
/7 LYS 416  
/7 LYS 429  
/7 ILE 432  
/7 PHE 454  
/7 PHE 478  
/7 GLU 484  
/7 LYS 488  
/7 GLN 496  
/7 LYS 502  
/7 LYS 526  
/7 TYR 637  
/7 LYS 646  
/7 LEU 653  
/7 LYS 676  
/7 ARG 711  
/7 GLU 714  
/7 LYS 724  
/7 ARG 746  
/7 GLU 754  
/7 LYS 770  
/7 PHE 777  
/9 GLU 643  
/9 LEU 677  
/9 LYS 749  
/9 LYS 767  
/9 LYS 788  
/9 GLU 825  
/9 GLU 826  
/9 ARG 852  
/9 THR 853  
/9 ARG 860  
/9 ARG 905  
/9 LEU 906  
/9 LEU 909  
/9 LEU 911  
/9 VAL 922  
/9 SER 923  
/9 LEU 925  
/A ASN 99  
/A THR 100  
/A THR 101  
/A THR 102  
/A LYS 298  
/A LYS 306  
/A LYS 372  
/A LYS 448  
/A LYS 749  
/A LYS 894  
/A ILE 1146  
/A LYS 1250  
/A ARG 1253  
/A PHE 1254  
/A LYS 1255  
/A LYS 1256  
/A VAL 1260  
/A LYS 1263  
/A LEU 1265  
/A TYR 1280  
/A TYR 1287  
/A LEU 1368  
/A ARG 1372  
/A GLN 1413  
/A ASN 1417  
/A LYS 1426  
/A SER 1428  
/A ASN 1673  
/A LYS 1676  
/A LYS 1814  
/A ASN 1932  
/A LYS 1935  
/B GLU 98  
/D PHE 82  
/E LYS 91  
/E THR 106  
/E GLU 243  
/E ASN 248  
/E LYS 496  
/E ARG 498  
/E ARG 674  
/E TRP 675  
/E LEU 678  
/F ARG 231  
/G PHE 326  
/G GLU 337  
/G ARG 343  
/G ARG 354  
/G ARG 358  
/G GLU 361  
/G ARG 372  
/G ARG 378  
/G LYS 384  
/G TYR 394  
/U ASP 93  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\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 "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 68, in assign_charges  
copy_a_to_orig[c_a] = o_a  
MemoryError  
  
MemoryError  
  
File "C:\Program Files\ChimeraX 1.4.dev202203080653\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 68, in assign_charges  
copy_a_to_orig[c_a] = o_a  
  
See log for complete Python traceback.  
  

QObject::~QObject: Timers cannot be stopped from another thread  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4.dev202203080653 (2022-03-08)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.9268
OpenGL renderer: Intel(R) UHD Graphics 615
OpenGL vendor: Intel

Locale: zh_CN.cp936
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Go 3
OS: Microsoft Windows 11 家庭版 (Build 22000)
Memory: 8,507,273,216
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-10100Y CPU @ 1.30GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203080653
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.2
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.7
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 3 years 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, 3 years ago

Resolution: → limitation
Status: accepted → closed

Hi,

Your machine ran out of memory while trying to compute the coulombic surface. There isn't really much that can be done about that other than only analyzing smaller structures on that machine, or using a more capable machine to analyze that structure.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by liuhao193@…, 3 years ago 

Hi，

Thank you!

Hao Liu  


> -----原始邮件-----
&gt; 发件人: ChimeraX <chimerax-bugs-admin@cgl.ucsf.edu>
&gt; 发送时间: 2022-05-06 06:12:59 (星期五)
&gt; 收件人: undisclosed-recipients: ;
&gt; 抄送: liuhao193@ibp.ac.cn, pett@cgl.ucsf.edu
&gt; 主题: Re: [ChimeraX] #6779: MemoryError running coulombic
&gt; 
&gt; #6779: MemoryError running coulombic
&gt; -----------------------------------------------+--------------------
&gt;           Reporter:  liuhao193@…               |      Owner:  pett
&gt;               Type:  defect                    |     Status:  closed
&gt;           Priority:  normal                    |  Milestone:
&gt;          Component:  Surface/Binding Analysis  |    Version:
&gt;         Resolution:  limitation                |   Keywords:
&gt;         Blocked By:                            |   Blocking:
&gt; Notify when closed:                            |   Platform:  all
&gt;            Project:  ChimeraX                  |
&gt; -----------------------------------------------+--------------------
&gt; Changes (by pett):
&gt; 
&gt;  * status:  accepted =&gt; closed
&gt;  * resolution:   =&gt; limitation
&gt; 
&gt; 
&gt; Comment:
&gt; 
&gt;  Hi,
&gt;          Your machine ran out of memory while trying to compute the
&gt;  coulombic surface.  There isn't really much that can be done about that
&gt;  other than only analyzing smaller structures on that machine, or using a
&gt;  more capable machine to analyze that structure.
&gt; 
&gt;  --Eric
&gt; 
&gt;          Eric Pettersen
&gt;          UCSF Computer Graphics Lab
&gt; 
&gt; --
&gt; Ticket URL: <https: www.rbvi.ucsf.edu="" trac="" chimerax="" ticket="" 6779#comment:2="">
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