id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6779 MemoryError running coulombic liuhao193@… Eric Pettersen "{{{ 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 }}} " defect closed normal Surface/Binding Analysis limitation all ChimeraX