id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8114 read_xyz: elements: list index out of range bdharding@… Tony Schaefer "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-52-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.4rc202205111743 (2022-05-11 17:43:38 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4rc202205111743 (2022-05-11) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/harding/dev/chimerax/CC_50ms_res.xyz Summary of feedback from opening /home/harding/dev/chimerax/CC_50ms_res.xyz --- error | unable to open CC_50ms_res.xyz warnings | WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Ce WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Ce WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Pr WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Ce WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Pr WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Nd WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Ce WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Pr WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Nd WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Pm WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Ce WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Pr WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Nd WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Pm WARNING AaronTools.atoms.Atom._set_vdw VDW Radii not found for element: Sm 60 messages similar to the above omitted Traceback (most recent call last): File ""/home/harding/.local/share/ChimeraX/1.4/site- packages/AaronTools/fileIO.py"", line 1309, in read_xyz int(line) ValueError: invalid literal for int() with base 10: '120 1 2190096.00000' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 457, in collated_open return remember_data_format() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/home/harding/.local/share/ChimeraX/1.4/site- packages/SEQCROW/__init__.py"", line 482, in open return open_aarontools( File ""/home/harding/.local/share/ChimeraX/1.4/site-packages/SEQCROW/io.py"", line 40, in open_aarontools raise e File ""/home/harding/.local/share/ChimeraX/1.4/site-packages/SEQCROW/io.py"", line 32, in open_aarontools fr = FileReader( File ""/home/harding/.local/share/ChimeraX/1.4/site- packages/AaronTools/fileIO.py"", line 1171, in __init__ self.read_xyz(f, get_all) File ""/home/harding/.local/share/ChimeraX/1.4/site- packages/AaronTools/fileIO.py"", line 1320, in read_xyz self.atoms += [Atom(element=line[0], coords=line[1:4], name=str(atom_count))] File ""/home/harding/.local/share/ChimeraX/1.4/site- packages/AaronTools/atoms.py"", line 111, in __init__ element = ELEMENTS[int(element)] IndexError: list index out of range IndexError: list index out of range File ""/home/harding/.local/share/ChimeraX/1.4/site- packages/AaronTools/atoms.py"", line 111, in __init__ element = ELEMENTS[int(element)] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 515.43.04 OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=Unity DISPLAY=:1 Manufacturer: System manufacturer Model: System Product Name OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virtual Machine: none CPU: 32 AMD Ryzen 9 5950X 16-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 125Gi 10Gi 82Gi 363Mi 32Gi 113Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 09:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:24b0] (rev a1) Subsystem: NVIDIA Corporation Device [10de:14ad] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 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: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4rc202205111743 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: 1.1 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: 1.2 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: 1.1.1 ChimeraX-LinuxSupport: 1.0 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: 1.5.5 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: 1.9 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: 2.6 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: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 distro: 1.6.0 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 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: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.4 msgpack: 1.0.3 nest-asyncio: 1.5.5 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 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 22.3.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 Send2Trash: 1.8.0 SEQCROW: 1.5.10 setuptools: 59.8.0 sfftk-rw: 0.7.2 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: 5.2.0 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect assigned normal Third Party all ChimeraX