id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18045 Problem reading .cmm file horvath.peter.3@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-6.14.9-200.fc41.x86_64-x86_64-with-glibc2.40 ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/user/CryoEM/E3_wt_sharp.mrc format mrc Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at level 0.136, step 1, values float32 > open ""/home/user/CryoEM/homology models/test1.pdb"" test1.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) e3_wt [more info...] Chain information for test1.pdb #2 --- Chain | Description A | No description available B | No description available Non-standard residues in test1.pdb #2 --- FAD — (FAD) > close session > open /home/user/CryoEM/E3_wt_sharp.mrc format mrc Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at level 0.136, step 1, values float32 > open ""/home/user/CryoEM/homology models/test2.cif"" Chain information for test2.cif #2 --- Chain | Description A | No description available B | No description available > volume #1 level 0.241 > close session > open /home/user/CryoEM/E3_wt_sharp.mrc format mrc Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at level 0.136, step 1, values float32 > open ""/home/user/CryoEM/homology models/test3.mol2"" Chain information for E3_WT_atomic_model_aligned.pdb #2 --- Chain | Description A | No description available B | No description available Opened test3.mol2 containing 1 structure (7195 atoms, 7315 bonds) > close session > open /home/user/CryoEM/E3_wt_sharp.mrc format mrc Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at level 0.136, step 1, values float32 > open ""/home/user/CryoEM/homology models/test4.dcd"" No atomic models open to read the coordinates into! > close session > open /home/user/CryoEM/E3_wt_sharp.mrc format mrc Opened E3_wt_sharp.mrc as #1, grid size 256,256,256, pixel 0.818, shown at level 0.136, step 1, values float32 > open ""/home/user/CryoEM/homology models/test5.cmm"" Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py"", line 217, in feed self._parser.Parse(data, isFinal) xml.parsers.expat.ExpatError: no element found: line 1, column 0 During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/open_command/dialog.py"", line 334, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 132, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 215, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 526, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 497, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/markers/__init__.py"", line 62, in open return cmmfiles.read_cmm(session, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/markers/cmmfiles.py"", line 7, in read_cmm msets = load_markerset_xml(session, f) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/markers/cmmfiles.py"", line 181, in load_markerset_xml xml_parser.parse(input) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py"", line 111, in parse xmlreader.IncrementalParser.parse(self, source) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/xmlreader.py"", line 127, in parse self.close() File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py"", line 240, in close self.feed(b"""", isFinal=True) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/expatreader.py"", line 221, in feed self._err_handler.fatalError(exc) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/handler.py"", line 38, in fatalError raise exception xml.sax._exceptions.SAXParseException: /home/user/CryoEM/homology models/test5.cmm:1:0: no element found xml.sax._exceptions.SAXParseException: /home/user/CryoEM/homology models/test5.cmm:1:0: no element found File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/xml/sax/handler.py"", line 38, in fatalError raise exception See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 575.57.08 OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=plasmax11 XDG_SESSION_DESKTOP=KDE XDG_CURRENT_DESKTOP=KDE DISPLAY=:0 Manufacturer: ASUSTeK COMPUTER INC. Model: ROG Strix G10DK_G10DK OS: Fedora Linux 41 Architecture: 64bit ELF Virtual Machine: none CPU: 12 AMD Ryzen 5 5600X 6-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 31Gi 9.8Gi 3.3Gi 261Mi 18Gi 21Gi Swap: 8.0Gi 764Ki 8.0Gi Graphics: 13:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106 [GeForce RTX 3060 Lite Hash Rate] [10de:2504] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:8811] Kernel driver in use: nvidia Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2024.8.30 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Input/Output limitation all ChimeraX