#10275 closed defect (fixed)
Syntax error in volume.py
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Volume Data | Version: | |
Keywords: | Cc: | Eric Pettersen | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.7rc202311300124 (2023-11-30 01:24:31 UTC) Description After I opened a structure by its ID, I want to superimpose with predicted structures in alphafold. But when I click fetch botton, r recieve this error: SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\__init__.py", line 29, in from .volume import open_map, volume_from_grid_data See log for complete Python traceback. Log: Startup Errors --- errors | Bundle 'ChimeraX-Map' custom initialization failed Bundle 'ChimeraX-Dicom' custom initialization failed warnings | Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 501, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen importlib._bootstrap>", line 1206, in _gcd_import File "<frozen importlib._bootstrap>", line 1178, in _find_and_load File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 690, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 940, in exec_module File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 375, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 503, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Map's module: invalid syntax (volume.py, line 3441) Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 501, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen importlib._bootstrap>", line 1206, in _gcd_import File "<frozen importlib._bootstrap>", line 1178, in _find_and_load File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 690, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 940, in exec_module File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\dicom\\__init__.py", line 15, in <module> from chimerax.map import add_map_format File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 375, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 503, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's module: invalid syntax (volume.py, line 3441) UCSF ChimeraX version: 1.7rc202311300124 (2023-11-30) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4DPZ Summary of feedback from opening 4DPZ fetched from pdb --- warning | Ignoring microheterogeneity for label_seq_id 113 in chain X 4dpz title: Crystal structure of human HRASLS2 [more info...] Chain information for 4dpz #1 --- Chain | Description | UniProt X | HRAS-like suppressor 2 | HRSL2_HUMAN 2001-2129 Non-standard residues in 4dpz #1 --- CSX — S-oxy cysteine > ui tool show AlphaFold > alphafold match #1 Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\panel.py", line 208, in _fetch self._run_command('match', options = options) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\panel.py", line 314, in _run_command run(self.session, cmd) File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\match.py", line 43, in alphafold_match seq_models = _fetch_by_uniprot_id(session, sequences, color_confidence=color_confidence, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\match.py", line 84, in _fetch_by_uniprot_id seq_models, missing_uids = _database_models(session, sequence_uids, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\match.py", line 150, in _database_models models, status = fetch(session, db_id.id, ^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\fetch.py", line 61, in alphafold_fetch _color_by_confidence(s) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\fetch.py", line 92, in _color_by_confidence color_by_attr(structure.session, 'bfactor', atoms = structure.atoms, File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\std_commands\color.py", line 1162, in color_by_attr acolors = _value_colors(palette, range, attr_vals) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\std_commands\color.py", line 1333, in _value_colors colors = cmap.interpolated_rgba8(values) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\colors.py", line 335, in interpolated_rgba8 c = self.interpolated_rgba(values) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\colors.py", line 328, in interpolated_rgba from chimerax import map File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in from .volume import open_map, volume_from_grid_data See log for complete Python traceback. > alphafold match #1 Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\panel.py", line 208, in _fetch self._run_command('match', options = options) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\panel.py", line 314, in _run_command run(self.session, cmd) File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\match.py", line 43, in alphafold_match seq_models = _fetch_by_uniprot_id(session, sequences, color_confidence=color_confidence, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\match.py", line 84, in _fetch_by_uniprot_id seq_models, missing_uids = _database_models(session, sequence_uids, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\match.py", line 150, in _database_models models, status = fetch(session, db_id.id, ^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\fetch.py", line 61, in alphafold_fetch _color_by_confidence(s) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\alphafold\fetch.py", line 92, in _color_by_confidence color_by_attr(structure.session, 'bfactor', atoms = structure.atoms, File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\std_commands\color.py", line 1162, in color_by_attr acolors = _value_colors(palette, range, attr_vals) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\std_commands\color.py", line 1333, in _value_colors colors = cmap.interpolated_rgba8(values) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\colors.py", line 335, in interpolated_rgba8 c = self.interpolated_rgba(values) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\colors.py", line 328, in interpolated_rgba from chimerax import map File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in from .volume import open_map, volume_from_grid_data See log for complete Python traceback. OpenGL version: 3.3.0 - Build 30.0.101.1692 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Python: 3.11.2 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Dell Inc. Model: Precision 3450 OS: Microsoft Windows 10 Pro (Build 19044) Memory: 16,899,969,024 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.13.1 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: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.2 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: 1.7rc202311300124 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 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: 1.5.13 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: 1.0.3 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: 1.12.3 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: 1.33.2 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: 0.2.0 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: 4.45.1 funcparserlib: 2.0.0a0 glfw: 2.6.3 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: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 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: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.0.0 prompt-toolkit: 3.0.41 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: 25.1.1 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 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: 4.8.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (4)
comment:1 by , 23 months ago
Cc: | added |
---|---|
Component: | Unassigned → Volume Data |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Syntax error in volume.py |
comment:2 by , 23 months ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
comment:3 by , 23 months ago
Eric, Thank you for Fixing the issue. How can I get the new version? Best, Zahra ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: Friday, December 1, 2023 11:50 AM To: Mashhadi, Zahra <zahra.mashhadi@vanderbilt.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu> Subject: Re: [ChimeraX] #10275: Syntax error in volume.py [You don't often get email from chimerax-bugs-admin@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] #10275: Syntax error in volume.py ---------------------------------------+------------------------- Reporter: zahra.mashhadi@… | Owner: Tom Goddard Type: defect | Status: closed Priority: normal | Milestone: Component: Volume Data | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------------+------------------------- Changes (by pett): * resolution: => fixed * status: assigned => closed Comment: Hi Zahra, There was an error (typo) in the release candidate available for part of yesterday. The error has been fixed so please get a newer version. Very sorry for the inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab -- Ticket URL: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F10275%23comment%3A2&data=05%7C01%7Czahra.mashhadi%40vanderbilt.edu%7Ced248ae0d16042ca97bd08dbf29613ea%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638370498635712816%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LNm0ARR44wM2KUtnxoGqyw%2BR82MyIKV1SEbHTALwUv4%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10275#comment:2>> ChimeraX <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Czahra.mashhadi%40vanderbilt.edu%7Ced248ae0d16042ca97bd08dbf29613ea%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638370498635712816%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4CmxPqAUWD%2F0CYf%2Bikxt7q6sX0GwRsBuJcfq0jCffro%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>> ChimeraX Issue Tracker
comment:4 by , 23 months ago
Hi Zahra,
Just go to the ChimeraX download page and download the release candidate again. That will be the fixed version. There is typically a new release candidate every few days as problems get reported and bug fixes get applied.
--Eric
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Hi Zahra,
--Eric