Opened 23 months ago

Closed 23 months ago

Last modified 23 months ago

#10275 closed defect (fixed)

Syntax error in volume.py

Reported by: zahra.mashhadi@… 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 Eric Pettersen, 23 months ago

Cc: Eric Pettersen added
Component: UnassignedVolume Data
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionSyntax error in volume.py

comment:2 by Eric Pettersen, 23 months ago

Resolution: fixed
Status: assignedclosed

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

comment:3 by zahra.mashhadi@…, 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

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#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
--
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ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 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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