Show sequence viewer: name 'Atoms' is not defined

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.2.dev202010150613 (2020-10-15 06:13:25 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.2.dev202010150613 (2020-10-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\desktop\Material and Method\gene\E_flic.fa" format fasta

Summary of feedback from opening D:\desktop\Material and Method\gene\E_flic.fa  
---  
note | Alignment identifier is E_flic.fa  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 319, in interceptRequest  
self._callback(info)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 84, in _intercept  
return interceptor(request_info, *args)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 352, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 447, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(qurl.None_), from_dir)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\gui.py", line 347, in thread_safe  
func(*args, **kw)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 104, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 165, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 402, in collated_open  
return func(*func_args, **func_kw)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seqalign\\__init__.py", line 61, in open  
return open_file(session, data, file_name,  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seqalign\parse.py", line 56, in open_file  
alignments = [session.alignments.new_alignment(seqs,  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 242, in new_alignment  
self._installed_viewers[viewer_name].run_provider(self.session, viewer_name,
self,  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1271, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\\__init__.py", line 42, in run_provider  
return _start_seq_viewer(session, "Sequence Viewer", alignment)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\tool.py", line 735, in _start_seq_viewer  
return SequenceViewer(session, tool_name, alignment)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\tool.py", line 55, in __init__  
self._finalize_init(alignment)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\tool.py", line 182, in _finalize_init  
self.region_browser = RegionBrowser(rb_window, self.seq_canvas)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\region_browser.py", line 461, in __init__  
self._show_sel_cb()  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\region_browser.py", line 1751, in _show_sel_cb  
self.show_chimerax_selection()  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\seq-view\region_browser.py", line 1140, in
show_chimerax_selection  
sel_residues = set(selected_residues(self.tool_window.session))  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2195, in selected_residues  
sel_atoms = concatenate((selected_atoms(session),)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2166, in selected_atoms  
return changes.selected_atoms(session)  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\atomic\changes.py", line 171, in selected_atoms  
return _ordered_sel if _ordered_sel is not None else (_full_sel if _full_sel
is not None else Atoms())  
NameError: name 'Atoms' is not defined  
  
NameError: name 'Atoms' is not defined  
  
File "D:\Program Files\ChimeraX 1.2.dev202010150613\bin\lib\site-
packages\chimerax\atomic\changes.py", line 171, in selected_atoms  
return _ordered_sel if _ordered_sel is not None else (_full_sel if _full_sel
is not None else Atoms())  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.1008
OpenGL renderer: AMD Radeon(TM) HD8490
OpenGL vendor: ATI Technologies Inc.
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 教育版 (Build 18363)
Memory: 17,040,502,784
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-2320 CPU @ 3.00GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202010150613
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
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    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
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    urllib3: 1.25.10
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    WMI: 1.5.1