Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8223 closed defect (duplicate)

mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'

Reported by: hzhan3@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-56-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5rc202211091945 (2022-11-09 19:45:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/mmcif/gui.py", line 130, in options_string
if self.compute_sheets.isChecked():

See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.5rc202211091945 (2022-11-09)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/hzhan/Documents/Project/EM_deposition_check/FHV_C12_multimere_checked_hz.pdb

Chain information for FHV_C12_multimere_checked_hz.pdb #1  
---  
Chain | Description  
A N O P Q R S T U V W X | No description available  
B C D E F G H I J K L M | No description available  
  

> style stick

Changed 76788 atom styles  

> hide atoms

> show cartoons

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
cmd += ' ' + save_mgr.save_args_string_from_widget(fmt, self._current_option)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/manager.py", line 110, in
save_args_string_from_widget  
return provider_info.bundle_info.run_provider(self.session,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 111, in
save_args_string_from_widget  
return widget.options_string()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mmcif/gui.py", line 130, in options_string  
if self.compute_sheets.isChecked():  
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'  
  
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mmcif/gui.py", line 130, in options_string  
if self.compute_sheets.isChecked():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
cmd += ' ' + save_mgr.save_args_string_from_widget(fmt, self._current_option)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/manager.py", line 110, in
save_args_string_from_widget  
return provider_info.bundle_info.run_provider(self.session,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 111, in
save_args_string_from_widget  
return widget.options_string()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mmcif/gui.py", line 130, in options_string  
if self.compute_sheets.isChecked():  
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'  
  
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/mmcif/gui.py", line 130, in options_string  
if self.compute_sheets.isChecked():  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 525.60.11
OpenGL renderer: NVIDIA TITAN RTX/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 Intel(R) Xeon(R) Gold 5118 CPU @ 2.30GHz
Cache Size: 16896 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           251Gi       5.0Gi       228Gi        77Mi        18Gi       244Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0000:73:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [TITAN RTX] [10de:1e02] (rev a1)	
	Subsystem: NVIDIA Corporation TU102 [TITAN RTX] [10de:12a3]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202211091945
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.0.5
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.0.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.3
    prompt-toolkit: 3.0.32
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.0
    starfile: 0.4.11
    superqt: 0.4.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.10.0

Change History (4)

comment:1 by pett, 3 years ago

Cc: pett added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'

comment:2 by pett, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Hi Hong,

Thanks for reporting this problem. It was fixed about 6 days ago, so if you get the current daily build it won't happen again.

--Eric

comment:3 by Greg Couch, 3 years ago

It is also fixed in the final ChimeraX 1.5 release. You have a 1.5 release candidate from November 9th. It was fixed on the 18th.

in reply to:  4 ; comment:4 by hzhan3@…, 3 years ago 

Thanks Eric!! sorry I was panic during the deposition....

I tried daily build, it worked!

Hong
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, December 21, 2022 12:34 PM
Cc: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; HONG ZHAN <hzhan3@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8223: mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'

#8223: mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'
-----------------------------------+------------------------
          Reporter:  hzhan3@…      |      Owner:  Greg Couch
              Type:  defect        |     Status:  closed
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:  duplicate     |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+------------------------
Changes (by pett):

 * status:  assigned => closed
 * resolution:   => duplicate


Comment:

 Hi Hong,
         Thanks for reporting this problem.  It was fixed about 6 days ago,
 so if you get the current daily build it won't happen again.

 --Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8223#comment:2>
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