Opened 5 years ago

Last modified 5 years ago

#4282 assigned defect

Toolshed using internal UI API

Reported by: zheng.ruan@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-65-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
isodle won't install

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.1.0-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.15.0 ChimeraX-ISOLDE-1.1.0  
Installed ChimeraX-Clipper (0.15.0)  
Installed ChimeraX-ISOLDE (1.1.0)  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7f7b41e72f90>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1993, in _forward_keystroke  
if not self.floating and not isinstance(self.ui_area.focusWidget(),
(QLineEdit, QComboBox)):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1826, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
AttributeError: 'NoneType' object has no attribute 'dock_widget'  
  
AttributeError: 'NoneType' object has no attribute 'dock_widget'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1826, in _get_floating  
return self.__toolkit.dock_widget.isFloating()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7f7b41e72f90>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2069, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7f7b41e72f90>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  

> open
> /home/zruan/Dropbox/shared_TRPM5/Figures/TRPM5_figures/local_density/5mM_Ca/representative_densities/script.cxc
> format cmd

> windowsize 600 600

> set bgColor white

> lighting simple

> set silhouettes false

> open 5mM_Ca_GDN_job461_open_order_post.mrc

Opened 5mM_Ca_GDN_job461_open_order_post.mrc, grid size 360,360,360, pixel
0.826, shown at level 0.0103, step 2, values float32  

> open zfM5_Ca_GDN_open_12052020_WL.pdb

Summary of feedback from opening zfM5_Ca_GDN_open_12052020_WL.pdb  
---  
warnings | Duplicate atom serial number found: 7584  
Duplicate atom serial number found: 7586  
Duplicate atom serial number found: 7589  
Duplicate atom serial number found: 7591  
Duplicate atom serial number found: 7594  
262 messages similar to the above omitted  
Ignored bad PDB record found on line 30983  
END  
  
Chain information for zfM5_Ca_GDN_open_12052020_WL.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> color #1 blue

> color #2 light green target c

> color #2 light green target a

> style #2 & sidechain stick

Changed 18300 atom styles  

> hide #2 cartoons

> hide #2 atoms

> show #2/A:3001 target a

> cartoon style width 1.2 thickness 0.4

> show #2/A:3001 & mainchain atoms

> molmap #2/A:3001 2.5

> wait 1

> volume mask #1 surfaces #3 extend 1

> hide #3

> volume #4 style mesh step 1 level 0.0245

> wait 1

> surface dust #4 size 2

> color #2 yellow

> color O red target a

> color N blue target a

> zoom pixelSize 0.02

executed script.cxc  




OpenGL version: 3.3.0 NVIDIA 450.102.04
OpenGL renderer: GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7C37
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 24 AMD Ryzen 9 3900X 12-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       5.0Gi        14Gi       495Mi        11Gi        25Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	23:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU116 [GeForce GTX 1660 Ti] [10de:2182] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd TU116 [GeForce GTX 1660 Ti] [1458:3fbe]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
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
    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: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    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: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    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: 2.0
    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: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    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
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    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: 1.2.3
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Toolshed using internal UI API

comment:2 by Eric Pettersen, 5 years ago

Hi,

ISOLDE did in fact install correctly. The error you saw was in later unrelated code that executes as the install tool closes. So you can safely ignore the error and if you restart ChimeraX then ISOLDE should be available. The error is fixed in the daily build (but ISOLDE doesn't work in the daily build).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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