Error in toolshed error message

[longphysics06@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

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  

> open D:/Molecule/B-Li/b13li/neutral/Shin2020/ELF/2c2e.pdb

Summary of feedback from opening
D:/Molecule/B-Li/b13li/neutral/Shin2020/ELF/2c2e.pdb  
---  
warning | Ignored bad PDB record found on line 16  
END  
  

> open D:/Molecule/B-Li/b13li/neutral/Shin2020/ELF/2c2e.cube

Opened 2c2e.cube, grid size 140,135,107, pixel 0.0529, shown at level
-0.972,0.972, step 1, values float32  

> set bgColor white

> size stickRadius 0.05

Changed 24 bond radii  

> volume #2 level 0.8 level 0.9716

> volume #2 level 0.82 level 0.9716

> volume #2 level 0.83 level 0.9716

> volume #2 level 0.84 level 0.9716

> volume #2 level 0.85 level 0.9716

> volume #2 level 0.86 level 0.9716

> volume #2 level 0.84 level 0.9716

> save D:/Molecule/TMP-transfer/done/2c-2e-084.gif width 1021 height 654
> supersample 3

> turn 1,0,0 -90

> turn 1,0,0 -90

> save D:/Molecule/TMP-transfer/done/2c-2e-084-top.gif width 1021 height 654
> supersample 3

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
longphysics06@gmail.com is subscribed to the ChimeraX announcements list  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\longp\Desktop\movie1.mp4

Movie saved to \C:Users\\...\Desktop\movie1.mp4  
  

> toolshed show

> close #2

> select #1

14 atoms, 24 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> close #1

> open D:/Molecule/TMP-transfer/done/2.pdb

Summary of feedback from opening D:/Molecule/TMP-transfer/done/2.pdb  
---  
warning | Ignored bad PDB record found on line 23  
END  
  
2.pdb title:  
title [more info...]  
  
Non-standard residues in 2.pdb #1  
---  
— ()  
  

> open D:/Molecule/TMP-transfer/done/1.pdb

Summary of feedback from opening D:/Molecule/TMP-transfer/done/1.pdb  
---  
warning | Ignored bad PDB record found on line 23  
END  
  
1.pdb title:  
title [more info...]  
  
Non-standard residues in 1.pdb #2  
---  
— ()  
  

> video

Unknown command: video  

>

Incomplete command: movie  

> size stickRadius 0.05

Changed 88 bond radii  

> ui tool show "Show Sequence Viewer"

> ui mousemode right clip

> ui mousemode right select

> save C:\Users\longp\Desktop\image1.png supersample 3

> save C:\Users\longp\Desktop\image2.png supersample 3

> open D:/Molecule/TMP-transfer/done/1.gjf

Unrecognized file suffix '.gjf'  

> close #2

> close

> open D:/Molecule/TMP-transfer/done/3.pdb

Summary of feedback from opening D:/Molecule/TMP-transfer/done/3.pdb  
---  
warning | Ignored bad PDB record found on line 23  
END  
  
3.pdb title:  
title [more info...]  
  
Non-standard residues in 3.pdb #1  
---  
— ()  
  

> open D:/Molecule/TMP-transfer/done/1.pdb

Summary of feedback from opening D:/Molecule/TMP-transfer/done/1.pdb  
---  
warning | Ignored bad PDB record found on line 23  
END  
  
1.pdb title:  
title [more info...]  
  
Non-standard residues in 1.pdb #2  
---  
— ()  
  

> open D:/Molecule/TMP-transfer/done/2.pdb

Summary of feedback from opening D:/Molecule/TMP-transfer/done/2.pdb  
---  
warning | Ignored bad PDB record found on line 23  
END  
  
2.pdb title:  
title [more info...]  
  
Non-standard residues in 2.pdb #3  
---  
— ()  
  

> hide #2 models

> hide #3 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> show #2 models

> show #3 models

> select #3

20 atoms, 44 bonds, 1 residue, 1 model selected  

> ~select #3

Nothing selected  

> select #2

20 atoms, 44 bonds, 1 residue, 1 model selected  

> ~select #2

Nothing selected  

> hide #1 models

> hide #3 models

> show #3 models

> hide #2 models

> show #1 models

> show #2 models

> show target m

> view clip false

> hide #3 models

> hide #2 models

> size stickRadius 0.05

Changed 133 bond radii  

> show #2 models

> hide #1 models

> hide #2 models

> show #2 models

> show #3 models

> hide #2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> ui tool show "Command Line Interface"

> ui tool show "Show Sequence Viewer"

> toolshed show

Downloading bundle MolecularDynamicsViewer-1.1-py3-none-any.whl  
Successfully installed MolecularDynamicsViewer-1.1  
Installed MolecularDynamicsViewer (1.1)  
Downloading bundle MolecularDynamicsViewer-1.1-py3-none-any.whl  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 840 G4
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 17,049,014,272
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-7600U CPU @ 2.80GHz"
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: 2.1.3
    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-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: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 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
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    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
    MolecularDynamicsViewer: 1.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

[Eric Pettersen]

Hi,

Thanks for reporting this problem. ChimeraX was trying to tell you that the MolecularDynamicsViewer tool was already installed, but there was an error in the code that generates that message, so you could safely ignore the error. If you want to avoid it in the future, it is fixed in the 1.2.5 release.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab