Opened 5 years ago

Closed 5 years ago

#4097 closed defect (duplicate)

Error in error message reinstalling bundle

Reported by: chimerax-bug-report@… 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:        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:\Activities Reseach Collabrators-Professors\Iqra
> China\Covid-19-hydrolase-mutations\ns8 modelled missing residues\WT.pdb"
> format pdb

Summary of feedback from opening D:\Activities Reseach Collabrators-
Professors\Iqra China\Covid-19-hydrolase-mutations\ns8 modelled missing
residues\WT.pdb  
---  
warning | Ignored bad PDB record found on line 857  
END  
  
Chain information for WT.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1

829 atoms, 855 bonds, 104 residues, 1 model selected  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> style sel stick

Changed 829 atom styles  

> rainbow sel

> color sel bychain

> rainbow sel

> color sel byhetero

> color sel byhetero

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel ball

Changed 829 atom styles  

> coulombic sel

Atoms with non-standard names found in standard residues: /A GLY 66 OXT.  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> coulombic sel

Atoms with non-standard names found in standard residues: /A GLY 66 OXT.  

> coulombic sel

Atoms with non-standard names found in standard residues: /A GLY 66 OXT.  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> color bfactor sel

829 atoms, 104 residues, 1 surfaces, atom bfactor range 0 to 113  

> color sel bynucleotide

> color bfactor sel

829 atoms, 104 residues, 1 surfaces, atom bfactor range 0 to 113  

> hbonds sel

Skipping possible acceptor with bad geometry: /A GLY 66 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 OXT  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  

Skipped 3 atom(s) with bad connectivities; see log for details  

65 hydrogen bonds found  

> hbonds sel

Skipping possible acceptor with bad geometry: /A GLY 66 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 OXT  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  

Skipped 3 atom(s) with bad connectivities; see log for details  

65 hydrogen bonds found  

> ~hbonds

> interfaces sel & ~solvent

0 buried areas:  

> interfaces sel & ~solvent

0 buried areas:  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> ~hbonds

> ~hbonds

> hbonds sel

Skipping possible acceptor with bad geometry: /A GLY 66 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 OXT  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  

Skipped 3 atom(s) with bad connectivities; see log for details  

65 hydrogen bonds found  

> hbonds sel

Skipping possible acceptor with bad geometry: /A GLY 66 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 OXT  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  
Skipping possible acceptor with bad geometry: /A GLY 66 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 66 O  
  

Skipped 3 atom(s) with bad connectivities; see log for details  

65 hydrogen bonds found  

> color sel bynucleotide

> color sel bynucleotide

> color bfactor sel

829 atoms, 104 residues, 1 surfaces, atom bfactor range 0 to 113  

> color bfactor sel

829 atoms, 104 residues, 1 surfaces, atom bfactor range 0 to 113  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> coulombic sel

Atoms with non-standard names found in standard residues: /A GLY 66 OXT.  

> rainbow sel

> color sel bychain

> rainbow sel

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> mlp sel

Map values for surface "WT.pdb_A SES surface": minimum -26.51, mean -3.524,
maximum 22.38  

> coulombic sel

Atoms with non-standard names found in standard residues: /A GLY 66 OXT.  

> rainbow sel

> style sel stick

Changed 829 atom styles  

> hide sel cartoons

> show sel cartoons

> color bfactor sel

829 atoms, 104 residues, 1 surfaces, atom bfactor range 0 to 113  

> show sel cartoons

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ~hbonds

> rainbow sel

> volume appearance airways

No volumes specified  

> show target m

> show target m

> hide target m

> hide target m

> show target m

> view clip false

> view clip false

> volume projectionMode 3d

No volumes specified  

> volume projectionMode 3d

No volumes specified  

> volume projectionMode 2d-xyz

No volumes specified  

> volume projectionMode 2d-xyz

No volumes specified  

> ~select #1

1 model selected  

> select #1

829 atoms, 855 bonds, 104 residues, 1 model selected  

> ~select #1

1 model selected  

> volume projectionMode 3d

No volumes specified  

> view orient

> view orient

> volume step 1

No volumes specified  

> volume step 2

No volumes specified  

> volume projectionMode 2d-xyz

No volumes specified  

> volume projectionMode 3d

No volumes specified  

> ui mousemode right "crop volume"

> ui mousemode right "move planes"

> ui mousemode right "rotate slab"

> ui mousemode right "tape measure"

> ui mousemode right windowing

> toolshed show

Downloading bundle MolecularDynamicsViewer-1.1-py3-none-any.whl  
Successfully installed MolecularDynamicsViewer-1.1  
Installed MolecularDynamicsViewer (1.1)  
Downloading bundle SEQCROW-0.23-py3-none-any.whl  
Successfully installed SEQCROW-0.23 Send2Trash-1.5.0 stripy-2.0.2  
Installed SEQCROW (0.23)  
resumed SEQCROW queue  

> ui tool show "Cage Builder"

Downloading bundle ChimeraX_HKCage-1.3-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.  
  
Downloading bundle ChimeraX_HKCage-1.3-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: 3.3.13540 Core Profile Forward-Compatible Context 25.20.14002.1
OpenGL renderer: AMD Radeon(TM) 535
OpenGL vendor: ATI Technologies Inc.
Manufacturer: LENOVO
Model: 81GA
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 8,494,747,648
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz"
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
    Send2Trash: 1.5.0
    SEQCROW: 0.23
    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
    stripy: 2.0.2
    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

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 → Error in error message reinstalling bundle

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: assigned → closed
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