Opened 4 years ago

Closed 4 years ago

#4728 closed defect (fixed)

AddH: 'Structure' object has no attribute 'num_coord_sets'

Reported by: aishen@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.8.0-55-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202106040028 (2021-06-04 00:28:40 UTC)
Description
hbonds :BTN showdist true color magenta display this bug windows


Log:
UCSF ChimeraX version: 1.3.dev202106040028 (2021-06-04)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1stp

1stp title:  
Structural origins of high-affinity biotin binding to streptavidin [more
info...]  
  
Chain information for 1stp #1  
---  
Chain | Description  
A | streptavidin complex with biotin  
  
Non-standard residues in 1stp #1  
---  
BTN — biotin  
  
1stp mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> delete solvent

> hbonds

112 hydrogen bonds found  

> hide hbonds

> hbonds :BTN

8 hydrogen bonds found  

> hbonds ligand

8 hydrogen bonds found  

> label @@display

> select clear

> color hbonds magenta

> hbonds :BTN showDist true

8 hydrogen bonds found  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/dist_monitor/monitor.py", line 107, in _changes_handler  
and pbg.structure.num_coord_sets > 1:  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'num_coord_sets'  
  
Error processing trigger "changes":  
AttributeError: 'Structure' object has no attribute 'num_coord_sets'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> hbonds :BTN showDist true color magenta

8 hydrogen bonds found  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/dist_monitor/monitor.py", line 107, in _changes_handler  
and pbg.structure.num_coord_sets > 1:  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'num_coord_sets'  
  
Error processing trigger "changes":  
AttributeError: 'Structure' object has no attribute 'num_coord_sets'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.80
OpenGL renderer: GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450M S2H
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       2.4Gi       8.5Gi       104Mi       4.8Gi        12Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	09:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 710] [10de:128b] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] GK208B [GeForce GT 710] [1462:8c93]	
	Kernel driver in use: nvidia
Locale: ('fr_FR', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.22.1
    ChimeraX-AtomicLibrary: 3.2.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    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-ColorKey: 1.3
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202106040028
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.3
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.6
    ChimeraX-PDB: 2.4.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    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: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.18
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.6.7.dev1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.5
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH: 'Structure' object has no attribute 'num_coord_sets'

Hi Aishen,

Thanks for reporting this problem. I don't think it will be too hard to fix and I will try to get it fixed today or Monday. The problem doesn't occur in the 1.2.5 production release.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by pett, 4 years ago

Resolution: → fixed
Status: accepted → closed

Fix available in next daily build

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