'Sequence' object has no attribute 'structure'

[cxk853@…]

The following bug report has been submitted:
Platform:        Darwin-21.4.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Hi

I've been running the attached script and this report a bug window opened. 

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> close all

> open 5UH6

5uh6 title:  
Crystal structure of Mycobacterium tuberculosis transcription initiation
complex containing 2ntRNA in complex with Rifampin [more info...]  
  
Chain information for 5uh6 #1  
---  
Chain | Description  
A B | DNA-directed RNA polymerase subunit α  
C | DNA-directed RNA polymerase subunit β  
D | DNA-directed RNA polymerase subunit beta'  
E | DNA-directed RNA polymerase subunit ω  
F | RNA polymerase σ factor SigA  
G | DNA (5'-D(*CP*ap*TP*CP*CP*GP*TP*GP*ap*GP*TP*CP*CP*ap*GP*G)-3')  
H | DNA
(5'-D(*TP*ap*TP*ap*ap*TP*GP*GP*GP*ap*GP*CP*TP*GP*TP*CP*ap*CP*GP*GP*ap*TP*G)-3')  
I | RNA (5'-R(*GP*A)-3')  
  
Non-standard residues in 5uh6 #1  
---  
MG — magnesium ion  
RFP — rifampicin  
ZN — zinc ion  
  

> open 5UHG

5uhg title:  
Crystal structure of Mycobacterium tuberculosis transcription initiation
complex in complex with D-AAP1 and Rifampin [more info...]  
  
Chain information for 5uhg #2  
---  
Chain | Description  
A B | DNA-directed RNA polymerase subunit α  
C | DNA-directed RNA polymerase subunit β  
D | DNA-directed RNA polymerase subunit beta'  
E | DNA-directed RNA polymerase subunit ω  
F | RNA polymerase σ factor SigA  
G | DNA (5'-D(*CP*ap*TP*CP*CP*GP*TP*GP*ap*GP*TP*CP*CP*ap*GP*G)-3')  
H | DNA
(5'-D(*TP*ap*TP*ap*ap*TP*GP*GP*GP*ap*GP*CP*TP*GP*TP*CP*ap*CP*GP*GP*ap*TP*G)-3')  
  
Non-standard residues in 5uhg #2  
---  
88G — Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide  
MG — magnesium ion  
RFP — rifampicin  
ZN — zinc ion  
  

> matchmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5uh6, chain D (#1) with 5uhg, chain D (#2), sequence alignment
score = 6484.6  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 5uh6 #1/D, 5uhg #2/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 1210 pruned atom pairs is 0.757 angstroms; (across all 1265
pairs: 0.916)  
  

> set bgColor white

> graphics silhouettes true

> view name start

> hide all

> select nucleic-acid

1538 atoms, 1725 bonds, 49 pseudobonds, 75 residues, 4 models selected  

> show sel ribbons

> show sel atoms

> nucleotides stubs

> name frozen NN sel

> select ~sel

50551 atoms, 51393 bonds, 29 pseudobonds, 6496 residues, 6 models selected  

> ~select :RFP

50433 atoms, 51267 bonds, 29 pseudobonds, 6494 residues, 6 models selected  

> name frozen SS sel

> show SS surfaces

> surface SS transparency 0

> select #1.6

8714 atoms, 1126 residues, 1 model selected  

> name frozen beta sel

> select clear

> select :RFP

118 atoms, 126 bonds, 2 residues, 2 models selected  

> name frozen rfp sel

> select #1.6

8714 atoms, 1126 residues, 1 model selected  

> select subtract /C:1036-1200

7824 atoms, 1008 residues, 1 model selected  

> name frozen beta2 sel

> select clear

> turn y 270

> surface SS transparency 70

> show :MG atoms

> view name init1

> turn y 50

> turn x 10

> zoom 2

> view name rfp_s

> view rfp_s

> cofr rfp

> turn y -50

> turn x -10

> move y -10

> zoom 4

> move x 15

> move y -4

> view name rfp_f

> view rfp_f

> zoom 0.6

> turn y 30

> view name rfp_fl

> turn y -80

> view name rfp_fr

> view init1

> view init1

> zoom 1.4

> move x 10

> view name dna

> split #1

Split 5uh6 (#1) into 9 models  
Chain information for 5uh6 A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 5uh6 B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 5uh6 C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 5uh6 D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 5uh6 E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 5uh6 F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 5uh6 G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 5uh6 H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 5uh6 I #1.9  
---  
Chain | Description  
I | No description available  
  
Associated 5uh6 D (1.4) chain D to 5uh6, chain D with 0 mismatches  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 355, in <lambda>  
self.associate([s for s in models if isinstance(s, AtomicStructure)],
force=False))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 317, in associate  
self._notify_observers(note_name, note_data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/alignment_headers/header_sequence.py", line 411, in
alignment_notification  
for x in self.alignment.associations if x not in added_sseqs]))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/alignment_headers/header_sequence.py", line 411, in
<listcomp>  
for x in self.alignment.associations if x not in added_sseqs]))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "add models":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Chains used in RMSD evaluation for alignment 1: 5uh6 D #1.4/D, 5uhg #2/D  

> close #1/A

> close #1/B

> close #1/C

> close #1/D

> close #1/E

> close #1/F

> close #1/H

> hide #2/G ribbons

> hide #2/G atoms

> style rfp stick

Changed 59 atom styles  

> hide rfp surfaces

> show rfp atoms

> color rfp yellow

> color rfp byhetero

> nucleotides atoms

> style nucleic stick

Changed 1062 atom styles  

> view dna

> turn y 180

> move y 7

> zoom 1.4

> view name daap1




OpenGL version: 4.1 INTEL-18.5.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 447.80.3.0.0
      OS Loader Version: 540.100.7~23
      SMC Version (system): 2.44f6

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 2 days 34 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 650:

      Chipset Model: Intel Iris Plus Graphics 650
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5927
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        SE2717H/HX:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 50.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: K9V8V88D00TU
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

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
    appnope: 0.1.0
    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: 1.1.1
    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
    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
File attachment: 5_DAAP1.cxc

5_DAAP1.cxc​

[cxk853@…]

Added by email2trac

[pett]

Hi Chris,

Thanks for reporting this problem. There are two ways you can fix it. You can use the current ChimeraX daily build, or you could change your script and remove "showAli true" from its matchmaker command.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab