id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6624 'Sequence' object has no attribute 'structure' cxk853@… Eric Pettersen "{{{ 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 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 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 }}} [attachment:""5_DAAP1.cxc""] " defect closed normal Sequence duplicate all ChimeraX