id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3975 Show sequence AttributeError: 'set' object has no attribute '_c_pointer' goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.dev202011130655 (2020-11-13 06:55:07 UTC) Description Pressed the Sequence button on the Molecule Display toolbar, pdb 6ugw. Log: UCSF ChimeraX version: 1.2.dev202011130655 (2020-11-13) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/goddard/Downloads/test.cxs format session Log from Tue Nov 24 16:16:06 2020UCSF ChimeraX version: 1.2.dev202011130655 (2020-11-13) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2gbp format mmcif fromDatabase pdb 2gbp title: Sugar and signal-transducer binding sites of the escherichia coli galactose chemoreceptor protein [more info...] Chain information for 2gbp #1 --- Chain | Description A | D-galactose/D-glucose binding protein Non-standard residues in 2gbp #1 --- BGC — β-D-glucose CA — calcium ion > close > open /Users/goddard/Downloads/6ugw.pdb 6ugw.pdb title: Crystal structure of the FC fragment of PF06438179/GP1111 an infliximab biosimilar In A C-centered orthorhombic crystal form, lot A [more info...] Chain information for 6ugw.pdb #1 --- Chain | Description A | PF-06438179/GP1111 FC Non-standard residues in 6ugw.pdb #1 --- ACT — acetate ion BMA — β-D-mannose FUC — α-L-fucose GAL — β-D-galactose MAN — α-D-mannose NAG — N-acetyl-D-glucosamine ZN — zinc ion > save /Users/goddard/Downloads/test.cxs ——— End of log from Tue Nov 24 16:16:06 2020 ——— opened ChimeraX session > save /Users/goddard/Desktop/image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/goddard/Desktop/movie1.mp4 Movie saved to /Users/goddard/Desktop/movie1.mp4 > show atoms > hide atoms > hide cartoons > show cartoons > show surfaces > hide surfaces > show atoms > style sphere Changed 1862 atom styles > style stick Changed 1862 atom styles > style ball Changed 1862 atom styles > set bgColor white > set bgColor black > lighting soft > lighting simple > lighting full > set bgColor white > graphics silhouettes true > hide atoms > show atoms > hide cartoons > show cartoons > show surfaces > hide surfaces > style stick Changed 1862 atom styles > style sphere Changed 1862 atom styles > style ball Changed 1862 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides fill > style nucleic stick Changed 0 atom styles > nucleotides fill > style nucleic stick Changed 0 atom styles > nucleotides ladder > nucleotides ladder > nucleotides ladder > nucleotides atoms > style nucleic stick Changed 0 atom styles > color bychain > color byhetero > rainbow > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A ASN 364 OD1, /A ASN 364 ND2, /A ASN 364 CG, /A LYS 249 CE, /A LYS 249 NZ, and 46 other atoms Coulombic values for 6ugw.pdb_A SES surface #1.2: minimum, -13.36, mean -2.38, maximum 9.64 > mlp Map values for surface ""6ugw.pdb_A SES surface"": minimum -26.84, mean -5.114, maximum 23.51 > color bfactor 1862 atoms, 371 residues, 1 surfaces, atom bfactor range 13.4 to 104 > color bynucleotide > hide surfaces > hbonds 555 hydrogen bonds found > ~hbonds Alignment identifier is 1/A Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/toolbar/tool.py"", line 202, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/toolshed/info.py"", line 361, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/toolshed/__init__.py"", line 1270, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/shortcuts.py"", line 1221, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/shortcuts.py"", line 376, in try_shortcut self.run_shortcut(keys) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/shortcuts.py"", line 394, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/shortcuts.py"", line 296, in run f(shortcut_atoms(s)) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/shortcuts.py"", line 933, in show_sequence run(session, 'sequence chain %s' % seq_chain_spec, log = False) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/shortcuts/shortcuts.py"", line 480, in run run_command(session, command, **kw) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/cmd.py"", line 140, in seqalign_chain alignment = session.alignments.new_alignment([chain], ident, seq_viewer=""sv"", File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/manager.py"", line 232, in new_alignment alignment = Alignment(self.session, seqs, identify_as, attrs, markups, auto_destroy, File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 128, in __init__ self._set_residue_attributes() File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 721, in _set_residue_attributes self.session.change_tracker.add_modified(assigned, attr_name + "" changed"") File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/atomic/molobject.py"", line 1914, in add_modified f(self._c_pointer, self._inst_to_int(item), modded._c_pointer, AttributeError: 'set' object has no attribute '_c_pointer' AttributeError: 'set' object has no attribute '_c_pointer' File ""/Users/goddard/ucsf/chimerax- pyside/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/atomic/molobject.py"", line 1914, in add_modified f(self._c_pointer, self._inst_to_int(item), modded._c_pointer, See log for complete Python traceback. OpenGL version: 4.1 ATI-3.10.18 OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,3 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H2) Kernel Version: Darwin 19.6.0 Time since boot: 12 days 27 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro Vega 20: Chipset Model: Radeon Pro Vega 20 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x69af Revision ID: 0x00c0 ROM Revision: 113-D2060I-087 VBIOS Version: 113-D20601MA0T-016 Option ROM Version: 113-D20601MA0T-016 EFI Driver Version: 01.01.087 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: ('en_US', 'UTF-8') PyQt version: 5.15.1 Compiled Qt version: 5.15.1 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.11.8 cftime: 1.2.1 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: 1.9.3 ChimeraX-AtomicLibrary: 1.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.2 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: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202011130655 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0.1 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: 2.1 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1 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: 2.1 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: 1.3.1 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-Read-Pbonds: 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: 1.2.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2.1 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: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.2.2 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: 1.3.1 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: 0.29.21 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: 0.17 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.6.3 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.5.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 netifaces: 0.10.9 networkx: 2.5 numexpr: 2.7.1 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 20.2.3 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.8 psutil: 5.7.2 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PySide2: 5.15.1 python-dateutil: 2.8.1 pytz: 2020.4 pyzmq: 19.0.2 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 Send2Trash: 1.5.0 setuptools: 50.3.0 sfftk-rw: 0.6.7.dev1 shiboken2: 5.15.1 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.35.1 }}} " defect closed normal Sequence fixed Eric Pettersen all ChimeraX