id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5623 rotamers table: 'setVisibile' doyeon.kim@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.3.dev202110080903 (2021-10-08 09:03:01 UTC) Description Hello, I am Doyeon Kim and I was trying to use the Rotamers tool. I selected a residue and changed it to another amino acid, and an error message that says ""AttributeError: 'QHeaderView' object has no attribute 'setVisibile'"" appeared. I attached the result in print screen in case it would helf figure out what the problem is. How can I resolve this? Thank you. Log: UCSF ChimeraX version: 1.3.dev202110080903 (2021-10-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5I57 format mmcif fromDatabase pdb Summary of feedback from opening 5I57 fetched from pdb --- warnings | Unknown polymer entity '3' near line 5964 Unknown polymer entity '4' near line 5969 Atom OXT is not in the residue template for GLY /A:1001 Atom OXT is not in the residue template for GLU /B:301 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 5i57 title: Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains [more info...] Chain information for 5i57 #1 --- Chain | Description | UniProt A | Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1 | NMDZ1_RAT B | Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A | NMDE1_RAT > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select > /A:6-10,18-21,42-47,58-64,82-86,95-97,104-106,120-121,136-137,142-151,173-174,220-224,238-250,253-254 570 atoms, 575 bonds, 69 residues, 1 model selected > select /A:83 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:83 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select sel @< 5 57 atoms, 47 bonds, 15 residues, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel TRP rotLib Dunbrack /A GLU 83: phi -132.6, psi 138.3 trans Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\swap_res\tool.py"", line 111, in launch_rotamers run(self.session, ""swapaa interactive sel %s rotLib %s"" % (res_type, lib_name)) File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\swap_res\cmd.py"", line 127, in rotamers RotamerDialog(session, ""%s Side-Chain Rotamers"" % r, mgr, res_type, rot_lib) File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\swap_res\tool.py"", line 184, in __init__ self.finalize_init(*args) File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\swap_res\tool.py"", line 223, in finalize_init self.table.verticalHeader().setVisibile(False) AttributeError: 'QHeaderView' object has no attribute 'setVisibile' AttributeError: 'QHeaderView' object has no attribute 'setVisibile' File ""C:\Program Files\ChimeraX 1.3.dev202110080903\bin\lib\site- packages\chimerax\swap_res\tool.py"", line 223, in finalize_init self.table.verticalHeader().setVisibile(False) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 471.11 OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: SAMSUNG ELECTRONICS CO., LTD. Model: 950XBE OS: Microsoft Windows 10 Home (Build 19043) Memory: 8,473,681,920 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz OSLanguage: ko-KR Locale: ('ko_KR', 'cp949') 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: 1.5.1 charset-normalizer: 2.0.6 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.2 ChimeraX-AtomicLibrary: 4.1.4 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202110080903 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 2.1.1 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 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: 2.0.2 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.2 ChimeraX-ModelPanel: 1.2 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.4 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 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: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.4 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: 2.1 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: 1.13.4 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 1.1 cycler: 0.10.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.4.0 html2text: 2020.1.16 idna: 3.2 ihm: 0.21 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: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.8.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.20 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 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: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 5.1.0 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 File attachment: Rotamer error 21-11-17 Doyeon Kim.png }}} [attachment:""Rotamer error 21-11-17 Doyeon Kim.png""] " defect closed normal Structure Editing fixed all ChimeraX