id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16165 swapaa: DunbrackRotamerLibrary' object has no attribute 'display_name' samira.alsadi@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-122-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.6rc202305021906 (2023-05-02 19:06:00 UTC) Description tried to change 2 residue side chains with the swapaa command following the syntax shown in the user guide. i tried: swapaa #3:469,218 gln,met swapaa #3:469,218 seq:QM but log showed the same error. Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.6rc202305021906 (2023-05-02) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8j03 Summary of feedback from opening 8j03 fetched from pdb --- note | Fetching compressed mmCIF 8j03 from http://files.rcsb.org/download/8j03.cif 8j03 title: Human KCNQ2(F104A)-CaM-PIP2-CBD complex in state I [more info...] Chain information for 8j03 #1 --- Chain | Description | UniProt A D G I | Potassium voltage-gated channel subfamily KQT member 2 | KCNQ2_HUMAN 64-703 E F H J | Calmodulin-1 | CALM1_HUMAN 1-149 Non-standard residues in 8j03 #1 --- P0T — cannabidiol ((1'R,2'R)-5'-methyl-4-pentyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,6-diol) > close > open 8p0q Summary of feedback from opening 8p0q fetched from pdb --- note | Fetching compressed mmCIF 8p0q from http://files.rcsb.org/download/8p0q.cif 8p0q title: Crystal structure of AaNGT complexed to UDP and a peptide [more info...] Chain information for 8p0q #1 --- Chain | Description | UniProt A B | Adhesin | A0A3M6PNT1_AGGAP 1-621 C D | PHE-GLY-ASN-TRP-THR-THR | Non-standard residues in 8p0q #1 --- UDP — uridine-5'-diphosphate 8p0q mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > set bgColor white > set bgColor #ffffff00 > open 8J30 Summary of feedback from opening 8J30 fetched from pdb --- note | Fetching compressed mmCIF 8j30 from http://files.rcsb.org/download/8j30.cif 8j30 title: Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP- GLC [more info...] Chain information for 8j30 #2 --- Chain | Description | UniProt A B | UDP-glucose:protein N-beta-glucosyltransferase | NGT_ACTP2 1-620 Non-standard residues in 8j30 #2 --- UDP — uridine-5'-diphosphate UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl- monophosphate ester) 8j30 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > ui tool show ""Selection Inspector"" > ui windowfill toggle [Repeated 1 time(s)] > open 8J30 8j30 title: Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP- GLC [more info...] Chain information for 8j30 #3 --- Chain | Description | UniProt A B | UDP-glucose:protein N-beta-glucosyltransferase | NGT_ACTP2 1-620 Non-standard residues in 8j30 #3 --- UDP — uridine-5'-diphosphate UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl- monophosphate ester) 8j30 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select #2 9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected > select #3 9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected > undo [Repeated 1 time(s)] > select #2 9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > close #2 > select #2:469,218 Nothing selected > select add #3 9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected > select add #1 19741 atoms, 20223 bonds, 3 pseudobonds, 2458 residues, 3 models selected > select subtract #1 9688 atoms, 9928 bonds, 3 pseudobonds, 1206 residues, 2 models selected > select subtract #3 Nothing selected > select #2:469 Nothing selected > select #3:469,218 20 atoms, 16 bonds, 4 residues, 1 model selected > select #3:469,218 stick Expected a keyword > style sel stick Changed 20 atom styles > hide sel cartoons > style sel stick Changed 20 atom styles > select #3:469,218 20 atoms, 16 bonds, 4 residues, 1 model selected > show sel atoms > show sel cartoons > show (sel-residues & sidechain) target ab > style sel stick Changed 20 atom styles > swapaa #3:469 gln 218 met Expected a keyword > swapaa #3:469,218 gln,met Using Dunbrack library 8j30 #3/A ALA 469: phi 75.1, psi 1.9 trans Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/cmd.py"", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/dunbrack_rotamer_lib/lib.py"", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) See log for complete Python traceback. > swapaa #3:469,218 gln,met Using Dunbrack library 8j30 #3/A ALA 469: phi 75.1, psi 1.9 trans Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/cmd.py"", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/dunbrack_rotamer_lib/lib.py"", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) See log for complete Python traceback. > swapaa #3:469,218 seq:QM Using Dunbrack library 8j30 #3/A ALA 469: phi 75.1, psi 1.9 trans Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/cmd.py"", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/dunbrack_rotamer_lib/lib.py"", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 535.183.01 OpenGL renderer: NVIDIA RTX A2000 12GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_GB.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Dell Inc. Model: Precision 3660 OS: Ubuntu 20.04 Focal Fossa Architecture: 64bit ELF Virtual Machine: none CPU: 20 12th Gen Intel(R) Core(TM) i7-12700 Cache Size: 25600 KB Memory: total used free shared buff/cache available Mem: 31Gi 2.7Gi 25Gi 298Mi 2.6Gi 27Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:4680] (rev 0c) Subsystem: Dell Device [1028:0a9f] Kernel driver in use: i915 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202305021906 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Structure Editing duplicate all ChimeraX