id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17817 Mutation Scores: NotImplementedError: cannot remove artist Ever.ODonnell@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3-arm64-arm-64bit ChimeraX Version: 1.9rc202412100036 (2024-12-10 00:36:39 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9rc202412100036 (2024-12-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7pqg 7pqg title: Structure of thermostabilised human NTCP in complex with nanobody 87 [more info...] Chain information for 7pqg #1 --- Chain | Description | UniProt A | Sodium/bile acid cotransporter | NTCP_HUMAN 3-328 B | Nanobody 87 | > select /B 955 atoms, 979 bonds, 124 residues, 1 model selected > hide sel cartoons > set bgColor white > lighting soft > graphics silhouettes true > ui tool show ""Color Actions"" > color sel slate gray > select /a 2296 atoms, 2346 bonds, 299 residues, 1 model selected > ui tool show ""Color Actions"" > color sel slate gray > select clear > open /Users/everodonnell/Documents/ntcp/ntcp_merged_scofes_.csv chain /A No such file/path: /Users/everodonnell/Documents/ntcp/ntcp_merged_scofes_.csv > open /Users/everodonnell/Documents/ntcp/ntcp_merged_scores_.csv chain /A Summary of feedback from opening /Users/everodonnell/Documents/ntcp/ntcp_merged_scores_.csv --- warning | Did not associate chain /A because sequence does not match mutation set ntcp_merged_scores_ at 7 positions, first mistmatch is VAL 33 note | Plotted 6471 mutations with effect_se_hbv_125 on x-axis and effect_se_hbv_187 on y-axis Opened deep mutational scan data for 6718 mutations of 341 residues with score names effect_se_hbv_125, effect_se_hbv_187, effect_se_hbv_250, effect_se_hbv_62, effect_se_nb79_125, effect_se_nb79_187, effect_se_nb79_250, effect_se_nb79_62, effect_se_nb79_93, effect_se_nb87_125, effect_se_nb87_187, effect_se_nb87_250, effect_se_nb87_62, effect_se_nb87_93, lfsr_abundance, lfsr_hbv_125, lfsr_hbv_187, lfsr_hbv_250, lfsr_hbv_62, lfsr_nb79_125, lfsr_nb79_187, lfsr_nb79_250, lfsr_nb79_62, lfsr_nb79_93, lfsr_nb87_125, lfsr_nb87_187, lfsr_nb87_250, lfsr_nb87_62, lfsr_nb87_93, pos_effect_abundance, pos_effect_hbv_125, pos_effect_hbv_187, pos_effect_hbv_250, pos_effect_hbv_62, pos_effect_nb79_125, pos_effect_nb79_187, pos_effect_nb79_250, pos_effect_nb79_62, pos_effect_nb79_93, pos_effect_nb87_125, pos_effect_nb87_187, pos_effect_nb87_250, pos_effect_nb87_62, pos_effect_nb87_93, pos_effect_se_abundance, pos_effect_se_hbv_125, pos_effect_se_hbv_187, pos_effect_se_hbv_250, pos_effect_se_hbv_62, pos_effect_se_nb79_125, pos_effect_se_nb79_187, pos_effect_se_nb79_250, pos_effect_se_nb79_62, pos_effect_se_nb79_93, pos_effect_se_nb87_125, pos_effect_se_nb87_187, pos_effect_se_nb87_250, pos_effect_se_nb87_62, pos_effect_se_nb87_93, pos_sd_abundance, pos_sd_hbv_125, pos_sd_hbv_187, pos_sd_hbv_250, pos_sd_hbv_62, pos_sd_nb79_125, pos_sd_nb79_187, pos_sd_nb79_250, pos_sd_nb79_62, pos_sd_nb79_93, pos_sd_nb87_125, pos_sd_nb87_187, pos_sd_nb87_250, pos_sd_nb87_62, pos_sd_nb87_93, pos_sd_se_abundance, pos_sd_se_hbv_125, pos_sd_se_hbv_187, pos_sd_se_hbv_250, pos_sd_se_hbv_62, pos_sd_se_nb79_125, pos_sd_se_nb79_187, pos_sd_se_nb79_250, pos_sd_se_nb79_62, pos_sd_se_nb79_93, pos_sd_se_nb87_125, pos_sd_se_nb87_187, pos_sd_se_nb87_250, pos_sd_se_nb87_62, pos_sd_se_nb87_93, position, score_abundance, score_hbv_125, score_hbv_187, score_hbv_250, score_hbv_62, score_nb79_125, score_nb79_187, score_nb79_250, score_nb79_62, score_nb79_93, score_nb87_125, score_nb87_187, score_nb87_250, score_nb87_62, score_nb87_93, score_tca_100, se_abundance. Assigned scores to 292 of 299 residues of chain /A. Found scores for 49 residues not present in atomic model. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mutation_scores/ms_scatter_plot.py"", line 119, in _menu_selection_changed self.set_plot_data(x_score_name, y_score_name, mutation_set_name, File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mutation_scores/ms_scatter_plot.py"", line 183, in set_plot_data self._set_nodes(xy, point_names=point_names, colors=colors, stack_order=stack_order, File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mutation_scores/ms_scatter_plot.py"", line 202, in _set_nodes self.draw_graph() File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/interfaces/graph.py"", line 237, in draw_graph node_pos = self._draw_nodes() ^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/interfaces/graph.py"", line 264, in _draw_nodes self._node_artist.remove() File ""/Users/everodonnell/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py"", line 256, in remove raise NotImplementedError('cannot remove artist') NotImplementedError: cannot remove artist NotImplementedError: cannot remove artist File ""/Users/everodonnell/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py"", line 256, in remove raise NotImplementedError('cannot remove artist') See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mutation_scores/ms_scatter_plot.py"", line 119, in _menu_selection_changed self.set_plot_data(x_score_name, y_score_name, mutation_set_name, File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mutation_scores/ms_scatter_plot.py"", line 183, in set_plot_data self._set_nodes(xy, point_names=point_names, colors=colors, stack_order=stack_order, File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mutation_scores/ms_scatter_plot.py"", line 202, in _set_nodes self.draw_graph() File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/interfaces/graph.py"", line 237, in draw_graph node_pos = self._draw_nodes() ^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9-rc2024.12.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/interfaces/graph.py"", line 264, in _draw_nodes self._node_artist.remove() File ""/Users/everodonnell/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py"", line 256, in remove raise NotImplementedError('cannot remove artist') NotImplementedError: cannot remove artist NotImplementedError: cannot remove artist File ""/Users/everodonnell/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/matplotlib/artist.py"", line 256, in remove raise NotImplementedError('cannot remove artist') See log for complete Python traceback. OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: MNEH3LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3 (23D56) Kernel Version: Darwin 23.3.0 Time since boot: 1 day, 13 hours, 18 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9rc202412100036 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.2 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 joblib: 1.4.2 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 llvmlite: 0.44.0 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.3 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 narwhals: 1.41.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numba: 0.61.0 numexpr: 2.10.2 numpy: 2.2.6 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 plotly: 6.0.1 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.8.0 pynmrstar: 3.3.4 pynndescent: 0.5.13 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scikit-learn: 1.6.1 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 threadpoolctl: 3.6.0 tifffile: 2024.7.24 tinyarray: 1.2.4 tomlkit: 0.13.2 tornado: 6.4.2 tqdm: 4.67.1 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 umap-learn: 0.5.7 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Structure Analysis fixed Eric Pettersen all ChimeraX