id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9861 Clipper installation Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-12.7-arm64-arm-64bit ChimeraX Version: 1.7.dev202309270131 (2023-09-27 01:31:04 UTC) Description Something seems to be wrong with Toolshed dependency resolution in the latest Mac daily builds (seems fine in Linux and Windows). Despite the fact that Clipper 0.22.0 is installed and working, trying to ""toolshed install"" the matching ISOLDE version fails with ""Error: No matching distribution found for ChimeraX-Clipper ~=0.22.0"". I did notice the below little bit of weirdness (""No bundles were installed"") when doing ""devel install"" on Clipper from the command line, but I'm not sure if that's actually related. I do note that the directory layout has changed since 1.6, and wonder if that has something to do with it: ~/Library/Application\ Support/ChimeraX/1.6/site-packages/ ~/Library/Application\ Support/ChimeraX/1.7/lib/python/site-packages/ removing build/bdist.macosx-10.9-universal2/wheel Distribution is in ./dist/ChimeraX_Clipper-0.22.0-cp311-cp311-macosx_10_13_universal2.whl Installing bundle Executing: toolshed install ./dist/ChimeraX_Clipper-0.22.0-cp311-cp311-macosx_10_13_universal2.whl reinstall true No bundles were installed Installed ChimeraX-Clipper (0.22.0) Executing: exit Exiting ... Log: > isolde shorthand Error running startup command 'isolde shorthand': Unknown command: isolde shorthand UCSF ChimeraX version: 1.7.dev202309270131 (2023-09-27) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed install > ./ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-macosx_10_13_universal2.whl ERROR: Could not find a version that satisfies the requirement ChimeraX- Clipper~=0.22.0 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Clipper~=0.22.0 > open 3io0 structureFactors true Summary of feedback from opening 3io0 fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""F_meas_au, F_meas_sigma_au"". notes | Resolution: 3.003 Launching live xmap mgr took 1.1706490516662598 seconds. Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 28,26,26, pixel 0.963, shown at level 0.0948, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 28,26,26, pixel 0.963, shown at level -0.0565,0.0565, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 28,26,26, pixel 0.963, shown at level 0.346, step 1, values float32 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 --- Chain | Description | UniProt 1.2/A | EtuB protein | A5N734_CLOK5 75-304 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > toolshed list List of installed bundles: * AddCharge (1.5.11): Add partial charges to atoms * AddH (2.2.5): Add hydrogens * AlignmentAlgorithms (2.0.1): Sequence alignment algorithms * AlignmentHdrs (3.4.1): Alignment header support * AlignmentMatrices (2.1): Sequence alignment similarity matrices * Alignments (2.11.1): Sequence alignment support * AlphaFold (1.0): Predict or fetch AlphaFold structures * AltlocExplorer (1.1.1): Examine/change alternate atomic locations * AmberInfo (1.0): Provide information about AmberTools installation * Arrays (1.1): C++ library for parsing numpy arrays * Atomic (1.48): Atomic-structure functionality * AtomicLibrary (10.1): Atomic-structure C++ library * AtomSearch (2.0.1): 3D atom search * AxesPlanes (2.3.2): Depict axes or planes * BasicActions (1.1.2): Basic actions for user-defined specifier names * BILD (1.0): BILD file reader * BlastProtein (2.1.2): Search PDB/NR/AlphaFold using BLAST * BondRot (2.0.4): Bond rotation support * BugReporter (1.0.1): Report bugs when an error occurs * BuildStructure (2.10.5): Create/modify structures * Bumps (1.0): Find protrusions in density maps * ButtonPanel (1.0.1): Create custom user interface panels * CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies * CellPack (1.0): Fetch cellPACK models from web * Centroids (1.3.2): Depict centroid of atoms * ChangeChains (1.0.3): Change chain IDs * CheckWaters (1.3.1): Check water placement in maps * ChemGroup (2.0.1): Detect chemically functional groups * Clashes (2.2.4): Find clashes/contacts in structures * Clipper (0.22.0): Clipper: Efficient handling of volumetric data and symmetry * ColorActions (1.0.3): Simple interface for coloring objects * ColorGlobe (1.0): Show directional resolution colored sphere * ColorKey (1.5.4): Add color key to graphics * CommandLine (1.2.5): Command line support * ConnectStructure (2.0.1): Add bonds to structures that lack them * Contacts (1.0.1): Display chain contact maps * Core (1.7.dev202309270131): ChimeraX Core Package * CoreFormats (1.2): ChimeraX session support * coulombic (1.4.2): Compute/show electrostatic potential * Crosslinks (1.0): Analyze crosslinks * Crystal (1.0): Crystal symmetries * CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal * DataFormats (1.2.3): Data format management * Dicom (1.2): Read medical imaging and segmentations in DICOM format * DistMonitor (1.4): Interactive distance display * DockPrep (1.1.2): Prepare structures for docking * Dssp (2.0): Compute/assign secondary structure * EMDB-SFF (1.0): EMDB SFF file reader * ESMFold (1.0): Predict or fetch ESMFold structures * FileHistory (1.0.1): File History Panel * FunctionKey (1.0.1): Assign function keys to run commands * Geometry (1.3): Vector and coordinate system routines * gltf (1.0): Read/write glTF 3d scene files * Graphics (1.1.1): OpenGL graphics rendering * Hbonds (2.4): Identify hydrogen bonds in and among structures * Help (1.2.2): Show ChimeraX Help * HKCage (1.3): Create icosahedral mesh of hexagons and pentagons * IHM (1.1): Integrative Hybrid Models file reader * ImageFormats (1.2): Support for saving images * IMOD (1.0): IMOD model file reader * IO (1.0.1): Python convenience input/output functions * ItemsInspection (1.0.1): Inspection of attributes of a set of items * IUPAC (1.0): IUPAC fetch * Label (1.1.8): Add text labels to graphics * ListInfo (1.2.1): Report attributes for selected atomic data * Log (1.1.6): Log support * LookingGlass (1.1): LookingGlass holographic display * Maestro (1.9.1): Maestro reader * Map (1.1.4): Density maps * MapData (2.0): Volume data file formats * MapEraser (1.0.1): Map eraser * MapFilter (2.0.1): Operations on maps * MapFit (2.0): Fit molecules into maps * MapSeries (2.1.1): Volume series * Markers (1.0.1): Place markers on density maps * Mask (1.0.2): Mask a volume to a surface * MatchMaker (2.1.2): Superimpose structures * MCopy (1.0): Copy atomic structure attributes to another structure * MDcrds (2.6): Molecular dynamics support * MedicalToolbar (1.0.2): Toolbar for medical image analysis * Meeting (1.0.1): Shared interactive VR sessions. * MLP (1.1.1): Molecular lipophilicity calculation * mmCIF (2.12.1): mmCIF format read/write * MMTF (2.2): MMTF format read/write * Modeller (1.5.12): Interface to Modeller * ModelPanel (1.4): ChimeraX Model Panel * ModelSeries (1.0.1): Display sequences of models one by one * Mol2 (2.0.3): Mol2 reader/writer * Mole (1.0): Open JSON tunnel files from Mole * Morph (1.0.2): Morph atomic structures * MouseModes (1.2): Provide right button mouse mode tool * Movie (1.0): Commands to record movies * Neuron (1.0): Read SWC neuron trace files * Nifti (1.1): Read medical images in NIfTI format * NRRD (1.1): Read medical images in NRRD format * Nucleotides (2.0.3): Create nucleotide-specific displays * OpenCommand (1.11): Manages 'open' command extensibility * PDB (2.7.2): PDB format read/write * PDBBio (1.0.1): PDB biological assembly fetch * PDBLibrary (1.0.2): C++ PDB support * PDBMatrices (1.0): Crystal and biological unit matrices * PickBlobs (1.0.1): Measure and color blobs * Positions (1.0): Read and write model position matrices * PresetMgr (1.1): Preset management * PubChem (2.1): PubChem fetch * ReadPbonds (1.0.1): Read in pseudobonds from a file * Registration (1.1.2): Register ChimeraX * RemoteControl (1.0): Control ChimeraX from other apps * RenderByAttr (1.1): Depict attribute values on structures * RenumberResidues (1.1): Renumber residues * ResidueFit (1.0.1): Display fit of residues to density map * RestServer (1.2): Starts REST server to execute commands from network requests * RNALayout (1.0): Make RNA models * RotamerLibMgr (4.0): Manage rotamer libraries * RotamerLibsDunbrack (2.0): Dunbrack rotamer library * RotamerLibsDynameomics (2.0): Dynameomics rotamer library * RotamerLibsRichardson (2.0): Richardson rotamer libraries * SaveCommand (1.5.1): Manages 'save' command extensibility * SchemeMgr (1.0): HTTP scheme management * SDF (2.0.1): SDF file reader * Segger (1.0): Segment map * Segment (1.0.1): Watershed segment calculation * SelInspector (1.0): Inspect contents of selection * SeqView (2.10): Sequence viewer * Shape (1.0.1): Make models for geometric shapes * Shell (1.0.1): Interactive Python shell * Shortcuts (1.1.1): Button and keyboard shortcuts * ShowSequences (1.0.2): Choose/show structure sequences * SideView (1.0.1): Side view of scene * Smiles (2.1.2): SMILES fetch * SmoothLines (1.0): Smooth network of lines * SpaceNavigator (1.0): Space Navigator device support * StdCommands (1.12.2): Standard commands * STL (1.0.1): STL file read/write * Storm (1.0): STORM file reader * StructMeasure (1.1.2): Structure measurement user interface * Struts (1.0.1): struts for 3D printing * Surface (1.0.1): Surface calculations * SwapAA (2.0.1): Swap amino acid * SwapRes (2.2.2): Swap residue side chains * TapeMeasure (1.0): Tape measure mouse mode * TaskManager (1.0): Manage background tasks in ChimeraX * Test (1.0): simple regression test * Toolbar (1.1.2): Toolbar * ToolshedUtils (1.2.4): Toolshed bundle utilities * Topography (1.0): Show a topographic surface for a 2D image * ToQuest (1.0): Copy scenes to VR Quest headset * Tug (1.0.1): Tug on atoms with molecular dynamics * UI (1.32.2): ChimeraX user interface * uniprot (2.3): UniProt database support * UnitCell (1.0.1): Show crystal unit cell * ViewDockX (1.3.1): Analyze ligand-receptor docking results * VIPERdb (1.0): Read Virus Particle Explorer .vdb files * Vive (1.1): Virtual reality headset support * VolumeMenu (1.0.1): Volume menu * VTK (1.0): Legacy VTK file reader and writer * WavefrontOBJ (1.0): Wavefront OBJ file read/write * WebCam (1.0.2): Combine camera video with graphics * WebServices (1.1.2): Web service and HTTP request support * Zone (1.0.1): Mouse mode to show atom and map zones OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: en_GB.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.1.1 OS Loader Version: 7459.141.1.700.1 Software: System Software Overview: System Version: macOS 12.7 (21G816) Kernel Version: Darwin 21.6.0 Time since boot: 25 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: HP Z27k G3: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.0 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.11.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.48 ChimeraX-AtomicLibrary: 10.1 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309270131 ChimeraX-CoreFormats: 1.2 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: 1.1.2 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: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.11 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.10 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.32.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.1 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: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.5 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed blocker 1.7 Tool Shed duplicate Zach Pearson all ChimeraX