id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9873 Installed version number not updated Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7.dev202309180647 (2023-09-18 06:47:42 UTC) Description Another subtle ToolShed problem: I incremented the version number of Clipper in its bundle_info.xml from 0.22.0 to 0.22.1 and rebuilt. The wheel file is correctly built with the version number 0.22.1 and it installs (I checked, and the bug I was fixing is gone) - but ChimeraX still believes the installed version is 0.22.0. Tail end of the terminal output from `make app-install` is below. removing build\bdist.win-amd64\wheel Distribution is in .\dist\ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl Installing bundle Executing: toolshed install .\dist\ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl Errors may have occurred when running pip: pip standard error: --- [notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: C:\Program Files\ChimeraX-daily\bin\python.exe -m pip install --upgrade pip --- pip standard output: --- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\tristan croll\my_gits\chimerax-clipper\dist\chimerax_clipper-0.22.1-cp311-cp311-win_amd64.whl Requirement already satisfied: ChimeraX-Core<1.8,>=1.7.dev202306142048 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (1.7.dev202309180647) Requirement already satisfied: ChimeraX-Atomic~=1.36 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (1.47.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (10.0.8) Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (1.1) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.3) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.1.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.12.1) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0.3) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.7.2) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.2) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.2.3) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.10.2) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.5.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.1) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.31.5) Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.1) Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.1.4) Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.12.2) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.2) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0.1) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.1.1) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.1) Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.4) Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0) Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0) Installing collected packages: ChimeraX-Clipper Successfully installed ChimeraX-Clipper-0.22.0 --- Successfully installed ChimeraX-Clipper-0.22.0 Installed ChimeraX-Clipper (0.22.0) UCSF ChimeraX version: 1.7.dev202309180647 (2023-09-18) © 2016-2023 Regents of the University of California. All rights reserved. Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.7.dev202309180647 (2023-09-18) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > 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): Alignment header support * AlignmentMatrices (2.1): Sequence alignment similarity matrices * Alignments (2.9.3): 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 (1.47.2): Atomic-structure functionality * AtomicLibrary (10.0.8): 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.dev202309180647): ChimeraX Core Package * CoreFormats (1.1): 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 * ISOLDE (1.7.dev0): ISOLDE: Interactive Structure Optimisation by Local Direct Exploration * 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 (1.1.5): 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 (1.10.2): 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 * SEQCROW (1.7.3): Structure Editing and Quantum Chemical Representation and Organization for Workflows * SeqView (2.9.1): 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 (1.0.1): 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 (1.31.5): ChimeraX user interface * uniprot (2.3): UniProt database support * UnitCell (1.0.1): Show crystal unit cell * ViewDockX (1.3): 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 * XMAS (1.1.2): Analyze and visualize crosslinking mass spectrometry data in a structural context * Zone (1.0.1): Mouse mode to show atom and map zones > ui tool show Shell 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. OpenGL version: 3.3.0 NVIDIA 529.08 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22621) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 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: 2023.7.22 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 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.47.2 ChimeraX-AtomicLibrary: 10.0.8 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.dev202309180647 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: 1.1.2 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-ISOLDE: 1.7.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.5 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: 1.10.2 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: 2.9.1 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: 2.1.2 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: 1.31.5 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3 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-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 comtypes: 1.1.14 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 et-xmlfile: 1.1.0 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: 2.8.6 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 23.1 pandas: 2.0.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 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 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 pywin32: 305 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.12.2 Send2Trash: 1.8.2 SEQCROW: 1.7.3 setuptools: 67.4.0 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: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1 }}} " defect closed blocker 1.7 Tool Shed duplicate all ChimeraX