Ticket #16791: chimerabug.txt

chimerax --debug
NOTE: Initializing core
Toolshed: __init__ False False None
Toolshed: cache dir: /home/jobilinux/.cache/ChimeraX/1.9/toolshed
Toolshed: site dir: /home/jobilinux/.local/share/ChimeraX/1.9/lib/python3.11/site-packages
Toolshed: loading bundles
available bundle cache has not been initialized yet
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-Atomic (installed) [version: 1.58.8] [api package: chimerax.atomic] [category: Structure Analysis, Structure Editing] [command: log chains [categories: General] [synopsis: show chain info in log]] [command: combine [categories: Structure Editing] [synopsis: copy or combine structure models]] [command: pbond [categories: Structure Editing] [synopsis: create a pseudobond]] [command: ~pbond [categories: Structure Analysis] [synopsis: delete a pseudobond]] [command: label missing [categories: Structure Analysis] [synopsis: label missing-structure pseudobonds]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-SwapAA (installed) [version: 2.0.1] [api package: chimerax.swapaa] [category: Structure Editing] [command: swapaa mousemode [categories: Replace an amino acid] [synopsis: Replaces amino acid with a specified standard amino acid]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-ESMFold (installed) [version: 1.0] [api package: chimerax.esmfold] [category: Structure Prediction] [tool: ESMFold [categories: Structure Prediction] [synopsis: Fetch or calculate ESMFold structures]] [tool: ESMFold Error Plot [categories: Structure Prediction] [synopsis: Plot ESMFold predicted aligned error]] [command: esmfold contacts [categories: Structure Prediction] [synopsis: Show ESMFold contact pseudobond colored by predicted aligned error]] [command: esmfold fetch [categories: Structure Prediction] [synopsis: Fetch ESM Metagenomic Atlas models for a MGnify accession code]] [command: esmfold match [categories: Structure Prediction] [synopsis: Fetch ESM Metagenomic Atlas models matching a structure]] [command: esmfold pae [categories: Structure Prediction] [synopsis: Show ESMFold predicted aligned error as heatmap]] [command: esmfold predict [categories: Structure Prediction] [synopsis: Predict a structure using ESMFold]] [command: esmfold search [categories: Structure Prediction] [synopsis: Search ESMFold database using BLAST]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-MutationScores (installed) [version: 1.0] [api package: chimerax.mutation_scores] [category: Molecular structure] [command: mutationscores label [categories: Molecular structure] [synopsis: Label residues with mutation scores]] [command: mutationscores define [categories: Molecular structure] [synopsis: Compute new scores from existing mutation scores]] [command: mutationscores undefine [categories: Molecular structure] [synopsis: Compute new scores from existing mutation scores]] [command: mutationscores scatterplot [categories: Molecular structure] [synopsis: Show a scatter plot for two mutations scores]] [command: mutationscores statistics [categories: Molecular structure] [synopsis: Report mean and standard deviation of mutation scores]] [command: mutationscores histogram [categories: Molecular structure] [synopsis: Show histogram of mutation scores]] [command: mutationscores umap [categories: Molecular structure] [synopsis: Show umap plot of residue mutation scores]] [command: mutationscores list [categories: Molecular structure] [synopsis: List names of sets of mutations scores]] [command: mutationscores structure [categories: Molecular structure] [synopsis: Associate a structure with a set of mutations scores]] [command: mutationscores close [categories: Molecular structure] [synopsis: Close a set of mutations scores]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-Movie (installed) [version: 1.0] [api package: chimerax.movie] [category: General] [command: movie [categories: General] [synopsis: record movies]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-uniprot (installed) [version: 2.3.1] [api package: chimerax.uniprot] [category: Sequence]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-coulombic (installed) [version: 1.4.4] [api package: chimerax.coulombic] [category: Surface/Binding Analysis] [command: coulombic [categories: Surface/Binding Analysis] [synopsis: Color surface based on electrostatics]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-PresetMgr (installed) [version: 1.1.2] [api package: chimerax.preset_mgr] [category: Depiction] [command: preset [categories: Depiction] [synopsis: apply "preset" depiction to models]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-Crosslinks (installed) [version: 1.0] [api package: chimerax.crosslinks] [category: General] [command: crosslinks [categories: General] [synopsis: Plot or minimize crosslink lengths]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-ResidueFit (installed) [version: 1.0.1] [api package: chimerax.residue_fit] [category: General] [command: resfit [categories: General] [synopsis: Display slider to show fit of each residue in density map]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-SpaceNavigator (installed) [version: 1.0] [api package: chimerax.spacenavigator] [category: General] [command: device snav [categories: General] [synopsis: Control SpaceNavigator device]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-ColorActions (installed) [version: 1.0.5] [api package: chimerax.color_actions] [category: Depiction] [tool: Color Actions [categories: Depiction] [synopsis: color items]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-ButtonPanel (installed) [version: 1.0.1] [api package: chimerax.buttonpanel] [category: General] [command: buttonpanel [categories: General] [synopsis: Create custom user interface panels]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDBMatrices (installed) [version: 1.0] [api package: chimerax.pdb_matrices] [category: Molecular structure]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-SmoothLines (installed) [version: 1.0] [api package: chimerax.smooth_lines] [category: General] [command: smoothlines [categories: General] [synopsis: Smooth networks of lines]]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-Arrays (installed) [version: 1.1] [api package: chimerax.arrays] [category: Utility]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-BlastProtein (installed) [version: 3.0.0] [api package: chimerax.blastprotein] [category: Sequence] [tool: Blast Protein [categories: Sequence] [synopsis: Search PDB/NR/AlphaFold using BLAST]] [command: blastprotein [categories: Sequence] [synopsis: Search PDB/NR/AlphaFold using BLAST]] [command: blastpdb [categories: Sequence] [synopsis: Search PDB/NR/AlphaFold using BLAST]] [command: blastprotein pull [categories: Sequence] [synopsis: Get results for a finished BlastProtein job]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfc10>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Positions (installed) [version: 1.0] [api package: chimerax.positions] [category: Generic 3D objects]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebde360>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-CellPack (installed) [version: 1.0] [api package: chimerax.cellpack] [category: Molecular structure]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfc60>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Toolbar (installed) [version: 1.2.3] [api package: chimerax.toolbar] [category: General] [tool: Toolbar [categories: General] [synopsis: a Windows ribbon-style toolbar]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdddc0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Maestro (installed) [version: 1.9.1] [api package: chimerax.maestro] [category: I/O]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdc060>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-AtomicLibrary (installed) [version: 14.1.11] [api package: chimerax.atomic_lib] [category: Structure Analysis, Structure Editing]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd500>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-PubChem (installed) [version: 2.2] [api package: chimerax.pubchem] [category: Molecular structure]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebde7c0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-UI (installed) [version: 1.41] [api package: chimerax.ui] [category: User Interface] [command: ui [categories: User interface] [synopsis: control user interface behavior]] [command: tool [categories: User interface] [synopsis: Manipulate tools]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdf620>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-PickBlobs (installed) [version: 1.0.1] [api package: chimerax.pick_blobs] [category: Volume data] [tool: Measure and Color Blobs [categories: Volume Data] [synopsis: Measure and color connected parts of surfaces]] [command: measure blob [categories: Measure and Color Blobs] [synopsis: Measure and color connected parts of surfaces]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdf170>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-WebServices (installed) [version: 1.1.4] [api package: chimerax.webservices] [category: General]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebddff0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-LinuxSupport (installed) [version: 1.0.1] [api package: chimerax.linux] [category: General] [command: linux xdg-install [categories: General] [synopsis: Integrate ChimeraX with Linux desktop]] [command: linux xdg-uninstall [categories: General] [synopsis: Remove integration with Linux desktop]] [command: linux flatpak-files [categories: General] [synopsis: Generate flatpak metainfo and desktop files]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfd50>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDBBio (installed) [version: 1.0.1] [api package: chimerax.pdb_bio] [category: Molecular structure]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd370>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-SchemeMgr (installed) [version: 1.0] [api package: chimerax.scheme_mgr] [category: Utilities]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebddfa0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-CoreFormats (installed) [version: 1.2] [api package: chimerax.core_formats] [category: Atomic Data]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdff80>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Core (installed) [version: 1.9] [api package: chimerax.core] [category: Core]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdc1a0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-MouseModes (installed) [version: 1.2] [api package: chimerax.mouse_modes] [category: Toolbar] [command: ui mousemode [categories: User interface] [synopsis: set/list mouse modes]] [command: mousemode [categories: User interface] [synopsis: set/list mouse modes]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfad0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-CommandLine (installed) [version: 1.2.5] [api package: chimerax.cmd_line] [category: General] [tool: Command Line Interface [categories: General] [synopsis: Command Line Interface]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfb20>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-ChemGroup (installed) [version: 2.0.1] [api package: chimerax.chem_group] [category: Structure Analysis]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdeb80>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapEraser (installed) [version: 1.0.1] [api package: chimerax.map_eraser] [category: Volume data] [tool: Map Eraser [categories: Volume Data] [synopsis: Erase part of a density map within a sphere]] [command: volume erase [categories: Erase image data] [synopsis: Erase part of a density map within a sphere]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebde680>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-SwapRes (installed) [version: 2.5] [api package: chimerax.swap_res] [category: Structure Editing] [tool: Rotamers [categories: Structure Editing] [synopsis: swap amino acid residue side chain]] [command: swapaa [categories: Structure Editing] [synopsis: swap amino acid residue side chain]] [command: swapna [categories: Structure Editing] [synopsis: swap nucleic acid residue side chain]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdec70>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-MatchMaker (installed) [version: 2.1.6] [api package: chimerax.match_maker] [category: Sequence] [tool: Matchmaker [categories: Structure Analysis] [synopsis: superimpose structures/chains]] [command: matchmaker [categories: Structure Comparison] [synopsis: Superimpose structures]] [command: mmaker [categories: Structure Analysis] [synopsis: alias of matchmaker]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdebd0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Shell (installed) [version: 1.0.1] [api package: chimerax.shell] [category: General] [tool: Shell [categories: General] [synopsis: Python shell]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdcab0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Bumps (installed) [version: 1.0] [api package: chimerax.bumps] [category: Volume Data] [command: bumps [categories: Volume Data] [synopsis: find protrusions in density maps]] [command: cbumps [categories: Volume Data] [synopsis: find convex surface patches]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdff30>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-RenderByAttr (installed) [version: 1.6.2] [api package: chimerax.render_by_attr] [category: Depiction, Structure Analysis] [tool: Render/Select by Attribute [categories: Structure Analysis, Depiction] [synopsis: depict attribute values on structures]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdf3f0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-RenumberResidues (installed) [version: 1.1] [api package: chimerax.renumber_residues] [category: Structure Editing] [tool: Renumber Residues [categories: Structure Editing] [synopsis: renumber residues]] [command: renumber [categories: Structure Editing] [synopsis: renumber residues]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebde1d0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlphaFold (installed) [version: 1.0.1] [api package: chimerax.alphafold] [category: Structure Prediction] [tool: AlphaFold [categories: Structure Prediction] [synopsis: Fetch or calculate AlphaFold structures]] [tool: AlphaFold Error Plot [categories: Structure Prediction] [synopsis: Plot AlphaFold predicted aligned error]] [command: alphafold match [categories: Structure Prediction] [synopsis: Fetch AlphaFold database models matching a structure]] [command: alphafold fetch [categories: Structure Prediction] [synopsis: Fetch AlphaFold database models for a UniProt identifier]] [command: alphafold search [categories: Structure Prediction] [synopsis: Search AlphaFold database using BLAST]] [command: alphafold predict [categories: Structure Prediction] [synopsis: Predict a structure using AlphaFold]] [command: alphafold pae [categories: Structure Prediction] [synopsis: Show AlphaFold predicted aligned error as heatmap]] [command: alphafold contacts [categories: Structure Prediction] [synopsis: Show AlphaFold contact pseudobond colored by predicted aligned error]] [command: alphafold dimers [categories: Structure Prediction] [synopsis: Setup AlphaFold dimer predictions]] [command: alphafold monomers [categories: Structure Prediction] [synopsis: Estimate time for AlphaFold predictions]] [command: alphafold interfaces [categories: Structure Prediction] [synopsis: Evaluate AlphaFold PAE scores at dimer interfaces]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdee00>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibsDunbrack (installed) [version: 2.0] [api package: chimerax.dunbrack_rotamer_lib] [category: Structure Editing]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdc290>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-ColorKey (installed) [version: 1.5.6] [api package: chimerax.color_key] [category: Depiction] [tool: Color Key [categories: Depiction] [synopsis: add color key to graphics]] [command: key [categories: General] [synopsis: add color key to graphics]] [command: ~key [categories: General] [synopsis: remove color key]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdcc90>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-ReadPbonds (installed) [version: 1.0.1] [api package: chimerax.read_pbonds] [category: Generic 3D objects]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdea40>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-ModelPanel (installed) [version: 1.5] [api package: chimerax.model_panel] [category: General] [tool: Model Panel [categories: General] [synopsis: model panel]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebde810>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-HKCage (installed) [version: 1.3] [api package: chimerax.hkcage] [category: Higher-Order Structure] [command: hkcage [categories: Higher-Order Structure] [synopsis: Create icosahedral cage]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdc600>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Map (installed) [version: 1.3] [api package: chimerax.map] [category: Volume Data] [tool: Volume Viewer [categories: Volume Data] [synopsis: Show density maps info]] [tool: Map Coordinates [categories: Volume Data] [synopsis: Adjust density map coordinates]] [tool: Map Statistics [categories: Volume Data] [synopsis: Report map minimum, maximum, mean, standard deviation, and root mean square]] [command: volume [categories: Volume data] [synopsis: control volume data display]] [command: molmap [categories: Volume data] [synopsis: create density map for molecule]] [command: measure mapstats [categories: Volume data] [synopsis: report map statistics]] [command: measure mapvalues [categories: Volume data] [synopsis: Intepolate map at atom positions]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfe40>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Meeting (installed) [version: 1.0.1] [api package: chimerax.meeting] [category: General] [tool: Meeting [categories: General] [synopsis: Multi-person sessions]] [command: meeting start [categories: General] [synopsis: Create a ChimeraX meeting]] [command: meeting join [categories: General] [synopsis: Join a ChimeraX meeting]] [command: meeting [categories: General] [synopsis: Same as meeting join]] [command: meeting close [categories: General] [synopsis: Close a ChimeraX meeting]] [command: meeting info [categories: General] [synopsis: Report ChimeraX meeting info]] [command: meeting settings [categories: General] [synopsis: Report or set meeting default settings]] [command: meeting server [categories: General] [synopsis: Report or define meeting server names]] [command: meeting unname [categories: General] [synopsis: Deregister a meeting name]] [command: meeting send [categories: General] [synopsis: Copy my scene to all other meeting participants]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd870>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-AltlocExplorer (installed) [version: 1.1.2] [api package: chimerax.altloc_explorer] [category: Structure Analysis] [tool: Altloc Explorer [categories: Structure Analysis] [synopsis: interact with alternate atom locations]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd000>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Struts (installed) [version: 1.0.1] [api package: chimerax.struts] [category: Molecular structure] [command: struts [categories: Molecular structure] [synopsis: provide struts for 3D printing]] [command: ~struts [categories: Molecular structure] [synopsis: remove 3D printing struts]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdf9e0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-DistMonitor (installed) [version: 1.4.2] [api package: chimerax.dist_monitor] [category: Structure Analysis] [command: distance [categories: Structure Analysis] [synopsis: determine distance]] [command: ~distance [categories: Structure Analysis] [synopsis: remove distance monitors]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebde270>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Mask (installed) [version: 1.0.2] [api package: chimerax.mask] [category: Volume Data] [command: volume mask [categories: Volume data] [synopsis: Mask a map to a surface]] [command: volume onesmask [categories: Volume data] [synopsis: Create a onesmask inside a surface]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdcfb0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Registration (installed) [version: 1.1.2] [api package: chimerax.registration] [category: Utilities] [tool: Registration [categories: Utilities] [synopsis: Register ChimeraX with RBVI]] [command: registration status [categories: Utilities] [synopsis: Report registration status]] [command: registration file [categories: Utilities] [synopsis: Report registration file location or apply registration file]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfda0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-StdCommands (installed) [version: 1.18.1] [api package: chimerax.std_commands] [category: Structure Analysis] [command: alias [categories: General Controls] [synopsis: create shorthand version of command]] [command: alias list [categories: General Controls] [synopsis: list command aliases]] [command: alias delete [categories: General Controls] [synopsis: remove command alias]] [command: ~alias [categories: General Controls] [synopsis: remove command alias]] [command: align [categories: Structure Comparison] [synopsis: superimpose specific parts of structures]] [command: altlocs [categories: Structure Editing] [synopsis: change/remove alternate atom locations]] [command: angle [categories: Structure Analysis] [synopsis: Report or set angle between atoms/objects]] [command: camera [categories: Viewing Controls] [synopsis: change "camera" parametrs of main viewing window]] [command: cartoon [categories: Depiction] [synopsis: show 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[command: color name [categories: General Controls] [synopsis: define custom color names]] [command: color show [categories: General Controls] [synopsis: show definition of custom color names]] [command: colordef [categories: General Controls] [synopsis: define custom color names]] [command: ~colordef [categories: General Controls] [synopsis: remove custom color names]] [command: colourdef [categories: General Controls] [synopsis: define custom color names]] [command: ~colourdef [categories: General Controls] [synopsis: remove custom color names]] [command: coordset [categories: General Controls] [synopsis: show specific coordinate set (a.k.a. frame or conformer)]] [command: crossfade [categories: Movie Making] [synopsis: fade from one view to another]] [command: defattr [categories: General Controls] [synopsis: set many Python attribute values for structure elements from a file]] [command: delete [categories: Structure Editing] [synopsis: delete parts of a structure]] [command: dssp 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Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebddc80>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentAlgorithms (installed) [version: 2.0.2] [api package: chimerax.alignment_algs] [category: Sequence alignment]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd320>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-IMOD (installed) [version: 1.0] [api package: chimerax.imod] [category: Volume Data]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd1e0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-ToolshedUtils (installed) [version: 1.2.4] [api package: chimerax.toolshed_utils] [category: Utilities] [tool: Updates [categories: Utilities] [synopsis: install/update ChimeraX bundles from the Toolshed (web repository)]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd780>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-Segger (installed) [version: 1.0] [api package: chimerax.segger] [category: Volume data] [tool: Segment Map [categories: Volume Data] [synopsis: Segment density maps using Segger algorithms]] [tool: Fit to Segments [categories: Volume Data] [synopsis: Fit atomic models in segmented maps]] [command: segger [categories: Volume data] [synopsis: Operate on Segger segmentations]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebddbe0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapData (installed) [version: 2.0] [api package: chimerax.map_data] [category: Volume Data]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdfbc0>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-KVFinder (installed) [version: 1.2.1] [api package: chimerax.kvfinder] [category: Binding Analysis, Structure Analysis] [tool: Find Cavities [categories: Binding Analysis, Structure Analysis] [synopsis: Find potential binding pockets]] [command: kvfinder [categories: Binding Analysis] [synopsis: Find pockets]]
Toolshed: InstalledBundleCache.load: package <importlib.metadata.PathDistribution object at 0x7f821ebdd190>
Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibMgr (installed) [version: 4.0] [api package: chimerax.rotamers] [category: Structure Editing]
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Toolshed: InstalledBundleCache.load: bundle ChimeraX-OrthoPick (installed) [version: 1.0.1] [api package: chimerax.orthopick] [category: Volume data] [tool: Orthopick [categories: Volume Data] [synopsis: Pick particles in tomograms]]
Toolshed: InstalledBundleCache.load: write_cache
Toolshed: InstalledBundleCache._write_cache /home/jobilinux/.cache/ChimeraX/1.9/toolshed/bundle_info.cache
Toolshed: register bundle ChimeraX-Core 1.9
Toolshed: register bundle ChimeraX-ToolshedUtils 1.2.4
Toolshed: register bundle ChimeraX-Arrays 1.1
Toolshed: register bundle ChimeraX-AtomicLibrary 14.1.11
Toolshed: register bundle ChimeraX-Umap 1.0
Toolshed: register bundle ChimeraX-PresetMgr 1.1.2
Toolshed: delay_registration preset
Toolshed: register bundle ChimeraX-RemoteControl 1.0
Toolshed: delay_registration remotecontrol xmlrpc
Toolshed: register bundle ChimeraX-IO 1.0.3
Toolshed: register bundle ChimeraX-ListInfo 1.2.2
Toolshed: delay_registration info
Toolshed: register bundle ChimeraX-SimilarStructures 1.0.1
Toolshed: delay_registration foldseek
Toolshed: delay_registration similarstructures open
Toolshed: delay_registration similarstructures close
Toolshed: delay_registration similarstructures list
Toolshed: delay_registration similarstructures sequences
Toolshed: delay_registration similarstructures traces
Toolshed: delay_registration similarstructures cluster
Toolshed: delay_registration similarstructures ligands
Toolshed: delay_registration similarstructures scrollto
Toolshed: delay_registration similarstructures pairing
Toolshed: delay_registration similarstructures seqalign
Toolshed: delay_registration similarstructures fetchcoords
Toolshed: delay_registration sequence search
Toolshed: delay_registration similarstructures blast
Toolshed: delay_registration similarstructures fromblast
Toolshed: register bundle ChimeraX-Movie 1.0
Toolshed: delay_registration movie
Toolshed: register bundle ChimeraX-Geometry 1.3
Toolshed: register bundle ChimeraX-RestServer 1.3.1
Toolshed: delay_registration remotecontrol rest
Toolshed: register bundle ChimeraX-Test 1.0
Toolshed: delay_registration debug test
Toolshed: delay_registration debug exectest
Toolshed: delay_registration debug expectfail
Toolshed: register bundle ChimeraX-WebServices 1.1.4
Toolshed: register bundle ChimeraX-RotamerLibMgr 4.0
Toolshed: register bundle ChimeraX-SchemeMgr 1.0
Toolshed: register bundle ChimeraX-ToQuest 1.0
Toolshed: register bundle ChimeraX-MCopy 1.0
Toolshed: delay_registration mcopy
Toolshed: register bundle ChimeraX-SmoothLines 1.0
Toolshed: delay_registration smoothlines
Toolshed: register bundle ChimeraX-AmberInfo 1.0
Toolshed: register bundle ChimeraX-Segment 1.0.1
Toolshed: delay_registration segmentation
Toolshed: register bundle ChimeraX-AtomSearch 2.0.1
Toolshed: register bundle ChimeraX-RotamerLibsDynameomics 2.0
Toolshed: register bundle ChimeraX-Shape 1.0.1
Toolshed: delay_registration shape boxPath
Toolshed: delay_registration shape cone
Toolshed: delay_registration shape cylinder
Toolshed: delay_registration shape ellipsoid
Toolshed: delay_registration shape icosahedron
Toolshed: delay_registration shape rectangle
Toolshed: delay_registration shape ribbon
Toolshed: delay_registration shape sphere
Toolshed: delay_registration shape triangle
Toolshed: delay_registration shape tube
Toolshed: register bundle ChimeraX-Dssp 2.0
Toolshed: register bundle ChimeraX-RotamerLibsDunbrack 2.0
Toolshed: register bundle ChimeraX-Struts 1.0.1
Toolshed: delay_registration struts
Toolshed: delay_registration ~struts
Toolshed: register bundle ChimeraX-SpaceNavigator 1.0
Toolshed: delay_registration device snav
Toolshed: register bundle ChimeraX-IMOD 1.0
Toolshed: register bundle ChimeraX-RotamerLibsRichardson 2.0
Toolshed: register bundle ChimeraX-DataFormats 1.2.3
Toolshed: register bundle ChimeraX-Graphics 1.4.1
Toolshed: register bundle ChimeraX-Crystal 1.0
Toolshed: register bundle ChimeraX-ConnectStructure 2.0.1
Toolshed: register bundle ChimeraX-MouseModes 1.2
Toolshed: delay_registration ui mousemode
Toolshed: delay_registration mousemode
Toolshed: register bundle ChimeraX-Vive 1.1
Toolshed: delay_registration vr
Toolshed: delay_registration xr
Toolshed: delay_registration device vr
Toolshed: register bundle ChimeraX-MapData 2.0
Toolshed: register bundle ChimeraX-WebCam 1.0.2
Toolshed: delay_registration webcam
Toolshed: delay_registration device webcam
Toolshed: register bundle ChimeraX-LookingGlass 1.1
Toolshed: delay_registration lookingglass
Toolshed: delay_registration device lookingglass
Toolshed: register bundle ChimeraX-vrml 1.0
Toolshed: register bundle ChimeraX-LinuxSupport 1.0.1
Toolshed: delay_registration linux xdg-install
Toolshed: delay_registration linux xdg-uninstall
Toolshed: delay_registration linux flatpak-files
Toolshed: register bundle ChimeraX-EMDB-SFF 1.0
Toolshed: register bundle ChimeraX-Shortcuts 1.2.0
Toolshed: delay_registration ks
Toolshed: delay_registration snapshot
Toolshed: register bundle ChimeraX-AlphaFold 1.0.1
Toolshed: delay_registration alphafold match
Toolshed: delay_registration alphafold fetch
Toolshed: delay_registration alphafold search
Toolshed: delay_registration alphafold predict
Toolshed: delay_registration alphafold pae
Toolshed: delay_registration alphafold contacts
Toolshed: delay_registration alphafold dimers
Toolshed: delay_registration alphafold monomers
Toolshed: delay_registration alphafold interfaces
Toolshed: register bundle ChimeraX-SideView 1.0.1
Toolshed: register bundle ChimeraX-Mask 1.0.2
Toolshed: delay_registration volume mask
Toolshed: delay_registration volume onesmask
Toolshed: register bundle ChimeraX-ColorKey 1.5.6
Toolshed: delay_registration key
Toolshed: delay_registration ~key
Toolshed: register bundle ChimeraX-CellPack 1.0
Toolshed: register bundle ChimeraX-BugReporter 1.0.1
Toolshed: register bundle ChimeraX-coulombic 1.4.4
Toolshed: delay_registration coulombic
Toolshed: register bundle ChimeraX-TapeMeasure 1.0
Toolshed: register bundle ChimeraX-CheckWaters 1.4
Toolshed: register bundle ChimeraX-Map 1.3
Toolshed: delay_registration volume
Toolshed: delay_registration molmap
Toolshed: delay_registration measure mapstats
Toolshed: delay_registration measure mapvalues
Toolshed: register bundle ChimeraX-Log 1.2
Toolshed: delay_registration echo
Toolshed: delay_registration log
Toolshed: register bundle ChimeraX-SwapRes 2.5
Toolshed: delay_registration swapaa
Toolshed: delay_registration swapna
Toolshed: register bundle ChimeraX-OrthoPick 1.0.1
Toolshed: register bundle ChimeraX-UI 1.41
Toolshed: delay_registration ui
Toolshed: delay_registration tool
Toolshed: register bundle ChimeraX-HKCage 1.3
Toolshed: delay_registration hkcage
Toolshed: register bundle ChimeraX-IHM 1.1
Toolshed: register bundle ChimeraX-BasicActions 1.1.2
Toolshed: delay_registration name
Toolshed: delay_registration name frozen
Toolshed: delay_registration name delete
Toolshed: delay_registration name list
Toolshed: register bundle ChimeraX-PDBLibrary 1.0.4
Toolshed: register bundle ChimeraX-Morph 1.0.2
Toolshed: delay_registration morph
Toolshed: register bundle ChimeraX-Crosslinks 1.0
Toolshed: delay_registration crosslinks
Toolshed: register bundle ChimeraX-AddCharge 1.5.18
Toolshed: delay_registration addcharge
Toolshed: delay_registration addcharge nonstd
Toolshed: register bundle ChimeraX-ModelPanel 1.5
Toolshed: register bundle ChimeraX-AlignmentHdrs 3.5
Toolshed: register bundle ChimeraX-Alignments 2.16.1
Toolshed: delay_registration sequence
Toolshed: register bundle ChimeraX-Bumps 1.0
Toolshed: delay_registration bumps
Toolshed: delay_registration cbumps
Toolshed: register bundle ChimeraX-ItemsInspection 1.0.1
Toolshed: register bundle ChimeraX-Neuron 1.0
Toolshed: register bundle ChimeraX-Smiles 2.1.2
Toolshed: register bundle ChimeraX-OpenCommand 1.14
Toolshed: delay_registration open
Toolshed: delay_registration usage open
Toolshed: register bundle ChimeraX-Modeller 1.5.18
Toolshed: delay_registration modeller comparative
Toolshed: delay_registration modeller loops
Toolshed: delay_registration modeller refine
Toolshed: delay_registration modeller scores
Toolshed: register bundle ChimeraX-MapEraser 1.0.1
Toolshed: delay_registration volume erase
Toolshed: register bundle ChimeraX-Shell 1.0.1
Toolshed: register bundle ChimeraX-MapSeries 2.1.1
Toolshed: delay_registration vseries
Toolshed: delay_registration measure motion
Toolshed: register bundle ChimeraX-MedicalToolbar 1.1
Toolshed: register bundle ChimeraX-MatchMaker 2.1.6
Toolshed: delay_registration matchmaker
Toolshed: delay_registration mmaker
Toolshed: register bundle ChimeraX-ReadPbonds 1.0.1
Toolshed: register bundle ChimeraX-SeqView 2.14
Toolshed: register bundle ChimeraX-Contacts 1.0.1
Toolshed: delay_registration interfaces
Toolshed: register bundle ChimeraX-StructMeasure 1.2.1
Toolshed: register bundle ChimeraX-Nucleotides 2.0.3
Toolshed: delay_registration nucleotides
Toolshed: delay_registration ~nucleotides
Toolshed: register bundle ChimeraX-STL 1.0.1
Toolshed: register bundle ChimeraX-FunctionKey 1.0.1
Toolshed: delay_registration ui functionkey
Toolshed: delay_registration functionkey
Toolshed: register bundle ChimeraX-FileHistory 1.0.1
Toolshed: register bundle ChimeraX-ModelArchive 1.0
Toolshed: delay_registration modelcif pae
Toolshed: register bundle ChimeraX-ChangeChains 1.1
Toolshed: delay_registration changechains
Toolshed: register bundle ChimeraX-MDcrds 2.7.2
Toolshed: register bundle ChimeraX-IUPAC 1.0
Toolshed: register bundle ChimeraX-MapFit 2.0
Toolshed: delay_registration fitmap
Toolshed: register bundle ChimeraX-MLP 1.1.1
Toolshed: delay_registration mlp
Toolshed: register bundle ChimeraX-Registration 1.1.2
Toolshed: delay_registration registration status
Toolshed: delay_registration registration file
Toolshed: register bundle ChimeraX-gltf 1.0
Toolshed: register bundle ChimeraX-TaskManager 1.0
Toolshed: delay_registration taskman
Toolshed: register bundle ChimeraX-Markers 1.0.1
Toolshed: delay_registration marker
Toolshed: register bundle ChimeraX-BlastProtein 3.0.0
Toolshed: delay_registration blastprotein
Toolshed: delay_registration blastpdb
Toolshed: delay_registration blastprotein pull
Toolshed: register bundle ChimeraX-BILD 1.0
Toolshed: register bundle ChimeraX-ButtonPanel 1.0.1
Toolshed: delay_registration buttonpanel
Toolshed: register bundle ChimeraX-UnitCell 1.0.1
Toolshed: delay_registration unitcell
Toolshed: register bundle ChimeraX-ColorActions 1.0.5
Toolshed: register bundle ChimeraX-PDB 2.7.6
Toolshed: register bundle ChimeraX-MapFilter 2.0.1
Toolshed: delay_registration volume add
Toolshed: delay_registration volume bin
Toolshed: delay_registration volume boxes
Toolshed: delay_registration volume copy
Toolshed: delay_registration volume cover
Toolshed: delay_registration volume falloff
Toolshed: delay_registration volume flatten
Toolshed: delay_registration volume flip
Toolshed: delay_registration volume fourier
Toolshed: delay_registration volume gaussian
Toolshed: delay_registration volume laplacian
Toolshed: delay_registration volume localCorrelation
Toolshed: delay_registration volume maximum
Toolshed: delay_registration volume minimum
Toolshed: delay_registration volume median
Toolshed: delay_registration volume morph
Toolshed: delay_registration volume multiply
Toolshed: delay_registration volume new
Toolshed: delay_registration volume octant
Toolshed: delay_registration volume ~octant
Toolshed: delay_registration volume permuteAxes
Toolshed: delay_registration volume resample
Toolshed: delay_registration volume ridges
Toolshed: delay_registration volume scale
Toolshed: delay_registration volume sharpen
Toolshed: delay_registration volume subtract
Toolshed: delay_registration volume threshold
Toolshed: delay_registration volume tile
Toolshed: delay_registration volume unbend
Toolshed: delay_registration volume unroll
Toolshed: delay_registration volume zone
Toolshed: delay_registration volume unzone
Toolshed: delay_registration vop
Toolshed: register bundle ChimeraX-ResidueFit 1.0.1
Toolshed: delay_registration resfit
Toolshed: register bundle ChimeraX-ImageFormats 1.2
Toolshed: register bundle ChimeraX-mmCIF 2.14.2
Toolshed: register bundle ChimeraX-Hbonds 2.5
Toolshed: delay_registration hbonds
Toolshed: delay_registration ~hbonds
Toolshed: register bundle ChimeraX-BuildStructure 2.13.1
Toolshed: delay_registration build
Toolshed: delay_registration bond
Toolshed: delay_registration ~bond
Toolshed: delay_registration bond length
Toolshed: register bundle ChimeraX-Surface 1.0.1
Toolshed: delay_registration color electrostatic
Toolshed: delay_registration color sample
Toolshed: delay_registration color gradient
Toolshed: delay_registration color radial
Toolshed: delay_registration color cylindrical
Toolshed: delay_registration color height
Toolshed: delay_registration color image
Toolshed: delay_registration surface
Toolshed: delay_registration ~surface
Toolshed: delay_registration surface showPatches
Toolshed: delay_registration surface hidePatches
Toolshed: delay_registration surface close
Toolshed: delay_registration surface style
Toolshed: delay_registration surface squaremesh
Toolshed: delay_registration surface showall
Toolshed: delay_registration surface cap
Toolshed: delay_registration surface dust
Toolshed: delay_registration surface undust
Toolshed: delay_registration surface hidefarblobs
Toolshed: delay_registration surface invertShown
Toolshed: delay_registration surface transform
Toolshed: delay_registration surface zone
Toolshed: delay_registration surface unzone
Toolshed: delay_registration surface check
Toolshed: delay_registration surface splitbycolor
Toolshed: delay_registration sop
Toolshed: delay_registration volume splitbyzone
Toolshed: delay_registration measure sasa
Toolshed: delay_registration measure volume
Toolshed: delay_registration measure area
Toolshed: delay_registration measure contactArea
Toolshed: register bundle ChimeraX-CageBuilder 1.0.1
Toolshed: delay_registration cage
Toolshed: register bundle ChimeraX-ViewDockX 1.4.4
Toolshed: delay_registration viewdockx
Toolshed: delay_registration viewdockx down
Toolshed: delay_registration viewdockx up
Toolshed: register bundle ChimeraX-MutationScores 1.0
Toolshed: delay_registration mutationscores label
Toolshed: delay_registration mutationscores define
Toolshed: delay_registration mutationscores undefine
Toolshed: delay_registration mutationscores scatterplot
Toolshed: delay_registration mutationscores statistics
Toolshed: delay_registration mutationscores histogram
Toolshed: delay_registration mutationscores umap
Toolshed: delay_registration mutationscores list
Toolshed: delay_registration mutationscores structure
Toolshed: delay_registration mutationscores close
Toolshed: register bundle ChimeraX-RenumberResidues 1.1
Toolshed: delay_registration renumber
Toolshed: register bundle ChimeraX-ShowSequences 1.0.3
Toolshed: register bundle ChimeraX-PubChem 2.2
Toolshed: register bundle ChimeraX-SwapAA 2.0.1
Toolshed: delay_registration swapaa mousemode
Toolshed: register bundle ChimeraX-Nifti 1.2
Toolshed: register bundle ChimeraX-CrystalContacts 1.0.1
Toolshed: delay_registration crystalcontacts
Toolshed: register bundle ChimeraX-ESMFold 1.0
Toolshed: delay_registration esmfold contacts
Toolshed: delay_registration esmfold fetch
Toolshed: delay_registration esmfold match
Toolshed: delay_registration esmfold pae
Toolshed: delay_registration esmfold predict
Toolshed: delay_registration esmfold search
Toolshed: register bundle ChimeraX-Label 1.1.14
Toolshed: delay_registration 2dlabels
Toolshed: delay_registration scalebar
Toolshed: delay_registration label
Toolshed: delay_registration ~label
Toolshed: register bundle ChimeraX-Mol2 2.0.3
Toolshed: register bundle ChimeraX-PickBlobs 1.0.1
Toolshed: delay_registration measure blob
Toolshed: register bundle ChimeraX-NMRSTAR 1.0.2
Toolshed: register bundle ChimeraX-Mole 1.0
Toolshed: register bundle ChimeraX-Dicom 1.2.6
Toolshed: register bundle ChimeraX-BondRot 2.0.4
Toolshed: delay_registration torsion
Toolshed: register bundle ChimeraX-Segger 1.0
Toolshed: delay_registration segger
Toolshed: register bundle ChimeraX-Topography 1.0
Toolshed: delay_registration topography
Toolshed: register bundle ChimeraX-PDBMatrices 1.0
Toolshed: register bundle ChimeraX-Help 1.3
Toolshed: delay_registration help
Toolshed: register bundle ChimeraX-SDF 2.0.2
Toolshed: register bundle ChimeraX-AltlocExplorer 1.1.2
Toolshed: register bundle ChimeraX-SelInspector 1.0
Toolshed: register bundle ChimeraX-AlignmentMatrices 2.1
Toolshed: register bundle ChimeraX-Clashes 2.3
Toolshed: delay_registration clashes
Toolshed: delay_registration contacts
Toolshed: delay_registration ~clashes
Toolshed: delay_registration ~contacts
Toolshed: register bundle ChimeraX-WavefrontOBJ 1.0
Toolshed: register bundle ChimeraX-DistMonitor 1.4.2
Toolshed: delay_registration distance
Toolshed: delay_registration ~distance
Toolshed: register bundle ChimeraX-NRRD 1.2
Toolshed: register bundle ChimeraX-VTK 1.0
Toolshed: register bundle ChimeraX-Centroids 1.4
Toolshed: delay_registration define centroid
Toolshed: register bundle ChimeraX-Storm 1.0
Toolshed: register bundle ChimeraX-CommandLine 1.2.5
Toolshed: register bundle ChimeraX-MMTF 2.2
Toolshed: register bundle ChimeraX-ChemGroup 2.0.1
Toolshed: register bundle ChimeraX-Atomic 1.58.8
Toolshed: delay_registration log chains
Toolshed: delay_registration combine
Toolshed: delay_registration pbond
Toolshed: delay_registration ~pbond
Toolshed: delay_registration label missing
Toolshed: register bundle ChimeraX-Zone 1.0.1
Toolshed: delay_registration zone
Toolshed: register bundle ChimeraX-VolumeMenu 1.0.1
Toolshed: register bundle ChimeraX-KVFinder 1.2.1
Toolshed: delay_registration kvfinder
Toolshed: register bundle ChimeraX-uniprot 2.3.1
Toolshed: register bundle ChimeraX-Positions 1.0
Toolshed: register bundle ChimeraX-Tug 1.0.1
Toolshed: delay_registration tug
Toolshed: register bundle ChimeraX-SaveCommand 1.5.1
Toolshed: delay_registration save
Toolshed: delay_registration usage save
Toolshed: register bundle ChimeraX-Toolbar 1.2.3
Toolshed: register bundle ChimeraX-AlignmentAlgorithms 2.0.2
Toolshed: register bundle ChimeraX-DockPrep 1.1.3
Toolshed: delay_registration dockprep
Toolshed: register bundle ChimeraX-ModelSeries 1.0.1
Toolshed: delay_registration mseries
Toolshed: register bundle ChimeraX-PDBBio 1.0.1
Toolshed: register bundle ChimeraX-AxesPlanes 2.4
Toolshed: delay_registration define plane
Toolshed: delay_registration define axis
Toolshed: register bundle ChimeraX-StdCommands 1.18.1
Toolshed: delay_registration alias
Toolshed: delay_registration alias list
Toolshed: delay_registration alias delete
Toolshed: delay_registration ~alias
Toolshed: delay_registration align
Toolshed: delay_registration altlocs
Toolshed: delay_registration angle
Toolshed: delay_registration camera
Toolshed: delay_registration cartoon
Toolshed: delay_registration ~cartoon
Toolshed: delay_registration cd
Toolshed: delay_registration clip
Toolshed: delay_registration ~clip
Toolshed: delay_registration close
Toolshed: delay_registration cofr
Toolshed: delay_registration ~cofr
Toolshed: delay_registration color
Toolshed: delay_registration colour
Toolshed: delay_registration color delete
Toolshed: delay_registration color list
Toolshed: delay_registration color name
Toolshed: delay_registration color show
Toolshed: delay_registration colordef
Toolshed: delay_registration ~colordef
Toolshed: delay_registration colourdef
Toolshed: delay_registration ~colourdef
Toolshed: delay_registration coordset
Toolshed: delay_registration crossfade
Toolshed: delay_registration defattr
Toolshed: delay_registration delete
Toolshed: delay_registration dssp
Toolshed: delay_registration exit
Toolshed: delay_registration quit
Toolshed: delay_registration fly
Toolshed: delay_registration getcrd
Toolshed: delay_registration graphics
Toolshed: delay_registration hide
Toolshed: delay_registration ~show
Toolshed: delay_registration ~display
Toolshed: delay_registration lighting
Toolshed: delay_registration lighting model
Toolshed: delay_registration material
Toolshed: delay_registration measure buriedarea
Toolshed: delay_registration measure center
Toolshed: delay_registration measure convexity
Toolshed: delay_registration measure correlation
Toolshed: delay_registration measure inertia
Toolshed: delay_registration measure length
Toolshed: delay_registration measure rotation
Toolshed: delay_registration measure symmetry
Toolshed: delay_registration measure weight
Toolshed: delay_registration move
Toolshed: delay_registration move cofr
Toolshed: delay_registration palette
Toolshed: delay_registration perframe
Toolshed: delay_registration ~perframe
Toolshed: delay_registration pwd
Toolshed: delay_registration rainbow
Toolshed: delay_registration rename
Toolshed: delay_registration ribbon
Toolshed: delay_registration ~ribbon
Toolshed: delay_registration rmsd
Toolshed: delay_registration rock
Toolshed: delay_registration roll
Toolshed: delay_registration runscript
Toolshed: delay_registration select
Toolshed: delay_registration ~select
Toolshed: delay_registration set
Toolshed: delay_registration ~set
Toolshed: delay_registration setattr
Toolshed: delay_registration show
Toolshed: delay_registration display
Toolshed: delay_registration size
Toolshed: delay_registration split
Toolshed: delay_registration stop
Toolshed: delay_registration style
Toolshed: delay_registration sym
Toolshed: delay_registration tile
Toolshed: delay_registration ~tile
Toolshed: delay_registration time
Toolshed: delay_registration transparency
Toolshed: delay_registration turn
Toolshed: delay_registration undo
Toolshed: delay_registration redo
Toolshed: delay_registration usage
Toolshed: delay_registration version
Toolshed: delay_registration view
Toolshed: delay_registration wait
Toolshed: delay_registration windowsize
Toolshed: delay_registration wobble
Toolshed: delay_registration worm
Toolshed: delay_registration ~worm
Toolshed: delay_registration select zone
Toolshed: delay_registration zoom
Toolshed: register bundle ChimeraX-Maestro 1.9.1
Toolshed: register bundle ChimeraX-AddH 2.2.6
Toolshed: delay_registration addh
Toolshed: register bundle ChimeraX-ColorGlobe 1.0
Toolshed: register bundle ChimeraX-Meeting 1.0.1
Toolshed: delay_registration meeting start
Toolshed: delay_registration meeting join
Toolshed: delay_registration meeting
Toolshed: delay_registration meeting close
Toolshed: delay_registration meeting info
Toolshed: delay_registration meeting settings
Toolshed: delay_registration meeting server
Toolshed: delay_registration meeting unname
Toolshed: delay_registration meeting send
Toolshed: register bundle ChimeraX-RenderByAttr 1.6.2
Toolshed: register bundle ChimeraX-RNALayout 1.0
Toolshed: delay_registration rna path
Toolshed: delay_registration rna model
Toolshed: register bundle ChimeraX-VIPERdb 1.0
Toolshed: register bundle ChimeraX-CoreFormats 1.2
Toolshed: register bundle ChimeraX-Segmentations 3.5.6
Toolshed: delay_registration ui view
Toolshed: delay_registration segmentations
Toolshed: Initiated toolshed check: 2025-02-06T12:19:31.798842
Toolshed: finished loading bundles
NOTE: Initializing bundles
Toolshed: initialize_bundles False
Toolshed: initialize manager presets for bundle 'ChimeraX-PresetMgr'
Toolshed: initialize manager rotamers for bundle 'ChimeraX-RotamerLibMgr'
Toolshed: initialize manager url_schemes for bundle 'ChimeraX-SchemeMgr'
Toolshed: initialize manager data formats for bundle 'ChimeraX-DataFormats'
Toolshed: initialize manager alignments for bundle 'ChimeraX-Alignments'
Toolshed: initialize manager items inspection for bundle 'ChimeraX-ItemsInspection'
Toolshed: find_bundle ChimeraX-DataFormats True None
Toolshed: initialize manager open command for bundle 'ChimeraX-OpenCommand'
Toolshed: skip non-autostart manager start structure for bundle 'ChimeraX-BuildStructure'
Toolshed: skip non-autostart manager start structure fragments for bundle 'ChimeraX-BuildStructure'
Toolshed: skip non-autostart manager sequence features for bundle 'ChimeraX-Atomic'
Toolshed: find_bundle ChimeraX-DataFormats True None
Toolshed: initialize manager save command for bundle 'ChimeraX-SaveCommand'
Toolshed: initialize manager toolbar for bundle 'ChimeraX-Toolbar'
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: skip non-autostart manager render by attribute for bundle 'ChimeraX-RenderByAttr'
Toolshed: custom initialization for bundle 'ChimeraX-ToolshedUtils'
Toolshed: custom initialization for bundle 'ChimeraX-RestServer'
Toolshed: custom initialization for bundle 'ChimeraX-MouseModes'
Toolshed: custom initialization for bundle 'ChimeraX-Vive'
Toolshed: custom initialization for bundle 'ChimeraX-BugReporter'
Toolshed: custom initialization for bundle 'ChimeraX-TapeMeasure'
Toolshed: custom initialization for bundle 'ChimeraX-Map'
Toolshed: custom initialization for bundle 'ChimeraX-Log'
Toolshed: custom initialization for bundle 'ChimeraX-SwapRes'
Toolshed: custom initialization for bundle 'ChimeraX-OrthoPick'
Toolshed: custom initialization for bundle 'ChimeraX-BasicActions'
Toolshed: custom initialization for bundle 'ChimeraX-MapEraser'
Toolshed: custom initialization for bundle 'ChimeraX-MapSeries'
Toolshed: custom initialization for bundle 'ChimeraX-StructMeasure'
Toolshed: custom initialization for bundle 'ChimeraX-FunctionKey'
Toolshed: custom initialization for bundle 'ChimeraX-Registration'
Toolshed: custom initialization for bundle 'ChimeraX-Markers'
Toolshed: custom initialization for bundle 'ChimeraX-BuildStructure'
Toolshed: custom initialization for bundle 'ChimeraX-Surface'
Toolshed: custom initialization for bundle 'ChimeraX-ViewDockX'
Toolshed: custom initialization for bundle 'ChimeraX-SwapAA'
Toolshed: custom initialization for bundle 'ChimeraX-Label'
Toolshed: custom initialization for bundle 'ChimeraX-PickBlobs'
Toolshed: custom initialization for bundle 'ChimeraX-NMRSTAR'
Toolshed: custom initialization for bundle 'ChimeraX-Dicom'
Toolshed: custom initialization for bundle 'ChimeraX-BondRot'
Toolshed: custom initialization for bundle 'ChimeraX-Help'
Toolshed: custom initialization for bundle 'ChimeraX-DistMonitor'
Toolshed: custom initialization for bundle 'ChimeraX-CommandLine'
Toolshed: custom initialization for bundle 'ChimeraX-ChemGroup'
Toolshed: custom initialization for bundle 'ChimeraX-Atomic'
Toolshed: custom initialization for bundle 'ChimeraX-Zone'
Toolshed: custom initialization for bundle 'ChimeraX-VolumeMenu'
Toolshed: custom initialization for bundle 'ChimeraX-Tug'
Toolshed: custom initialization for bundle 'ChimeraX-StdCommands'
Toolshed: custom initialization for bundle 'ChimeraX-Segmentations'
Starting main interface
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-SelInspector True None
Toolshed: AvailableBundleCache.load: toolshed_url https://cxtoolshed.rbvi.ucsf.edu
Toolshed: AvailableBundleCache.load: url https://cxtoolshed.rbvi.ucsf.edu/bundle/?uuid=773cf03f-db23-5226-968d-1f624be4b082&format_version=2
Toolshed: find_bundle ChimeraX-Core True None
malloc(): unsorted double linked list corrupted
Aborted (core dumped)
jobilinux@SCMB-2DN9BY3:~$