| Accelerators | HappyDoc Generated Documentation: Accelerators
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| AddH | Add hydrogens to structures
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| AlignPlot | HappyDoc Generated Documentation: AlignPlot
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| Benchmark | HappyDoc Generated Documentation: Benchmark
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| CGLtk | Generically useful CGL Tk additions
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| CGLutil | Generically useful modules
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| Categorizer | Categorize atoms into solvent, ligand, etc. categories
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| ChemGroup | Find chemical groups in a structure
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| Collaboratory | Initialization code for the Collaboratory Chimera Extension
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| DOCKGridViewer | HappyDoc Generated Documentation: DOCKGridViewer
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| DelphiViewer | View Delphi output in Chimera
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| EnsembleMatch | HappyDoc Generated Documentation: EnsembleMatch
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| FindHBond | Find hydrogen bonds
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| Idle | HappyDoc Generated Documentation: Idle
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| MSFViewer | HappyDoc Generated Documentation: MSFViewer
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| MainChain | HappyDoc Generated Documentation: MainChain
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| Midas | Emulate UCSF Midas command set
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| MinrmsPlot | HappyDoc Generated Documentation: MinrmsPlot
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| ModelBrowser | HappyDoc Generated Documentation: ModelBrowser
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| ModelPanel | GUI to perform functions on models
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| Movie | HappyDoc Generated Documentation: Movie
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| MultAlignViewer | HappyDoc Generated Documentation: MultAlignViewer
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| OpenSave | Standard open/save panels for Chimera
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| PBReader | Show pseudobonds described in a file
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| Phantom | HappyDoc Generated Documentation: Phantom
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| PipesAndPlanks | HappyDoc Generated Documentation: PipesAndPlanks
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| PythonModel | Access Chimera OpenGL drawing
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| ResProp | Color residues by property (e.g. aliphatic)
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| Ribbon | HappyDoc Generated Documentation: Ribbon
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| RibbonStyleEditor | HappyDoc Generated Documentation: RibbonStyleEditor
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| ScaleBar | HappyDoc Generated Documentation: ScaleBar
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| SessionUtil | HappyDoc Generated Documentation: SessionUtil
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| SimpleSession | Save/restore most aspects of a Chimera modeling session
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| StructMeasure | Interface to structure measurements (e.g. distances, angles)
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| Surfnet | HappyDoc Generated Documentation: Surfnet
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| SwapRes | Change residue side chains
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| Texturer | Convenience classes for making small 2D textures
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| Trajectory | HappyDoc Generated Documentation: Trajectory
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| ViewDock | HappyDoc Generated Documentation: ViewDock
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| VolumeData | HappyDoc Generated Documentation: VolumeData
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| VolumePath | HappyDoc Generated Documentation: VolumePath
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| VolumeViewer | HappyDoc Generated Documentation: VolumeViewer
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| _chimera | Declarations of basic Chimera classes (Molecule, Atom, etc.)
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| _contour | _contour module
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| _cubes | _cubes module
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| _dockgrid | _dockgrid module
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| _surface | _surface module
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| _surfnet | _surfnet module
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| _volume | _volume module
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| blast | HappyDoc Generated Documentation: blast
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| chimera | Chimera module
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| grailif | HappyDoc Generated Documentation: grailif
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| mpose | HappyDoc Generated Documentation: mpose
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| registration | HappyDoc Generated Documentation: registration
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