Concept Index

• .coot: Scheme
• .coot.py: Python
• alternate conformation: Adding Alternative Conformations
• anisotropic atoms: Anisotropic Atoms
• annotations: 3D Annotations
• atom colouring: Atom Colouring
• atom colouring: Display Manager
• atom info: Atom Info
• atom label, brief: Atom Labeling
• atom labeling: Atom Labeling
• atom picking: Clear Pending Picks
• atomic dots: Atomic Dots
• auto-fit rotamer: Rotamers
• average map: Make an Averaged Map
• B-Factor, New Atoms: Temperature Factor for New Atoms
• background colour: Background colour
• backrub rotamers: Rotamers
• backups: Backups and Undo
• backups, clearing: Clearing Backups
• ball and stick: Ball and Stick Representation
• baton build: Baton Building
• baton mode: Baton Building
• big maps: Dynamic Map Sampling and Display Size
• blobs: sec_blobs
• bond thickness: Bond Parameters
• bones: Skeletonization
• C-terminus: Add OXT Atom to Residue
• C\alpha representation: Display Manager
• C\alpha symmetry: Symmetry
• carbohydrates: Refining Carbohydrates
• chain id: Changing Chain IDs
• change contour level: Maps in General
• changing chain ids: Changing Chain IDs
• changing the Refinement Map: Changing the Map for Building/Refinement
• chi angles: Editing Chi Angles
• cif dictionary: Dictionary
• citing coot: Citing Coot
• clashing residues: Rotamers
• Clear Pending Picks: Clear Pending Picks
• clearing backups: Clearing Backups
• clipping: Clipping Manipulation
• colour by chain: Display Manager
• colouring, atoms: Atom Colouring
• colouring, map: Map colouring
• command line arguments: Command Line Arguments
• contouring, map: Map Contouring
• contouring, map: Scrollwheel
• coordinates format: Reading coordinates
• coot droppings: Coot Droppings
• crash: Crash
• crash recovery: Crash
• crosshairs: Crosshairs
• debugger: Crash
• default refmac executable: Running Refmac
• delete: Delete
• density line thickness: Map Line Width
• depth-cueing: Display Issues
• dictionary, cif: Find Ligands
• dictionary, cif: Environment Variables
• dictionary, ligands: Environment Variables
• difference map: Make a Difference Map
• difference map: Map Contouring
• difference map colours: Map Contouring
• directory for save coordinates: The file selector
• Display Manager: Display Manager
• DNA, ideal: Building Ideal DNA and RNA
• DNA, mutating: Mutation
• docking sidechains: Docking Sidechains
• droppings: Coot Droppings
• dual conformations: Adding Alternative Conformations
• edit \chi angles: Editing Chi Angles
• edit B-factors: Atom Info
• edit occupancy: Atom Info
• Electron Density Server: Get Coordinates and Map from EDS
• executing commands: Scripting
• export map: Export Map
• EYC-TIED: Maps in General
• file-name filtering: The file selector
• fill partial residues: Fill Partial Residues
• findligand: findligand
• flip peptide: Pep-flip
• fragment direction change: Reversing Direction of Fragment
• frame rate: Frame Rate
• gdb: Crash
• GLN and ASN B-factor Outliers: GLN and ASN B-factor Outliers
• goose: Download coordinates
• guano: Coot Droppings
• guile: Scheme
• helix placement: Place Helix
• hydrogens: Bond Parameters
• initialization file: Scheme
• Least Squares Fitting: Least-Squares Fitting
• ligand orientation: Flip Ligand
• ligand torsion angles: Torsion General
• ligand, overlay: Ligand Overlaying
• ligands: Find Ligands
• ligands: Importing Ligands/Monomers
• ligands, flexible: Find Ligands
• mainchain: C-alpha -> Mainchain
• mainchain torsions: Backbone Torsion Angles
• map box radius: Map Extent
• map changing (for refinement/building): Changing the Map for Building/Refinement
• map extent: Map Extent
• map line width: Map Line Width
• map scrolling: Scrollwheel
• map transformation: Map Transformation
• masks: masks
• mean B-factor: Mean and Median Temperature Factors
• median B-factor: Mean and Median Temperature Factors
• merge molecules: Merge Molecules
• missing symmetry: Symmetry
• mmCIF dictionary: Dictionary
• modelling toolbar: The Modelling Toolbar
• modified labels: Modifying the Labels on the Model/Fit/Refine dialog
• molecule centre: Moving Molecules/Ligands
• molecule number: Molecule Number
• Molprobity Tools: Molprobity Tools Interface
• monomers: Importing Ligands/Monomers
• mouse: Hardware Requirements
• mouse buttons: Mousing and Keyboarding
• moving ligands: Moving Molecules/Ligands
• moving molecules: Moving Molecules/Ligands
• Moving Zero Occupancy Atoms: Moving Zero Occupancy Atoms
• multi-mutate: Mutation
• multiple coordinates files: Reading coordinates
• mutate: Mutation
• mutating DNA: Mutation
• mutating RNA: Mutation
• NCS: Bond Parameters
• NCS averaging: Bond Parameters
• NCS edits: Applying NCS Edits
• negative contour levels: Map Contour ``Scrolling'' Limits
• OCA: Download coordinates
• OpenGL: Display Issues
• Orientation Axes: Orientation Axes
• origin marker: Display Issues
• output: Program Output
• overlaying ligands: Ligand Overlaying
• OXT atom: Add OXT Atom to Residue
• packing diagram: Symmetry
• Patterson: Pattersons
• pepflip: Pep-flip
• peptide restraints, planar: Planar Peptide Restraints
• PHS data: Create a Map
• PHS data format: Create a Map
• picking: sec_picking
• pink pointer: Rotation Centre Pointer
• planar peptide restraints: Planar Peptide Restraints
• planes: Regularization and Real Space Refinement
• polynucleotides: Building Ideal DNA and RNA
• post-manipulation-hook: Post-manipulation-hook
• Print Sequence: Print Sequence
• probe: Molprobity Tools Interface
• python: Python
• Ramachandran plot: Ramachandran Plots
• Raster3D: Raster3D
• reading multiple pdb files: Reading coordinates
• recentring view: Recentring View
• recover session: Crash
• redo: Backups and Undo
• reduce: Molprobity Tools Interface
• reference manual: Introduction
• reference structures: Environment Variables
• refine single click: Regularization and Real Space Refinement
• refinement: Regularization and Real Space Refinement
• refinement weight: Regularization and Real Space Refinement
• refinement, rigid body: Rigid Body Refinement
• refinement, simplex: Simplex Refinement
• refining residues: Refining Specific Residues
• refmac: Running Refmac
• refmac map colour: Running Refmac
• refmac parameters: Running Refmac
• refmac, default: Running Refmac
• regularization: Regularization and Real Space Refinement
• render: Raster3D
• renumbering residues: Mutation
• residue info: Atom Info
• resizing view: Resizing View
• restore after crash: Backups and Undo
• reverse direction: Reversing Direction of Fragment
• rigid body fit: Rigid Body Refinement
• RNA, ideal: Building Ideal DNA and RNA
• RNA, mutating: Mutation
• rotamers: Rotamers
• rotate/translate, manual: Rotate/Translate Zone
• rotation centre: Recentring View
• rotation centre pointer: Rotation Centre Pointer
• running refmac: Running Refmac
• running SHELXL: Running SHELXL
• save coordinates directory: The file selector
• scheme: Scheme
• screenshot.: Screenshot
• scripting: Scripting
• Scroll: Display Manager
• scroll wheel, map for: Scroll-wheel
• scroll, map contour change by: Scrollwheel
• scroll-wheel: Scrollwheel
• Secondary Structure Matching (SSM): Secondary Structure Matching (SSM)
• sequence view: Sequence View
• set-matrix: Regularization and Real Space Refinement
• set-rotation-centre: Recentring View
• setting space group: Setting the Space Group
• sharpening, map: Map Sharpening
• SHELX .ins: Reading coordinates
• SHELXL: Running SHELXL
• sidechains: Docking Sidechains
• simplex refinement: Simplex Refinement
• single click refine: Regularization and Real Space Refinement
• skeleton updating: Skeletonization
• skeleton, missing: Baton Building
• skeletonization: Skeletonization
• slab: Clipping Manipulation
• sliding: Recentring View
• slow computer: Slow Computer Configuration
• SMILES strings: Ligand from SMILES strings
• space group names: Reading coordinates
• space group operators: Space Group and Symmetry
• sphere refinement: Sphere Refinement
• startup dialog (state): Coot State
• startup settings (python): Python
• startup settings (scheme): Scheme
• state: Coot State
• superposition: Secondary Structure Matching (SSM)
• symmetry: Symmetry
• symmetry operators: Space Group and Symmetry
• terminal oxygen: Add OXT Atom to Residue
• terminal residue: Add Terminal Residue
• thickness of density lines: Map Line Width
• tooltips: General Features
• torsion angles, ligand: Torsion General
• torsion general: Torsion General
• torsion restraints: Regularization and Real Space Refinement
• torsions: Editing Chi Angles
• trackball, virtual: Virtual Trackball
• traffic lights: Regularization and Real Space Refinement
• translate molecule: Moving Molecules/Ligands
• translation, keyboard: Keyboard Z Translation
• translation, mouse: Mouse Z Translation
• trimming atoms: Trimming Atoms
• undo: Backups and Undo
• unexplained density: sec_blobs
• unit cell: Unit Cell
• UNK residue: The UNK residue type
• unmodelled density: sec_blobs
• Validation Graphs: Validation Graphs
• version number: Version number
• view matrix: View Matrix
• waters, finding: Find Waters
• web page: Web Page
• weight, real space refinement: Regularization and Real Space Refinement
• width, bonds: Bond Parameters
• write map: Export Map
• writing PDBs: Writing PDB files
• yellow box: Display Issues
• z-rotation: Virtual Trackball
• zero occupancy: Zero Occupancy Marker
• zoom: Resizing View
• zoom, slider: more on zooming