The Coot User Manual

Table of Contents

• Coot User Manual
• 1 Introduction
  • 1.1 Citing Coot and Friends
  • 1.2 What is Coot?
  • 1.3 What Coot is Not
  • 1.4 Hardware Requirements
    • 1.4.1 Mouse
  • 1.5 Environment Variables
  • 1.6 Command Line Arguments
  • 1.7 Web Page
  • 1.8 Crash
• 2 Mousing and Keyboarding
  • 2.1 Next Residue
  • 2.2 Keyboard Contouring
  • 2.3 Mouse Z Translation and Clipping
  • 2.4 Keyboard Translation
  • 2.5 Keyboard Zoom and Clip
  • 2.6 Scrollwheel
  • 2.7 Selecting Atoms
  • 2.8 Virtual Trackball
  • 2.9 More on Zooming
• 3 General Features
  • 3.1 Version number
  • 3.2 Antialiasing
  • 3.3 Molecule Number
  • 3.4 Display Issues
    • 3.4.1 Stereo
    • 3.4.2 Pick Cursor
    • 3.4.3 Origin Marker
  • 3.5 Screenshot
  • 3.6 Raster3D output
  • 3.7 Display Manager
  • 3.8 The Modelling Toolbar
  • 3.9 The file selector
    • 3.9.1 File-name Filtering
    • 3.9.2 Filename Sorting
    • 3.9.3 Save Coordinates Directory
  • 3.10 Scripting
    • 3.10.1 Python
      • 3.10.1.1 Python Commands
    • 3.10.2 Scheme
    • 3.10.3 Coot State
    • 3.10.4 Key Binding
    • 3.10.5 User-Defined Functions
  • 3.11 Backups and Undo
    • 3.11.1 Redo
    • 3.11.2 Restoring from Backup
  • 3.12 View Matrix
  • 3.13 Space Group and Symmetry
  • 3.14 Recentring View
  • 3.15 Views
  • 3.16 Clipping Manipulation
  • 3.17 Background colour
  • 3.18 Unit Cell
  • 3.19 Rotation Centre Pointer
  • 3.20 Pointer Distances
  • 3.21 Crosshairs
  • 3.22 3D Annotations
  • 3.23 Frame Rate
  • 3.24 Program Output
• 4 Coordinate-Related Features
  • 4.1 Reading coordinates
    • 4.1.1 A Note on Space Groups Names
    • 4.1.2 Read multiple coordinate files
    • 4.1.3 SHELX .ins/.res files
  • 4.2 Atom Info
  • 4.3 Atom Labeling
  • 4.4 Atom Colouring
  • 4.5 Bond Parameters
    • 4.5.1 Bond Thickness
    • 4.5.2 Display Hydrogens
    • 4.5.3 NCS Ghosts Coordinates
    • 4.5.4 NCS Maps
    • 4.5.5 Using Strict NCS
  • 4.6 Download coordinates
  • 4.7 Get Coordinates and Map from EDS
  • 4.8 Save Coordinates
  • 4.9 Setting the Space Group
  • 4.10 Anisotropic Atoms
  • 4.11 Symmetry
    • 4.11.1 Missing symmetry
  • 4.12 Sequence View
  • 4.13 Print Sequence
  • 4.14 Environment Distances
  • 4.15 Distances and Angles
  • 4.16 Zero Occupancy Marker
  • 4.17 Atomic Dots
  • 4.18 Ball and Stick Representation
  • 4.19 Mean, Median Temperature Factors
  • 4.20 Secondary Structure Matching (SSM)
  • 4.21 Least-Squares Fitting
  • 4.22 Ligand Overlaying
  • 4.23 Writing PDB files
• 5 Modelling and Building
  • 5.1 Regularization and Real Space Refinement
    • 5.1.1 Dictionary
    • 5.1.2 Sphere Refinement
    • 5.1.3 Refining Specific Residues
    • 5.1.4 Refining Carbohydrates
    • 5.1.5 Planar Peptide Restraints
    • 5.1.6 The UNK residue type
    • 5.1.7 Moving Zero Occupancy Atoms
  • 5.2 Changing the Map for Building/Refinement
  • 5.3 Rotate/Translate Zone
  • 5.4 Rigid Body Refinement
  • 5.5 Simplex Refinement
  • 5.6 Post-manipulation-hook
  • 5.7 Baton Building
    • 5.7.1 Undo
    • 5.7.2 Missing Skeleton
    • 5.7.3 Building Backwards
  • 5.8 Reversing Direction of Fragment
  • 5.9 C\alpha -> Mainchain
  • 5.10 Backbone Torsion Angles
  • 5.11 Docking Sidechains
  • 5.12 Rotamers
    • 5.12.1 Auto Fit Rotamer
      • 5.12.1.1 Backrub Rotamers
    • 5.12.2 De-clashing residues
  • 5.13 Editing chi Angles
  • 5.14 Torsion General
    • 5.14.1 Ligand Torsion angles
  • 5.15 Pep-flip
  • 5.16 Add Alternate Conformation
  • 5.17 Mutation
    • 5.17.1 Mutating DNA/RNA
    • 5.17.2 Multiple mutations
    • 5.17.3 Mutating to a Non-Standard Residue
    • 5.17.4 Mutate and Autofit
    • 5.17.5 Renumbering
  • 5.18 Importing Lignds/Monomers
  • 5.19 Ligand from SMILES strings
  • 5.20 Find Ligands
    • 5.20.1 Flexible Ligands
    • 5.20.2 Adding Ligands to Model
  • 5.21 Flip Ligand
  • 5.22 Find Waters
    • 5.22.1 Refinement Failure
    • 5.22.2 Blobs
  • 5.23 Add Terminal Residue
  • 5.24 Add OXT Atom to Residue
  • 5.25 Add Atom at Pointer
  • 5.26 Place Helix
  • 5.27 Building Ideal DNA and RNA
  • 5.28 Merge Molecules
  • 5.29 Temperature Factor for New Atoms
  • 5.30 Applying NCS Edits
  • 5.31 Running Refmac
  • 5.32 Running SHELXL
  • 5.33 Clear Pending Picks
  • 5.34 Delete
  • 5.35 Sequence Assignment
  • 5.36 Building Links and Loops
  • 5.37 Fill Partial Residues
  • 5.38 Changing Chain IDs
  • 5.39 Setting Occupancies
  • 5.40 Fix Nomenclature Errors
  • 5.41 Rotamer Fix Whole Protein
  • 5.42 Refine All Waters
  • 5.43 Moving Molecules/Ligands
  • 5.44 Modifying the Labels on the Model/Fit/Refine dialog
• 6 Map-Related Features
  • 6.1 Maps in General
    • 6.1.1 Map Reading Bug
  • 6.2 Create a Map
    • 6.2.1 Auto-read MTZ file
    • 6.2.2 Reading CIF data
    • 6.2.3 Reading PHS data
  • 6.3 Map Contouring
  • 6.4 Map Extent
  • 6.5 Map Contour “Scrolling” Limits
  • 6.6 Map Line Width
  • 6.7 “Dynamic” Map colouring
  • 6.8 Difference Map Colouring
  • 6.9 Make a Difference Map
  • 6.10 Make an Averaged Map
  • 6.11 Map Sampling
  • 6.12 Dragged Map
  • 6.13 Dynamic Map Sampling and Display Size
  • 6.14 Skeletonization
  • 6.15 Map Sharpening
  • 6.16 Pattersons
  • 6.17 Masks
    • 6.17.1 Example
  • 6.18 Trimming
  • 6.19 Map Transformation
  • 6.20 Export Map
• 7 Validation
  • 7.1 Ramachandran Plots
  • 7.2 Geometry Analysis
  • 7.3 Chiral Volumes
    • 7.3.1 Fixing Chiral Volume Errors
  • 7.4 Blobs: a.k.a. Unmodelled density
  • 7.5 Difference Map Peaks
  • 7.6 Check Waters by Difference Map
  • 7.7 Molprobity Tools Interface
  • 7.8 GLN and ASN B-factor Outliers
  • 7.9 Validation Graphs
    • 7.9.1 Residue Density Fit
    • 7.9.2 Rotamer Analysis
    • 7.9.3 Temperature Factor Variance
    • 7.9.4 Peptide Omega Angle Distortion
• 8 Representation
  • 8.1 Surfaces
• 9 Hints and Usage Tips
  • 9.1 Documentation
  • 9.2 Low Resolution
  • 9.3 Coot Droppings
  • 9.4 Clearing Backups
  • 9.5 Getting out of “Translate” Mode
  • 9.6 Getting out of “Continuous Rotation” Mode
  • 9.7 Getting out of “Label Atom Only” Mode
  • 9.8 Button Labels
  • 9.9 Picking
  • 9.10 Resizing View
  • 9.11 Scroll-wheel
  • 9.12 Slow Computer Configuration
• 10 Other Programs
  • 10.1 findligand
• 11 Scripting Functions
  • 11.1 The Virtual Trackball
    • 11.1.1 vt-surface
    • 11.1.2 vt-surface-status
  • 11.2 Startup Functions
    • 11.2.1 set-prefer-python
    • 11.2.2 prefer-python
  • 11.3 File System Functions
    • 11.3.1 make-directory-maybe
    • 11.3.2 set-show-paths-in-display-manager
    • 11.3.3 show-paths-in-display-manager-state
    • 11.3.4 add-coordinates-glob-extension
    • 11.3.5 add-data-glob-extension
    • 11.3.6 add-dictionary-glob-extension
    • 11.3.7 add-map-glob-extension
    • 11.3.8 remove-coordinates-glob-extension
    • 11.3.9 remove-data-glob-extension
    • 11.3.10 remove-dictionary-glob-extension
    • 11.3.11 remove-map-glob-extension
    • 11.3.12 set-sticky-sort-by-date
    • 11.3.13 unset-sticky-sort-by-date
    • 11.3.14 set-filter-fileselection-filenames
    • 11.3.15 filter-fileselection-filenames-state
    • 11.3.16 file-type-coords
    • 11.3.17 open-coords-dialog
  • 11.4 Widget Utilities
    • 11.4.1 info-dialog
  • 11.5 MTZ and data handling utilities
    • 11.5.1 manage-column-selector
  • 11.6 Molecule Info Functions
    • 11.6.1 chain-n-residues
    • 11.6.2 resname-from-serial-number
    • 11.6.3 seqnum-from-serial-number
    • 11.6.4 insertion-code-from-serial-number
    • 11.6.5 n-models
    • 11.6.6 n-chains
    • 11.6.7 is-solvent-chain-p
    • 11.6.8 n-residues
    • 11.6.9 sort-chains
    • 11.6.10 remarks-dialog
    • 11.6.11 print-header-secondary-structure-info
    • 11.6.12 copy-molecule
    • 11.6.13 add-ligand-delete-residue-copy-molecule
    • 11.6.14 exchange-chain-ids-for-seg-ids
  • 11.7 Library and Utility Functions
    • 11.7.1 coot-version
    • 11.7.2 svn-revision
    • 11.7.3 molecule-name
    • 11.7.4 set-molecule-name
    • 11.7.5 coot-real-exit
    • 11.7.6 first-coords-imol
    • 11.7.7 first-small-coords-imol
    • 11.7.8 first-unsaved-coords-imol
    • 11.7.9 mmcif-sfs-to-mtz
  • 11.8 Graphics Utility Functions
    • 11.8.1 set-do-anti-aliasing
    • 11.8.2 do-anti-aliasing-state
    • 11.8.3 set-do-GL-lighting
    • 11.8.4 do-GL-lighting-state
    • 11.8.5 use-graphics-interface-state
    • 11.8.6 start-graphics-interface
    • 11.8.7 reset-view
    • 11.8.8 graphics-n-molecules
    • 11.8.9 toggle-idle-spin-function
    • 11.8.10 toggle-idle-rock-function
    • 11.8.11 set-rocking-factors
    • 11.8.12 set-idle-function-rotate-angle
    • 11.8.13 handle-read-draw-molecule
    • 11.8.14 set-convert-to-v2-atom-names
    • 11.8.15 handle-read-draw-molecule-with-recentre
    • 11.8.16 handle-read-draw-molecule-and-move-molecule-here
    • 11.8.17 read-pdb
    • 11.8.18 assign-hetatms
    • 11.8.19 hetify-residue
    • 11.8.20 residue-has-hetatms
    • 11.8.21 replace-fragment
    • 11.8.22 copy-residue-range
    • 11.8.23 clear-and-update-model-molecule-from-file
    • 11.8.24 screendump-image
    • 11.8.25 set-draw-solid-density-surface
    • 11.8.26 set-draw-map-standard-lines
    • 11.8.27 set-solid-density-surface-opacity
    • 11.8.28 set-flat-shading-for-solid-density-surface
  • 11.9 Interface Preferences
    • 11.9.1 set-scroll-by-wheel-mouse
    • 11.9.2 scroll-by-wheel-mouse-state
    • 11.9.3 set-default-initial-contour-level-for-map
    • 11.9.4 set-default-initial-contour-level-for-difference-map
    • 11.9.5 print-view-matrix
    • 11.9.6 get-view-quaternion-internal
    • 11.9.7 set-view-quaternion
    • 11.9.8 apply-ncs-to-view-orientation
    • 11.9.9 apply-ncs-to-view-orientation-and-screen-centre
    • 11.9.10 set-show-origin-marker
    • 11.9.11 show-origin-marker-state
    • 11.9.12 hide-modelling-toolbar
    • 11.9.13 show-modelling-toolbar
    • 11.9.14 hide-main-toolbar
    • 11.9.15 show-main-toolbar
    • 11.9.16 show-model-toolbar-all-icons
    • 11.9.17 show-model-toolbar-main-icons
    • 11.9.18 reattach-modelling-toolbar
    • 11.9.19 set-model-toolbar-docked-position
    • 11.9.20 suck-model-fit-dialog
    • 11.9.21 add-status-bar-text
  • 11.10 Mouse Buttons
    • 11.10.1 set-control-key-for-rotate
    • 11.10.2 control-key-for-rotate-state
    • 11.10.3 blob-under-pointer-to-screen-centre
  • 11.11 Cursor Function
    • 11.11.1 set-pick-cursor-index
  • 11.12 Model/Fit/Refine Functions
    • 11.12.1 post-model-fit-refine-dialog
    • 11.12.2 show-select-map-dialog
    • 11.12.3 set-model-fit-refine-rotate-translate-zone-label
    • 11.12.4 set-model-fit-refine-place-atom-at-pointer-label
    • 11.12.5 post-other-modelling-tools-dialog
    • 11.12.6 set-refinement-move-atoms-with-zero-occupancy
    • 11.12.7 refinement-move-atoms-with-zero-occupancy-state
  • 11.13 Backup Functions
    • 11.13.1 make-backup
    • 11.13.2 turn-off-backup
    • 11.13.3 turn-on-backup
    • 11.13.4 backup-state
    • 11.13.5 set-have-unsaved-changes
    • 11.13.6 have-unsaved-changes-p
    • 11.13.7 set-undo-molecule
    • 11.13.8 show-set-undo-molecule-chooser
    • 11.13.9 set-unpathed-backup-file-names
    • 11.13.10 unpathed-backup-file-names-state
    • 11.13.11 backup-compress-files-state
    • 11.13.12 set-backup-compress-files
  • 11.14 Recover Session Function
    • 11.14.1 recover-session
  • 11.15 Map Functions
    • 11.15.1 calc-phases-generic
    • 11.15.2 map-from-mtz-by-refmac-calc-phases
    • 11.15.3 map-from-mtz-by-calc-phases
    • 11.15.4 set-scroll-wheel-map
    • 11.15.5 set-scrollable-map
    • 11.15.6 scroll-wheel-map
    • 11.15.7 save-previous-map-colour
    • 11.15.8 restore-previous-map-colour
    • 11.15.9 set-active-map-drag-flag
    • 11.15.10 get-active-map-drag-flag
    • 11.15.11 set-last-map-colour
    • 11.15.12 set-map-colour
    • 11.15.13 set-last-map-sigma-step
    • 11.15.14 set-contour-by-sigma-step-by-mol
    • 11.15.15 data-resolution
    • 11.15.16 model-resolution
    • 11.15.17 export-map
    • 11.15.18 difference-map
  • 11.16 Density Increment
    • 11.16.1 set-iso-level-increment
    • 11.16.2 set-diff-map-iso-level-increment
    • 11.16.3 set-map-sampling-rate
    • 11.16.4 get-map-sampling-rate
    • 11.16.5 change-contour-level
    • 11.16.6 set-last-map-contour-level
    • 11.16.7 set-last-map-contour-level-by-sigma
    • 11.16.8 set-stop-scroll-diff-map
    • 11.16.9 set-stop-scroll-iso-map
    • 11.16.10 set-stop-scroll-iso-map-level
    • 11.16.11 set-stop-scroll-diff-map-level
    • 11.16.12 set-residue-density-fit-scale-factor
  • 11.17 Density Functions
    • 11.17.1 set-map-line-width
    • 11.17.2 map-line-width-state
    • 11.17.3 make-and-draw-map
    • 11.17.4 make-and-draw-map-with-refmac-params
    • 11.17.5 make-and-draw-map-with-reso-with-refmac-params
    • 11.17.6 valid-labels
    • 11.17.7 auto-read-make-and-draw-maps
    • 11.17.8 set-auto-read-do-difference-map-too
    • 11.17.9 auto-read-do-difference-map-too-state
    • 11.17.10 set-auto-read-column-labels
    • 11.17.11 set-map-radius
    • 11.17.12 set-density-size
    • 11.17.13 set-display-intro-string
    • 11.17.14 get-map-radius
    • 11.17.15 set-esoteric-depth-cue
    • 11.17.16 esoteric-depth-cue-state
    • 11.17.17 set-swap-difference-map-colours
    • 11.17.18 set-map-is-difference-map
    • 11.17.19 another-level
    • 11.17.20 another-level-from-map-molecule-number
    • 11.17.21 residue-density-fit-scale-factor
    • 11.17.22 density-at-point
  • 11.18 Parameters from map
    • 11.18.1 mtz-hklin-for-map
    • 11.18.2 mtz-fp-for-map
    • 11.18.3 mtz-phi-for-map
    • 11.18.4 mtz-weight-for-map
    • 11.18.5 mtz-use-weight-for-map
  • 11.19 PDB Functions
    • 11.19.1 write-pdb-file
    • 11.19.2 write-residue-range-to-pdb-file
    • 11.19.3 quick-save
  • 11.20 Refmac Functions
    • 11.20.1 set-refmac-counter
    • 11.20.2 refmac-name
    • 11.20.3 swap-map-colours
    • 11.20.4 set-keep-map-colour-after-refmac
    • 11.20.5 keep-map-colour-after-refmac-state
  • 11.21 Symmetry Functions
    • 11.21.1 set-symmetry-size
    • 11.21.2 get-show-symmetry
    • 11.21.3 set-show-symmetry-master
    • 11.21.4 set-show-symmetry-molecule
    • 11.21.5 symmetry-as-calphas
    • 11.21.6 get-symmetry-as-calphas-state
    • 11.21.7 set-symmetry-molecule-rotate-colour-map
    • 11.21.8 symmetry-molecule-rotate-colour-map-state
    • 11.21.9 has-unit-cell-state
    • 11.21.10 undo-symmetry-view
    • 11.21.11 first-molecule-with-symmetry-displayed
    • 11.21.12 save-symmetry-coords
    • 11.21.13 new-molecule-by-symmetry
    • 11.21.14 new-molecule-by-symmetry-with-atom-selection
    • 11.21.15 new-molecule-by-symop
    • 11.21.16 set-space-group
    • 11.21.17 set-symmetry-shift-search-size
  • 11.22 History Functions
    • 11.22.1 print-all-history-in-scheme
    • 11.22.2 print-all-history-in-python
    • 11.22.3 set-console-display-commands-state
    • 11.22.4 set-console-display-commands-hilights
  • 11.23 State Functions
    • 11.23.1 save-state
    • 11.23.2 save-state-file
    • 11.23.3 set-save-state-file-name
    • 11.23.4 set-run-state-file-status
    • 11.23.5 run-state-file
    • 11.23.6 run-state-file-maybe
  • 11.24 Unit Cell interface
    • 11.24.1 get-show-unit-cell
    • 11.24.2 set-show-unit-cells-all
    • 11.24.3 set-show-unit-cell
  • 11.25 Colour
    • 11.25.1 set-colour-map-rotation-on-read-pdb
    • 11.25.2 set-colour-map-rotation-on-read-pdb-flag
    • 11.25.3 set-colour-map-rotation-on-read-pdb-c-only-flag
    • 11.25.4 set-colour-by-chain
    • 11.25.5 set-colour-by-molecule
    • 11.25.6 set-symmetry-colour
  • 11.26 Map colour
    • 11.26.1 set-colour-map-rotation-for-map
    • 11.26.2 set-molecule-bonds-colour-map-rotation
    • 11.26.3 get-molecule-bonds-colour-map-rotation
  • 11.27 Display Functions
    • 11.27.1 set-graphics-window-size
    • 11.27.2 set-graphics-window-position
    • 11.27.3 graphics-draw
    • 11.27.4 zalman-stereo-mode
    • 11.27.5 hardware-stereo-mode
    • 11.27.6 stereo-mode-state
    • 11.27.7 mono-mode
    • 11.27.8 side-by-side-stereo-mode
    • 11.27.9 set-hardware-stereo-angle-factor
    • 11.27.10 hardware-stereo-angle-factor-state
    • 11.27.11 set-model-fit-refine-dialog-position
    • 11.27.12 set-display-control-dialog-position
    • 11.27.13 set-go-to-atom-window-position
    • 11.27.14 set-delete-dialog-position
    • 11.27.15 set-rotate-translate-dialog-position
    • 11.27.16 set-accept-reject-dialog-position
    • 11.27.17 set-ramachandran-plot-dialog-position
    • 11.27.18 set-edit-chi-angles-dialog-position
    • 11.27.19 set-rotamer-selection-dialog-position
  • 11.28 Smooth Scrolling
    • 11.28.1 set-smooth-scroll-flag
    • 11.28.2 get-smooth-scroll
    • 11.28.3 set-smooth-scroll-steps
    • 11.28.4 set-smooth-scroll-limit
  • 11.29 Font Size
    • 11.29.1 set-font-size
    • 11.29.2 get-font-size
    • 11.29.3 set-font-colour
  • 11.30 Rotation Centre
    • 11.30.1 go-to-ligand
  • 11.31 Atom Selection Utilities
    • 11.31.1 clear-pending-picks
    • 11.31.2 set-default-temperature-factor-for-new-atoms
    • 11.31.3 default-new-atoms-b-factor
    • 11.31.4 set-reset-b-factor-moved-atoms
    • 11.31.5 get-reset-b-factor-moved-atoms-state
    • 11.31.6 set-atom-attribute
    • 11.31.7 set-atom-string-attribute
    • 11.31.8 set-residue-name
  • 11.32 Skeletonization Interface
    • 11.32.1 skeletonize-map
    • 11.32.2 unskeletonize-map
    • 11.32.3 set-max-skeleton-search-depth
    • 11.32.4 set-skeleton-box-size
  • 11.33 Read Maps
    • 11.33.1 handle-read-ccp4-map
  • 11.34 Save Coordinates
    • 11.34.1 save-coordinates
  • 11.35 Read Phases File Functions
    • 11.35.1 read-phs-and-coords-and-make-map
    • 11.35.2 read-phs-and-make-map-using-cell-symm-from-previous-mol
    • 11.35.3 read-phs-and-make-map-using-cell-symm-from-mol
    • 11.35.4 read-phs-and-make-map-using-cell-symm
    • 11.35.5 read-phs-and-make-map-with-reso-limits
  • 11.36 Graphics Move
    • 11.36.1 undo-last-move
    • 11.36.2 translate-molecule-by
    • 11.36.3 transform-molecule-by
  • 11.37 Go To Atom Widget Functions
    • 11.37.1 post-go-to-atom-window
    • 11.37.2 set-go-to-atom-chain-residue-atom-name
    • 11.37.3 update-go-to-atom-from-current-position
    • 11.37.4 atom-spec-to-atom-index
    • 11.37.5 full-atom-spec-to-atom-index
    • 11.37.6 update-go-to-atom-window-on-changed-mol
    • 11.37.7 update-go-to-atom-window-on-new-mol
    • 11.37.8 set-go-to-atom-molecule
  • 11.38 Map and Molecule Control
    • 11.38.1 post-display-control-window
    • 11.38.2 set-map-displayed
    • 11.38.3 set-mol-displayed
    • 11.38.4 set-mol-active
    • 11.38.5 mol-is-displayed
    • 11.38.6 mol-is-active
    • 11.38.7 map-is-displayed
    • 11.38.8 set-all-maps-displayed
    • 11.38.9 set-all-models-displayed-and-active
    • 11.38.10 show-spacegroup
  • 11.39 Align and Mutate
    • 11.39.1 align-and-mutate
    • 11.39.2 set-alignment-gap-and-space-penalty
    • 11.39.3 align-to-closest-chain
  • 11.40 Renumber Residue Range
    • 11.40.1 renumber-residue-range
    • 11.40.2 change-residue-number
  • 11.41 Scripting Interface
    • 11.41.1 probe-available-p
    • 11.41.2 post-scripting-window
    • 11.41.3 post-scheme-scripting-window
    • 11.41.4 post-python-scripting-window
  • 11.42 Monomer
    • 11.42.1 get-coords-for-accession-code
    • 11.42.2 get-monomer
    • 11.42.3 run-script
  • 11.43 Regularization and Refinement
    • 11.43.1 add-planar-peptide-restraints
    • 11.43.2 remove-planar-peptide-restraints
    • 11.43.3 add-omega-torsion-restriants
    • 11.43.4 remove-omega-torsion-restriants
    • 11.43.5 set-refinement-immediate-replacement
    • 11.43.6 refinement-immediate-replacement-state
    • 11.43.7 set-residue-selection-flash-frames-number
    • 11.43.8 accept-regularizement
    • 11.43.9 set-refine-with-torsion-restraints
    • 11.43.10 refine-with-torsion-restraints-state
    • 11.43.11 set-matrix
    • 11.43.12 matrix-state
    • 11.43.13 set-refine-auto-range-step
    • 11.43.14 set-refine-max-residues
    • 11.43.15 refine-zone-atom-index-define
    • 11.43.16 refine-zone
    • 11.43.17 refine-auto-range
    • 11.43.18 regularize-zone
    • 11.43.19 set-dragged-refinement-steps-per-frame
    • 11.43.20 dragged-refinement-steps-per-frame
    • 11.43.21 set-refinement-refine-per-frame
    • 11.43.22 refinement-refine-per-frame-state
    • 11.43.23 set-refine-ramachandran-angles
    • 11.43.24 set-fix-chiral-volumes-before-refinement
    • 11.43.25 check-chiral-volumes
    • 11.43.26 set-show-chiral-volume-errors-dialog
    • 11.43.27 set-secondary-structure-restraints-type
    • 11.43.28 secondary-structure-restraints-type
    • 11.43.29 imol-refinement-map
    • 11.43.30 set-imol-refinement-map
    • 11.43.31 does-residue-exist-p
    • 11.43.32 add-extra-bond-restraint
    • 11.43.33 delete-all-extra-restraints
  • 11.44 Simplex Refinement Interface
    • 11.44.1 fit-residue-range-to-map-by-simplex
    • 11.44.2 score-residue-range-fit-to-map
  • 11.45 Nomenclature Errors
    • 11.45.1 fix-nomenclature-errors
    • 11.45.2 set-nomenclature-errors-on-read
  • 11.46 Atom Info Interface
    • 11.46.1 output-atom-info-as-text
  • 11.47 Residue Environment Functions
    • 11.47.1 set-show-environment-distances
    • 11.47.2 set-show-environment-distances-bumps
    • 11.47.3 set-show-environment-distances-h-bonds
    • 11.47.4 show-environment-distances-state
    • 11.47.5 set-environment-distances-distance-limits
  • 11.48 Pointer Functions
    • 11.48.1 set-show-pointer-distances
    • 11.48.2 show-pointer-distances-state
  • 11.49 Zoom Functions
    • 11.49.1 scale-zoom
    • 11.49.2 zoom-factor
    • 11.49.3 set-smooth-scroll-do-zoom
    • 11.49.4 smooth-scroll-do-zoom
  • 11.50 CNS Data Functions
    • 11.50.1 handle-cns-data-file
    • 11.50.2 handle-cns-data-file-with-cell
  • 11.51 mmCIF Functions
    • 11.51.1 open-cif-dictionary-file-selector-dialog
  • 11.52 SHELXL Functions
    • 11.52.1 read-shelx-ins-file
    • 11.52.2 write-shelx-ins-file
  • 11.53 Validation Functions
    • 11.53.1 difference-map-peaks
    • 11.53.2 gln-asn-b-factor-outliers
  • 11.54 Ramachandran Plot Functions
    • 11.54.1 do-ramachandran-plot
    • 11.54.2 set-kleywegt-plot-n-diffs
    • 11.54.3 set-ramachandran-plot-contour-levels
    • 11.54.4 set-ramachandran-plot-background-block-size
    • 11.54.5 ramachandran-plot-differences
    • 11.54.6 ramachandran-plot-differences-by-chain
  • 11.55 Sequence View Interface
    • 11.55.1 do-sequence-view
  • 11.56 Atom Labelling
    • 11.56.1 set-brief-atom-labels
    • 11.56.2 brief-atom-labels-state
  • 11.57 Screen Rotation
    • 11.57.1 rotate-y-scene
    • 11.57.2 rotate-x-scene
    • 11.57.3 rotate-z-scene
    • 11.57.4 spin-zoom-trans
  • 11.58 Views Interface
    • 11.58.1 add-view-here
    • 11.58.2 add-view-raw
    • 11.58.3 remove-named-view
    • 11.58.4 remove-view
    • 11.58.5 add-view-description
    • 11.58.6 add-action-view
    • 11.58.7 insert-action-view-after-view
    • 11.58.8 save-views
    • 11.58.9 clear-all-views
  • 11.59 Background Colour
    • 11.59.1 set-background-colour
    • 11.59.2 redraw-background
    • 11.59.3 background-is-black-p
  • 11.60 Ligand Fitting Functions
    • 11.60.1 set-ligand-acceptable-fit-fraction
    • 11.60.2 set-ligand-cluster-sigma-level
    • 11.60.3 set-ligand-flexible-ligand-n-samples
    • 11.60.4 set-find-ligand-n-top-ligands
    • 11.60.5 set-find-ligand-mask-waters
    • 11.60.6 set-ligand-search-protein-molecule
    • 11.60.7 set-ligand-search-map-molecule
    • 11.60.8 add-ligand-search-ligand-molecule
    • 11.60.9 add-ligand-search-wiggly-ligand-molecule
    • 11.60.10 ligand-expert
    • 11.60.11 do-find-ligands-dialog
    • 11.60.12 match-ligand-atom-names
    • 11.60.13 flip-ligand
  • 11.61 Water Fitting Functions
    • 11.61.1 execute-find-waters-real
    • 11.61.2 move-waters-to-around-protein
    • 11.61.3 move-hetgroups-to-around-protein
    • 11.61.4 max-water-distance
    • 11.61.5 set-water-check-spherical-variance-limit
    • 11.61.6 set-ligand-water-to-protein-distance-limits
    • 11.61.7 set-ligand-water-n-cycles
    • 11.61.8 execute-find-blobs
  • 11.62 Bond Representation
    • 11.62.1 set-default-bond-thickness
    • 11.62.2 set-bond-thickness
    • 11.62.3 set-bond-thickness-intermediate-atoms
    • 11.62.4 set-default-representation-type
    • 11.62.5 get-default-bond-thickness
    • 11.62.6 set-draw-zero-occ-markers
    • 11.62.7 set-draw-hydrogens
    • 11.62.8 draw-hydrogens-state
    • 11.62.9 graphics-to-ca-representation
    • 11.62.10 graphics-to-ca-plus-ligands-representation
    • 11.62.11 graphics-to-bonds-no-waters-representation
    • 11.62.12 graphics-to-bonds-representation
    • 11.62.13 graphics-to-ca-plus-ligands-sec-struct-representation
    • 11.62.14 graphics-to-sec-struct-bonds-representation
    • 11.62.15 graphics-to-rainbow-representation
    • 11.62.16 graphics-to-b-factor-representation
    • 11.62.17 graphics-to-b-factor-cas-representation
    • 11.62.18 graphics-to-occupancy-representation
    • 11.62.19 graphics-molecule-bond-type
    • 11.62.20 set-b-factor-bonds-scale-factor
    • 11.62.21 change-model-molecule-representation-mode
    • 11.62.22 make-ball-and-stick
    • 11.62.23 clear-ball-and-stick
    • 11.62.24 additional-representation-by-string
    • 11.62.25 additional-representation-by-attributes
  • 11.63 Dots Representation
    • 11.63.1 dots
    • 11.63.2 set-dots-colour
    • 11.63.3 clear-dots
    • 11.63.4 clear-dots-by-name
    • 11.63.5 n-dots-sets
  • 11.64 Pep-flip Interface
    • 11.64.1 pepflip
  • 11.65 Rigid Body Refinement Interface
    • 11.65.1 rigid-body-refine-zone
    • 11.65.2 set-rigid-body-fit-acceptable-fit-fraction
  • 11.66 Add Terminal Residue Functions
    • 11.66.1 set-add-terminal-residue-immediate-addition
    • 11.66.2 add-terminal-residue
    • 11.66.3 add-terminal-residue-using-phi-psi
    • 11.66.4 set-add-terminal-residue-default-residue-type
    • 11.66.5 set-add-terminal-residue-do-post-refine
    • 11.66.6 add-terminal-residue-do-post-refine-state
  • 11.67 Delete Residues
    • 11.67.1 delete-residue-range
    • 11.67.2 delete-residue
    • 11.67.3 delete-residue-with-full-spec
    • 11.67.4 delete-residue-hydrogens
    • 11.67.5 delete-atom
    • 11.67.6 delete-residue-sidechain
    • 11.67.7 delete-hydrogens
  • 11.68 Mainchain Building Functions
    • 11.68.1 db-mainchain
  • 11.69 Rotatmer Functions
    • 11.69.1 set-rotamer-search-mode
    • 11.69.2 set-rotamer-lowest-probability
    • 11.69.3 set-rotamer-check-clashes
    • 11.69.4 auto-fit-best-rotamer
    • 11.69.5 set-auto-fit-best-rotamer-clash-flag
    • 11.69.6 n-rotamers
    • 11.69.7 set-residue-to-rotamer-number
    • 11.69.8 fill-partial-residues
  • 11.70 180 Flip Side chain
    • 11.70.1 do-180-degree-side-chain-flip
  • 11.71 Mutate Functions
    • 11.71.1 setup-mutate-auto-fit
    • 11.71.2 mutate
    • 11.71.3 mutate-base
    • 11.71.4 set-mutate-auto-fit-do-post-refine
    • 11.71.5 mutate-auto-fit-do-post-refine-state
    • 11.71.6 set-rotamer-auto-fit-do-post-refine
    • 11.71.7 rotamer-auto-fit-do-post-refine-state
    • 11.71.8 mutate-single-residue-by-serial-number
    • 11.71.9 set-residue-type-chooser-stub-state
  • 11.72 Pointer Atom Functions
    • 11.72.1 create-pointer-atom-molecule-maybe
    • 11.72.2 pointer-atom-molecule
  • 11.73 Baton Build Interface Functions
    • 11.73.1 set-baton-mode
    • 11.73.2 try-set-draw-baton
    • 11.73.3 accept-baton-position
    • 11.73.4 baton-try-another
    • 11.73.5 shorten-baton
    • 11.73.6 lengthen-baton
    • 11.73.7 baton-build-delete-last-residue
    • 11.73.8 set-baton-build-params
  • 11.74 Crosshairs Interface
    • 11.74.1 set-draw-crosshairs
  • 11.75 Edit Chi Angles
    • 11.75.1 set-find-hydrogen-torsions
    • 11.75.2 edit-chi-angles
    • 11.75.3 setup-torsion-general
  • 11.76 Masks
    • 11.76.1 mask-map-by-molecule
    • 11.76.2 set-map-mask-atom-radius
    • 11.76.3 map-mask-atom-radius
  • 11.77 check Waters Interface
    • 11.77.1 delete-checked-waters-baddies
  • 11.78 Trim
    • 11.78.1 trim-molecule-by-map
  • 11.79 External Ray-Tracing
    • 11.79.1 raster3d
    • 11.79.2 set-raster3d-bond-thickness
    • 11.79.3 set-raster3d-atom-radius
    • 11.79.4 set-raster3d-density-thickness
    • 11.79.5 set-renderer-show-atoms
    • 11.79.6 set-raster3d-bone-thickness
    • 11.79.7 set-raster3d-shadows-enabled
    • 11.79.8 set-raster3d-water-sphere
    • 11.79.9 raster-screen-shot
  • 11.80 Superposition (SSM)
    • 11.80.1 superpose
    • 11.80.2 superpose-with-chain-selection
    • 11.80.3 superpose-with-atom-selection
  • 11.81 NCS
    • 11.81.1 set-draw-ncs-ghosts
    • 11.81.2 draw-ncs-ghosts-state
    • 11.81.3 set-ncs-ghost-bond-thickness
    • 11.81.4 ncs-update-ghosts
    • 11.81.5 make-dynamically-transformed-ncs-maps
    • 11.81.6 add-ncs-matrix
    • 11.81.7 add-strict-ncs-matrix
    • 11.81.8 show-strict-ncs-state
    • 11.81.9 set-show-strict-ncs
    • 11.81.10 set-ncs-homology-level
    • 11.81.11 copy-chain
    • 11.81.12 copy-from-ncs-master-to-others
    • 11.81.13 copy-residue-range-from-ncs-master-to-others
    • 11.81.14 ncs-control-change-ncs-master-to-chain
    • 11.81.15 ncs-control-change-ncs-master-to-chain-id
    • 11.81.16 ncs-control-display-chain
  • 11.82 Helices and Strands
    • 11.82.1 place-helix-here
    • 11.82.2 place-strand-here
    • 11.82.3 place-strand-here-dialog
    • 11.82.4 find-helices
    • 11.82.5 find-strands
    • 11.82.6 find-secondary-structure
    • 11.82.7 find-secondary-structure-local
  • 11.83 New Molecule by Section Interface
    • 11.83.1 new-molecule-by-residue-type-selection
    • 11.83.2 new-molecule-by-atom-selection
    • 11.83.3 new-molecule-by-sphere-selection
  • 11.84 RNA/DNA
    • 11.84.1 ideal-nucleic-acid
    • 11.84.2 watson-crick-pair
    • 11.84.3 watson-crick-pair-for-residue-range
  • 11.85 Sequence (Assignment)
    • 11.85.1 print-sequence-chain
    • 11.85.2 assign-fasta-sequence
    • 11.85.3 assign-pir-sequence
    • 11.85.4 assign-sequence-from-file
    • 11.85.5 assign-sequence-from-string
    • 11.85.6 delete-all-sequences-from-molecule
    • 11.85.7 delete-sequence-by-chain-id
  • 11.86 Surface Interface
    • 11.86.1 do-surface
    • 11.86.2 set-transparent-electrostatic-surface
    • 11.86.3 get-electrostatic-surface-opacity
  • 11.87 FFFearing
    • 11.87.1 fffear-search
    • 11.87.2 set-fffear-angular-resolution
    • 11.87.3 fffear-angular-resolution
  • 11.88 Remote Control
    • 11.88.1 make-socket-listener-maybe
  • 11.89 Display Lists for Maps
    • 11.89.1 set-display-lists-for-maps
    • 11.89.2 display-lists-for-maps-state
  • 11.90 Browser Interface
    • 11.90.1 browser-url
    • 11.90.2 set-browser-interface
    • 11.90.3 handle-online-coot-search-request
  • 11.91 Generic Objects
    • 11.91.1 new-generic-object-number
    • 11.91.2 to-generic-object-add-line
    • 11.91.3 to-generic-object-add-dashed-line
    • 11.91.4 to-generic-object-add-point
    • 11.91.5 to-generic-object-add-display-list-handle
    • 11.91.6 set-display-generic-object
    • 11.91.7 generic-object-is-displayed-p
    • 11.91.8 generic-object-index
    • 11.91.9 number-of-generic-objects
    • 11.91.10 generic-object-info
    • 11.91.11 generic-object-has-objects-p
    • 11.91.12 close-generic-object
    • 11.91.13 is-closed-generic-object-p
    • 11.91.14 generic-object-clear
    • 11.91.15 generic-objects-gui-wrapper
  • 11.92 Molprobity Interface
    • 11.92.1 handle-read-draw-probe-dots
    • 11.92.2 handle-read-draw-probe-dots-unformatted
    • 11.92.3 set-do-probe-dots-on-rotamers-and-chis
    • 11.92.4 do-probe-dots-on-rotamers-and-chis-state
    • 11.92.5 set-do-probe-dots-post-refine
    • 11.92.6 do-probe-dots-post-refine-state
    • 11.92.7 unmangle-hydrogen-name
    • 11.92.8 set-interactive-probe-dots-molprobity-radius
    • 11.92.9 interactive-probe-dots-molprobity-radius
  • 11.93 Map Sharpening Interface
    • 11.93.1 sharpen
    • 11.93.2 set-map-sharpening-scale-limit
  • 11.94 Marking Fixed Atom Interface
    • 11.94.1 clear-all-fixed-atoms
  • 11.95 Partial Charges
    • 11.95.1 show-partial-charge-info
  • 11.96 EM interface
    • 11.96.1 scale-cell
  • 11.97 CCP4mg Interface
    • 11.97.1 write-ccp4mg-picture-description
    • 11.97.2 get-atom-colour-from-mol-no
  • 11.98 Aux functions
    • 11.98.1 laplacian
  • 11.99 SMILES
    • 11.99.1 do-smiles-gui
  • 11.100 PHENIX Support
    • 11.100.1 set-button-label-for-external-refinement
  • 11.101 Graphics Text
    • 11.101.1 place-text
    • 11.101.2 remove-text
    • 11.101.3 text-index-near-position
  • 11.102 PISA Interaction
    • 11.102.1 pisa-interaction
  • 11.103 Jiggle Fit
    • 11.103.1 fit-to-map-by-random-jiggle
  • 11.104 SBase interface
    • 11.104.1 get-sbase-monomer
  • 11.105 LSQ-improve
    • 11.105.1 lsq-improve
  • 11.106 single-model view
    • 11.106.1 single-model-view-model-number
    • 11.106.2 single-model-view-this-model-number
    • 11.106.3 single-model-view-next-model-number
    • 11.106.4 single-model-view-prev-model-number
  • 11.107 Sectionless functions
    • 11.107.1 get-write-conect-record-state
    • 11.107.2 set-write-conect-record-state
    • 11.107.3 make-and-draw-patterson
• 12 More Scripting Functions
  • 12.1 More Symmetry Functions
    • 12.1.1 get-symmetry
  • 12.2 Extra Map Functions
    • 12.2.1 map-colour-components
  • 12.3 Execute Refmac
    • 12.3.1 execute-refmac-real
  • 12.4 Dictionary Functions
    • 12.4.1 dictionaries-read
  • 12.5 Restraints Interface
    • 12.5.1 set-monomer-restraints
  • 12.6 Atom Information functions
    • 12.6.1 residue-info
    • 12.6.2 add-molecule
    • 12.6.3 clear-and-update-molecule
    • 12.6.4 active-residue
    • 12.6.5 closest-atom
    • 12.6.6 residues-near-residue
  • 12.7 Refinement with specs
    • 12.7.1 refine-zone-with-full-residue-spec-scm
  • 12.8 Water Chain Functions
    • 12.8.1 water-chain-from-shelx-ins-scm
    • 12.8.2 water-chain-scm
  • 12.9 Spin Search Functions
    • 12.9.1 spin-search
  • 12.10 protein-db
    • 12.10.1 protein-db-loops
  • 12.11 Coot's Hole implementation
    • 12.11.1 hole
  • 12.12 Drag and Drop
    • 12.12.1 handle-drag-and-drop-string
• 13 Scheme Scripting Functions
  • 13.1 cns2coot
  • 13.2 group-settings
  • 13.3 clear-backup
  • 13.4 quat-convert
  • 13.5 filter
  • 13.6 coot-gui
  • 13.7 ncs
  • 13.8 shelx
  • 13.9 what-check
  • 13.10 refmac-problems
  • 13.11 get-ebi
  • 13.12 brute-lsqman
  • 13.13 entry+do-button
  • 13.14 prodrg-import
  • 13.15 fascinating-things
  • 13.16 libcheck
  • 13.17 generic-objects
  • 13.18 fitting
  • 13.19 refmac
  • 13.20 a-rapper-gui
  • 13.21 extra-top-level
  • 13.22 raster3d-from-scheme
  • 13.23 check-for-updates
  • 13.24 mutate-from-scheme
  • 13.25 tips
  • 13.26 americanisms
  • 13.27 exercise-scm-mol
  • 13.28 remote-control
  • 13.29 coot
  • 13.30 hello
  • 13.31 parse-pisa-xml
  • 13.32 coot-utils
  • 13.33 snarf-coot-docs
  • 13.34 tips-gui
  • 13.35 background-demo
  • 13.36 coot-crash-catcher
  • 13.37 mutate-in-scheme
  • 13.38 coot-lsq
• Concept Index
• Function Index