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Table of Contents
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 Anti-aliasing
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
3.11 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 Clipping manipulation
3.16 Background colour
3.17 Unit Cell
3.18 Rotation Centre Pointer
3.18.1 Pointer Distances
3.19 Crosshairs
3.20 3D Annotations
3.21 Frame Rate
3.22 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 Refining Carbohydrates
5.1.3 Planar Peptide Restraints
5.1.4 The UNK residue type
5.1.5 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 Baton Building
5.6.1 Undo
5.6.2 Missing Skeleton
5.6.3 Building Backwards
5.7 Reversing Direction of Fragment
5.8 C
\alpha
-> Mainchain
5.9 Backbone Torsion Angles
5.10 Rotamers
5.10.1 Auto Fit Rotamer
5.10.2 De-clashing residues
5.11 Editing
\chi
Angles
5.12 Torsion General
5.12.1 Ligand Torsion angles
5.13 Pep-flip
5.14 Add Alternate Conformation
5.15 Mutation
5.15.1 Mutating DNA/RNA
5.15.2 Multiple mutations
5.15.3 Mutating to a Non-Standard Residue
5.15.4 Mutate and Autofit
5.15.5 Renumbering
5.16 Importing Lignds/Monomers
5.17 Ligand from SMILES strings
5.18 Find Ligands
5.18.1 Flexible Ligands
5.18.2 Adding Ligands to Model
5.19 Flip Ligand
5.20 Find Waters
5.20.1 Refinement Failure
5.20.2 Blobs
5.21 Add Terminal Residue
5.22 Add OXT Atom to Residue
5.23 Add Atom at Pointer
5.24 Place Helix
5.25 Building Ideal DNA and RNA
5.26 Merge Molecules
5.27 Temperature Factor for New Atoms
5.28 Applying NCS Edits
5.29 Running Refmac
5.30 Running SHELXL
5.31 Clear Pending Picks
5.32 Delete
5.33 Sequence Assignment
5.34 Building Links and Loops
5.35 Fill Partial Residues
5.36 Setting Occupancies
5.37 Fix Nomenclature Errors
5.38 Rotamer Fix Whole Protein
5.39 Refine All Waters
5.40 Moving Molecules/Ligands
5.41 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 Map Sampling
6.11 Dragged Map
6.12 Dynamic Map Sampling and Display Size
6.13 Skeletonization
6.14 Masks
6.14.1 Example
6.15 Trimming
6.16 Map Transformation
6.17 Export Map
7. Validation
7.1 Ramachandran Plots
7.2 Chiral Volumes
7.2.1 Fixing Chiral Volume Errors
7.3 Blobs: a.k.a. Unmodelled density
7.4 Check Waters by Difference Map
7.5 Check Waters via Difference Map
7.6 Molprobity Tools Interface
7.7 GLN and ASN B-factor Outliers
7.8 Validation Graphs
7.8.1 Residue Density Fit
7.8.2 Rotamer Analysis
7.8.3 Temperature Factor Variance
7.8.4 Peptide
\omega
Distortion
8. Hints and Usage Tips
8.1 Documentation
8.2 Low Resolution
8.3 Coot Droppings
8.4 Clearing Backups
8.5 Getting out of "Translate" Mode
8.6 Getting out of "Continuous Rotation" Mode
8.7 Getting out of "Label Atom Only" Mode
8.8 Button Labels
8.9 Picking
8.10 Resizing View
8.11 Scroll-wheel
8.12 Slow Computer Configuration
9. Other Programs
9.1 findligand
10. Scripting Functions
10.1 The Virtual Trackball
10.1.1 vt-surface
10.1.2 vt-surface-status
10.2 File System Functions
10.2.1 make-directory-maybe
10.2.2 set-show-paths-in-display-manager
10.2.3 show-paths-in-display-manager-state
10.2.4 add-coordinates-glob-extension
10.2.5 add-data-glob-extension
10.2.6 add-dictionary-glob-extension
10.2.7 add-map-glob-extension
10.2.8 remove-coordinates-glob-extension
10.2.9 remove-data-glob-extension
10.2.10 remove-dictionary-glob-extension
10.2.11 remove-map-glob-extension
10.2.12 set-sticky-sort-by-date
10.2.13 unset-sticky-sort-by-date
10.2.14 set-filter-fileselection-filenames
10.2.15 filter-fileselection-filenames-state
10.3 Widget Utilities
10.3.1 info-dialog
10.4 MTZ and data handling utilities
10.4.1 manage-column-selector
10.5 Molecule Info Functions
10.5.1 chain-n-residues
10.5.2 resname-from-serial-number
10.5.3 seqnum-from-serial-number
10.5.4 insertion-code-from-serial-number
10.5.5 chain-id
10.5.6 n-chains
10.5.7 is-solvent-chain-p
10.5.8 sort-chains
10.5.9 copy-molecule
10.5.10 exchange-chain-ids-for-seg-ids
10.6 Library and Utility Functions
10.6.1 coot-version
10.6.2 molecule-name
10.6.3 set-molecule-name
10.6.4 coot-real-exit
10.6.5 first-coords-imol
10.6.6 first-unsaved-coords-imol
10.7 Graphics Utility Functions
10.7.1 set-do-anti-aliasing
10.7.2 do-anti-aliasing-state
10.7.3 set-do-GL-lighting
10.7.4 do-GL-lighting-state
10.7.5 use-graphics-interface-state
10.7.6 start-graphics-interface
10.7.7 reset-view
10.7.8 graphics-n-molecules
10.7.9 toggle-idle-spin-function
10.7.10 set-idle-function-rotate-angle
10.7.11 handle-read-draw-molecule
10.7.12 handle-read-draw-molecule-with-recentre
10.7.13 handle-read-draw-molecule-and-move-molecule-here
10.7.14 read-pdb
10.7.15 assign-hetatms
10.7.16 replace-fragment
10.7.17 clear-and-update-model-molecule-from-file
10.7.18 screendump-image
10.8 Interface Preferences
10.8.1 set-scroll-by-wheel-mouse
10.8.2 scroll-by-wheel-mouse-state
10.8.3 set-default-initial-contour-level-for-map
10.8.4 set-default-initial-contour-level-for-difference-map
10.8.5 print-view-matrix
10.8.6 get-view-quaternion-internal
10.8.7 set-view-quaternion
10.8.8 apply-ncs-to-view-orientation
10.8.9 set-show-origin-marker
10.8.10 show-origin-marker-state
10.8.11 hide-modelling-toolbar
10.8.12 show-modelling-toolbar
10.8.13 show-model-toolbar-all-icons
10.8.14 show-model-toolbar-main-icons
10.8.15 reattach-modelling-toolbar
10.8.16 set-model-toolbar-docked-position
10.8.17 suck-model-fit-dialog
10.8.18 add-status-bar-text
10.9 Mouse Buttons
10.9.1 set-control-key-for-rotate
10.9.2 control-key-for-rotate-state
10.9.3 blob-under-pointer-to-screen-centre
10.10 Cursor Function
10.10.1 set-pick-cursor-index
10.11 Model/Fit/Refine Functions
10.11.1 post-model-fit-refine-dialog
10.11.2 show-select-map-dialog
10.11.3 set-model-fit-refine-rotate-translate-zone-label
10.11.4 set-model-fit-refine-place-atom-at-pointer-label
10.11.5 post-other-modelling-tools-dialog
10.11.6 set-refinement-move-atoms-with-zero-occupancy
10.11.7 refinement-move-atoms-with-zero-occupancy-state
10.12 Backup Functions
10.12.1 make-backup
10.12.2 turn-off-backup
10.12.3 turn-on-backup
10.12.4 backup-state
10.12.5 set-have-unsaved-changes
10.12.6 have-unsaved-changes-p
10.12.7 set-undo-molecule
10.12.8 show-set-undo-molecule-chooser
10.12.9 set-unpathed-backup-file-names
10.12.10 unpathed-backup-file-names-state
10.13 Recover Session Function
10.13.1 recover-session
10.14 Map Functions
10.14.1 calc-phases-generic
10.14.2 map-from-mtz-by-refmac-calc-phases
10.14.3 map-from-mtz-by-calc-phases
10.14.4 set-scroll-wheel-map
10.14.5 scroll-wheel-map
10.14.6 save-previous-map-colour
10.14.7 restore-previous-map-colour
10.14.8 set-active-map-drag-flag
10.14.9 get-active-map-drag-flag
10.14.10 set-last-map-colour
10.14.11 set-map-colour
10.14.12 set-last-map-sigma-step
10.14.13 set-contour-by-sigma-step-by-mol
10.14.14 data-resolution
10.14.15 export-map
10.14.16 difference-map
10.15 Density Increment
10.15.1 set-iso-level-increment
10.15.2 set-diff-map-iso-level-increment
10.15.3 set-map-sampling-rate
10.15.4 get-map-sampling-rate
10.15.5 set-scrollable-map
10.15.6 change-contour-level
10.15.7 set-last-map-contour-level
10.15.8 set-last-map-contour-level-by-sigma
10.15.9 set-stop-scroll-diff-map
10.15.10 set-stop-scroll-iso-map
10.15.11 set-stop-scroll-iso-map-level
10.15.12 set-stop-scroll-diff-map-level
10.15.13 set-residue-density-fit-scale-factor
10.16 Density Functions
10.16.1 set-map-line-width
10.16.2 map-line-width-state
10.16.3 make-and-draw-map
10.16.4 make-and-draw-map-with-refmac-params
10.16.5 make-and-draw-map-with-reso-with-refmac-params
10.16.6 valid-labels
10.16.7 auto-read-make-and-draw-maps
10.16.8 set-auto-read-do-difference-map-too
10.16.9 auto-read-do-difference-map-too-state
10.16.10 set-auto-read-column-labels
10.16.11 set-map-radius
10.16.12 set-density-size
10.16.13 set-display-intro-string
10.16.14 get-map-radius
10.16.15 set-esoteric-depth-cue
10.16.16 esoteric-depth-cue-state
10.16.17 set-swap-difference-map-colours
10.16.18 set-map-is-difference-map
10.16.19 another-level
10.16.20 another-level-from-map-molecule-number
10.16.21 residue-density-fit-scale-factor
10.16.22 density-at-point
10.17 Parameters from map
10.17.1 mtz-hklin-for-map
10.17.2 mtz-fp-for-map
10.17.3 mtz-phi-for-map
10.17.4 mtz-weight-for-map
10.17.5 mtz-use-weight-for-map
10.18 PDB Functions
10.18.1 write-pdb-file
10.18.2 write-residue-range-to-pdb-file
10.19 Refmac Functions
10.19.1 set-refmac-counter
10.19.2 refmac-name
10.19.3 swap-map-colours
10.19.4 set-keep-map-colour-after-refmac
10.19.5 keep-map-colour-after-refmac-state
10.20 Symmetry Functions
10.20.1 set-symmetry-size
10.20.2 get-show-symmetry
10.20.3 set-show-symmetry-master
10.20.4 set-show-symmetry-molecule
10.20.5 symmetry-as-calphas
10.20.6 get-symmetry-as-calphas-state
10.20.7 set-symmetry-molecule-rotate-colour-map
10.20.8 symmetry-molecule-rotate-colour-map-state
10.20.9 has-unit-cell-state
10.20.10 save-symmetry-coords
10.20.11 new-molecule-by-symmetry
10.20.12 set-space-group
10.20.13 set-symmetry-shift-search-size
10.21 History Functions
10.21.1 print-all-history-in-scheme
10.21.2 print-all-history-in-python
10.21.3 set-console-display-commands-state
10.22 State Functions
10.22.1 save-state
10.22.2 save-state-file
10.22.3 set-save-state-file-name
10.22.4 set-run-state-file-status
10.22.5 run-state-file
10.22.6 run-state-file-maybe
10.23 Unit Cell interface
10.23.1 get-show-unit-cell
10.23.2 set-show-unit-cells-all
10.23.3 set-show-unit-cell
10.24 Colour
10.24.1 set-colour-map-rotation-on-read-pdb
10.24.2 set-colour-map-rotation-on-read-pdb-flag
10.24.3 set-colour-map-rotation-on-read-pdb-c-only-flag
10.24.4 set-colour-by-chain
10.24.5 set-colour-by-molecule
10.24.6 set-symmetry-colour
10.25 Map colour
10.25.1 set-colour-map-rotation-for-map
10.25.2 set-molecule-bonds-colour-map-rotation
10.25.3 get-molecule-bonds-colour-map-rotation
10.26 Display Functions
10.26.1 set-graphics-window-size
10.26.2 set-graphics-window-position
10.26.3 graphics-draw
10.26.4 zalman-stereo-mode
10.26.5 hardware-stereo-mode
10.26.6 stereo-mode-state
10.26.7 mono-mode
10.26.8 side-by-side-stereo-mode
10.26.9 set-hardware-stereo-angle-factor
10.26.10 hardware-stereo-angle-factor-state
10.26.11 set-model-fit-refine-dialog-position
10.26.12 set-display-control-dialog-position
10.26.13 set-go-to-atom-window-position
10.26.14 set-delete-dialog-position
10.26.15 set-rotate-translate-dialog-position
10.26.16 set-accept-reject-dialog-position
10.26.17 set-ramachandran-plot-dialog-position
10.27 Smooth Scrolling
10.27.1 set-smooth-scroll-flag
10.27.2 get-smooth-scroll
10.27.3 set-smooth-scroll-steps
10.27.4 set-smooth-scroll-limit
10.28 Font Size
10.28.1 set-font-size
10.28.2 get-font-size
10.28.3 set-font-colour
10.29 Atom Selection Utilities
10.29.1 set-default-temperature-factor-for-new-atoms
10.29.2 default-new-atoms-b-factor
10.29.3 set-reset-b-factor-moved-atoms
10.29.4 get-reset-b-factor-moved-atoms-state
10.29.5 set-atom-attribute
10.29.6 set-atom-string-attribute
10.30 Skeletonization Interface
10.30.1 skeletonize-map
10.30.2 unskeletonize-map
10.30.3 set-max-skeleton-search-depth
10.30.4 set-skeleton-box-size
10.31 Read Maps
10.31.1 handle-read-ccp4-map
10.32 Save Coordinates
10.32.1 save-coordinates
10.33 Read Phases File Functions
10.33.1 read-phs-and-coords-and-make-map
10.33.2 read-phs-and-make-map-using-cell-symm-from-previous-mol
10.33.3 read-phs-and-make-map-using-cell-symm-from-mol
10.33.4 read-phs-and-make-map-using-cell-symm
10.33.5 read-phs-and-make-map-with-reso-limits
10.34 Graphics Move
10.34.1 undo-last-move
10.34.2 translate-molecule-by
10.34.3 transform-molecule-by
10.35 Go To Atom Widget Functions
10.35.1 post-go-to-atom-window
10.35.2 set-go-to-atom-chain-residue-atom-name
10.35.3 update-go-to-atom-from-current-position
10.35.4 atom-spec-to-atom-index
10.35.5 full-atom-spec-to-atom-index
10.35.6 update-go-to-atom-window-on-changed-mol
10.35.7 update-go-to-atom-window-on-new-mol
10.35.8 set-go-to-atom-molecule
10.36 Map and Molecule Control
10.36.1 post-display-control-window
10.36.2 set-map-displayed
10.36.3 set-mol-displayed
10.36.4 set-mol-active
10.36.5 mol-is-displayed
10.36.6 mol-is-active
10.36.7 map-is-displayed
10.36.8 set-all-maps-displayed
10.36.9 set-all-models-displayed-and-active
10.36.10 show-spacegroup
10.37 Renumber Residue Range
10.37.1 renumber-residue-range
10.37.2 change-residue-number
10.38 Scripting Interface
10.38.1 post-scripting-window
10.38.2 post-scheme-scripting-window
10.38.3 post-python-scripting-window
10.39 Monomer
10.39.1 get-monomer
10.39.2 run-script
10.40 Regularization and Refinement
10.40.1 add-planar-peptide-restraints
10.40.2 remove-planar-peptide-restraints
10.40.3 add-omega-torsion-restriants
10.40.4 remove-omega-torsion-restriants
10.40.5 set-refinement-immediate-replacement
10.40.6 refinement-immediate-replacement-state
10.40.7 set-residue-selection-flash-frames-number
10.40.8 accept-regularizement
10.40.9 set-refine-with-torsion-restraints
10.40.10 refine-with-torsion-restraints-state
10.40.11 set-matrix
10.40.12 matrix-state
10.40.13 set-refine-auto-range-step
10.40.14 set-refine-max-residues
10.40.15 refine-zone-atom-index-define
10.40.16 refine-zone
10.40.17 refine-zone-with-full-residue-spec
10.40.18 refine-auto-range
10.40.19 regularize-zone
10.40.20 set-dragged-refinement-steps-per-frame
10.40.21 dragged-refinement-steps-per-frame
10.40.22 set-refinement-refine-per-frame
10.40.23 refinement-refine-per-frame-state
10.40.24 set-refine-ramachandran-angles
10.40.25 set-fix-chiral-volumes-before-refinement
10.40.26 check-chiral-volumes
10.40.27 set-show-chiral-volume-errors-dialog
10.40.28 set-secondary-structure-restraints-type
10.40.29 secondary-structure-restraints-type
10.40.30 imol-refinement-map
10.40.31 set-imol-refinement-map
10.40.32 does-residue-exist-p
10.41 Simplex Refinement Interface
10.41.1 fit-residue-range-to-map-by-simplex
10.41.2 score-residue-range-fit-to-map
10.42 Nomenclature Errors
10.42.1 fix-nomenclature-errors
10.43 Atom Info Interface
10.43.1 output-atom-info-as-text
10.44 Zoom Functions
10.44.1 scale-zoom
10.44.2 zoom-factor
10.44.3 set-smooth-scroll-do-zoom
10.44.4 smooth-scroll-do-zoom
10.45 CNS Data Functions
10.45.1 handle-cns-data-file
10.45.2 handle-cns-data-file-with-cell
10.46 SHELXL Functions
10.46.1 read-shelx-ins-file
10.46.2 write-shelx-ins-file
10.47 Validation Functions
10.47.1 difference-map-peaks
10.47.2 gln-asn-b-factor-outliers
10.48 Ramachandran Plot Functions
10.48.1 do-ramachandran-plot
10.48.2 set-kleywegt-plot-n-diffs
10.48.3 set-ramachandran-plot-contour-levels
10.48.4 set-ramachandran-plot-background-block-size
10.48.5 ramachandran-plot-differences
10.48.6 ramachandran-plot-differences-by-chain
10.49 Sequence View Interface
10.49.1 do-sequence-view
10.50 Atom Labelling
10.50.1 set-brief-atom-labels
10.50.2 brief-atom-labels-state
10.51 Screen Rotation
10.51.1 rotate-y-scene
10.51.2 rotate-x-scene
10.51.3 rotate-z-scene
10.51.4 spin-zoom-trans
10.52 Background Colour
10.52.1 set-background-colour
10.52.2 redraw-background
10.52.3 background-is-black-p
10.53 Ligand Fitting Functions
10.53.1 set-ligand-acceptable-fit-fraction
10.53.2 set-ligand-cluster-sigma-level
10.53.3 set-ligand-flexible-ligand-n-samples
10.53.4 set-find-ligand-n-top-ligands
10.53.5 set-find-ligand-mask-waters
10.53.6 set-ligand-search-protein-molecule
10.53.7 set-ligand-search-map-molecule
10.53.8 add-ligand-search-ligand-molecule
10.53.9 add-ligand-search-wiggly-ligand-molecule
10.53.10 ligand-expert
10.53.11 do-find-ligands-dialog
10.53.12 execute-get-mols-ligand-search
10.53.13 flip-ligand
10.54 Water Fitting Functions
10.54.1 execute-find-waters-real
10.54.2 set-ligand-water-to-protein-distance-limits
10.54.3 set-ligand-water-n-cycles
10.54.4 execute-find-blobs
10.55 Bond Representation
10.55.1 set-default-bond-thickness
10.55.2 set-bond-thickness
10.55.3 set-bond-thickness-intermediate-atoms
10.55.4 get-default-bond-thickness
10.55.5 set-draw-zero-occ-markers
10.55.6 set-draw-hydrogens
10.55.7 draw-hydrogens-state
10.55.8 graphics-to-ca-representation
10.55.9 graphics-to-ca-plus-ligands-representation
10.55.10 graphics-to-bonds-no-waters-representation
10.55.11 graphics-to-bonds-representation
10.55.12 graphics-to-ca-plus-ligands-sec-struct-representation
10.55.13 graphics-to-sec-struct-bonds-representation
10.55.14 graphics-to-rainbow-representation
10.55.15 graphics-to-b-factor-representation
10.55.16 graphics-to-b-factor-cas-representation
10.55.17 graphics-to-occupancy-representation
10.55.18 graphics-molecule-bond-type
10.55.19 set-b-factor-bonds-scale-factor
10.55.20 make-ball-and-stick
10.55.21 clear-ball-and-stick
10.56 Dots Representation
10.56.1 dots
10.56.2 clear-dots
10.56.3 n-dots-sets
10.57 Pep-flip Interface
10.57.1 pepflip
10.58 Rigid Body Refinement Interface
10.58.1 rigid-body-refine-zone
10.58.2 set-rigid-body-fit-acceptable-fit-fraction
10.59 Add Terminal Residue Functions
10.59.1 set-add-terminal-residue-immediate-addition
10.59.2 add-terminal-residue
10.59.3 set-add-terminal-residue-default-residue-type
10.59.4 set-add-terminal-residue-do-post-refine
10.59.5 add-terminal-residue-do-post-refine-state
10.60 Delete Residues
10.60.1 delete-residue-range
10.60.2 delete-residue
10.60.3 delete-residue-with-altconf
10.60.4 delete-residue-hydrogens
10.60.5 delete-atom
10.60.6 delete-residue-sidechain
10.61 Mainchain Building Functions
10.61.1 db-mainchain
10.62 Rotatmer Functions
10.62.1 set-rotamer-lowest-probability
10.62.2 set-rotamer-check-clashes
10.62.3 auto-fit-best-rotamer
10.62.4 set-auto-fit-best-rotamer-clash-flag
10.62.5 n-rotamers
10.62.6 set-residue-to-rotamer-number
10.62.7 fill-partial-residues
10.63 180 Flip Side chain
10.63.1 do-180-degree-side-chain-flip
10.64 Mutate Functions
10.64.1 setup-mutate-auto-fit
10.64.2 mutate
10.64.3 mutate-base
10.64.4 set-mutate-auto-fit-do-post-refine
10.64.5 mutate-auto-fit-do-post-refine-state
10.64.6 set-rotamer-auto-fit-do-post-refine
10.64.7 rotamer-auto-fit-do-post-refine-state
10.64.8 mutate-single-residue-by-serial-number
10.64.9 set-residue-type-chooser-stub-state
10.65 Baton Build Interface Functions
10.65.1 set-baton-mode
10.65.2 set-draw-baton
10.65.3 accept-baton-position
10.65.4 baton-try-another
10.65.5 shorten-baton
10.65.6 lengthen-baton
10.65.7 baton-build-delete-last-residue
10.65.8 set-baton-build-params
10.66 Crosshairs Interface
10.66.1 set-draw-crosshairs
10.67 Edit Chi Angles
10.67.1 set-find-hydrogen-torsions
10.67.2 edit-chi-angles
10.67.3 setup-torsion-general
10.68 Masks
10.68.1 mask-map-by-molecule
10.68.2 set-map-mask-atom-radius
10.68.3 map-mask-atom-radius
10.69 check Waters Interface
10.69.1 delete-checked-waters-baddies
10.70 Trim
10.70.1 trim-molecule-by-map
10.71 External Ray-Tracing
10.71.1 raster3d
10.71.2 set-raster3d-bond-thickness
10.71.3 set-raster3d-atom-radius
10.71.4 set-raster3d-density-thickness
10.71.5 set-renderer-show-atoms
10.71.6 set-raster3d-bone-thickness
10.71.7 set-raster3d-shadows-enabled
10.71.8 raster-screen-shot
10.72 Superposition (SSM)
10.72.1 superpose
10.72.2 superpose-with-chain-selection
10.72.3 superpose-with-atom-selection
10.73 NCS
10.73.1 set-draw-ncs-ghosts
10.73.2 draw-ncs-ghosts-state
10.73.3 set-ncs-ghost-bond-thickness
10.73.4 ncs-update-ghosts
10.73.5 make-dynamically-transformed-ncs-maps
10.73.6 add-ncs-matrix
10.73.7 add-strict-ncs-matrix
10.73.8 show-strict-ncs-state
10.73.9 set-show-strict-ncs
10.73.10 set-ncs-homology-level
10.73.11 copy-chain
10.73.12 copy-from-ncs-master-to-others
10.73.13 copy-residue-range-from-ncs-master-to-others
10.73.14 ncs-control-change-ncs-master-to-chain
10.73.15 ncs-control-change-ncs-master-to-chain-id
10.73.16 ncs-control-display-chain
10.74 Helices and Strands
10.74.1 place-helix-here
10.74.2 place-strand-here
10.74.3 find-helices
10.74.4 find-strands
10.74.5 find-secondary-structure
10.74.6 find-secondary-structure-local
10.75 RNA/DNA
10.75.1 ideal-nucleic-acid
10.75.2 watson-crick-pair
10.76 Sequence (Assignment)
10.76.1 print-sequence-chain
10.76.2 assign-fasta-sequence
10.76.3 assign-pir-sequence
10.76.4 assign-sequence-from-file
10.76.5 assign-sequence-from-string
10.76.6 delete-all-sequences-from-molecule
10.76.7 delete-sequence-by-chain-id
10.77 Surfaces
10.77.1 do-surface
10.78 FFFearing
10.78.1 fffear-search
10.78.2 set-fffear-angular-resolution
10.78.3 fffear-angular-resolution
10.79 Remote Control
10.79.1 make-socket-listener-maybe
10.80 Browser Interface
10.80.1 browser-url
10.80.2 set-browser-interface
10.80.3 handle-online-coot-search-request
10.81 Generic Objects
10.81.1 new-generic-object-number
10.81.2 to-generic-object-add-line
10.81.3 to-generic-object-add-dashed-line
10.81.4 to-generic-object-add-point
10.81.5 to-generic-object-add-display-list-handle
10.81.6 set-display-generic-object
10.81.7 generic-object-is-displayed-p
10.81.8 generic-object-index
10.81.9 number-of-generic-objects
10.81.10 generic-object-info
10.81.11 generic-object-has-objects-p
10.81.12 close-generic-object
10.81.13 is-closed-generic-object-p
10.81.14 generic-object-clear
10.81.15 generic-objects-gui-wrapper
10.82 Molprobity Interface
10.82.1 handle-read-draw-probe-dots
10.82.2 handle-read-draw-probe-dots-unformatted
10.82.3 set-do-probe-dots-on-rotamers-and-chis
10.82.4 do-probe-dots-on-rotamers-and-chis-state
10.82.5 set-do-probe-dots-post-refine
10.82.6 do-probe-dots-post-refine-state
10.82.7 unmangle-hydrogen-name
10.82.8 set-interactive-probe-dots-molprobity-radius
10.82.9 interactive-probe-dots-molprobity-radius
10.82.10 probe-available-p
10.83 Map Sharpening Interface
10.83.1 sharpen
10.83.2 set-map-sharpening-scale-limit
10.84 Marking Fixed Atom Interface
10.84.1 clear-all-fixed-atoms
10.85 Partial Charges
10.85.1 show-partial-charge-info
10.86 EM interface
10.86.1 scale-cell
10.87 CCP4mg Interface
10.87.1 write-ccp4mg-picture-description
10.87.2 get-atom-colour-from-mol-no
10.88 Aux functions
10.88.1 laplacian
10.89 SMILES
10.89.1 do-smiles-gui
10.90 PHENIX Support
10.90.1 set-button-label-for-external-refinement
10.91 Graphics Text
10.91.1 place-text
10.91.2 remove-text
Index
This document was generated by
Paul Emsley
on
June, 6 2009
using
texi2html