MolViewSpec tree schema v1

This is the exhaustive list of MolViewSpec node kinds, their parameters, and parent-child relationships. Parameters with ?: are optional, i.e. they may be omitted, meaning that the default value should be used. Parameters with : are required, i.e. omitting them will result in an invalid MolViewSpec tree.

This specification is formalized by the OpenAPI JSON schema.

(This document was auto-generated by node lib/commonjs/cli/mvs/mvs-print-schema --markdown in Mol*.)

root

[Root of the tree must be of this kind]

Auxiliary node kind that only appears as the tree root.

Parent: none

Params:

download

This node instructs to retrieve a data resource.

Parent: root

Params:

• url:string

  URL of the data resource.

parse

This node instructs to parse a data resource.

Parent: download

Params:

• format:"mmcif" | "bcif" | "pdb" | "pdbqt" | "gro" | "xyz" | "mol" | "sdf" | "mol2" | "lammpstrj" | "xtc" | "nctraj" | "dcd" | "trr" | "psf" | "prmtop" | "top" | "map" | "dx" | "dxbin"

  Format of the input data resource.

coordinates

This node instructs to retrieve molecular coordinates from a parsed data resource.

Parent: parse

Params:

structure

This node instructs to create a structure from a parsed data resource. “Structure” refers to an internal representation of molecular coordinates without any visual representation.

Parent: parse

Params:

• type:"model" | "assembly" | "symmetry" | "symmetry_mates"

  Type of structure to be created ("model" for original model coordinates, "assembly" for assembly structure, "symmetry" for a set of crystal unit cells based on Miller indices, "symmetry_mates" for a set of asymmetric units within a radius from the original model).

• block_header?:string | null

  Header of the CIF block to read coordinates from (only applies when the input data are from CIF or BinaryCIF). If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read coordinates from (only applies when the input data are from CIF or BinaryCIF and block_header is null).

  Default: 0

• model_index?:Integer

  0-based index of model in case the input data contain multiple models.

  Default: 0

• assembly_id?:string | null

  Assembly identifier (only applies when kind is "assembly"). If null, the first assembly is selected.

  Default: null

• radius?:number

  Distance (in Angstroms) from the original model in which asymmetric units should be included (only applies when kind is "symmetry_mates").

  Default: 5

• ijk_min?:[Integer, Integer, Integer]

  Miller indices of the bottom-left unit cell to be included (only applies when kind is "symmetry").

  Default: [-1, -1, -1]

• ijk_max?:[Integer, Integer, Integer]

  Miller indices of the top-right unit cell to be included (only applies when kind is "symmetry").

  Default: [1, 1, 1]

• coordinates_ref?:string | null

  Reference to a specific set of coordinates.

  Default: null

transform

This node instructs to rotate and/or translate coordinates OR provide a transformation matrix.

Parent: structure or component or volume

Params:

• rotation?:Array<number>

  Rotation matrix (3x3 matrix flattened in column major format (j*3+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. The default value is the identity matrix (corresponds to no rotation).

  Default: [1, 0, 0, 0, 1, 0, 0, 0, 1]

• translation?:[number, number, number]

  Translation vector, applied to the structure coordinates after rotation. The default value is the zero vector (corresponds to no translation).

  Default: [0, 0, 0]

• rotation_center?:[number, number, number] | "centroid" | null

  Point to rotate the object around. Can be either a 3D vector or dynamically computed object centroid.

  Default: null

• matrix?:Array<number> | null

  Transform matrix (4x4 matrix flattened in column major format (j*4+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. Takes precedence over rotation and translation.

  Default: null

instance

This node allows instantiation using the provided transformation parameters.

Parent: structure or component or volume

Params:

• rotation?:Array<number>

  Rotation matrix (3x3 matrix flattened in column major format (j*3+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. The default value is the identity matrix (corresponds to no rotation).

  Default: [1, 0, 0, 0, 1, 0, 0, 0, 1]

• translation?:[number, number, number]

  Translation vector, applied to the structure coordinates after rotation. The default value is the zero vector (corresponds to no translation).

  Default: [0, 0, 0]

• rotation_center?:[number, number, number] | "centroid" | null

  Point to rotate the object around. Can be either a 3D vector or dynamically computed object centroid.

  Default: null

• matrix?:Array<number> | null

  Transform matrix (4x4 matrix flattened in column major format (j*4+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. Takes precedence over rotation and translation.

  Default: null

component

This node instructs to create a component (i.e. a subset of the parent structure).

Parent: structure

Params:

• selector:("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water" | "coarse") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>

  Defines what part of the parent structure should be included in this component.

component_from_uri

This node instructs to create a component defined by an external annotation resource.

Parent: structure

Params:

• uri:string

  URL of the annotation resource.

• format:"cif" | "bcif" | "json"

  Format of the annotation resource.

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the component identifier.

  Default: "component"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

• field_values?:Array<string> | null

  List of component identifiers (i.e. values in the field given by field_name) which should be included in this component. If null, component identifiers are ignored (all annotation rows are included), and field_name field can be dropped from the annotation.

  Default: null

component_from_source

This node instructs to create a component defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: structure

Params:

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from. If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from. If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the component identifier.

  Default: "component"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

• field_values?:Array<string> | null

  List of component identifiers (i.e. values in the field given by field_name) which should be included in this component. If null, component identifiers are ignored (all annotation rows are included), and field_name field can be dropped from the annotation.

  Default: null

representation

This node instructs to create a visual representation of a component.

Parent: component or component_from_uri or component_from_source

Params:

• type:cartoon | backbone | ball_and_stick | line | spacefill | carbohydrate | surface

  Representation type

  [This parameter determines the rest of parameters]

  Case type: "cartoon":

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  • tubular_helices?:boolean

    Simplify corkscrew helices to tubes.

    Default: false

  Case type: "backbone":

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  Case type: "ball_and_stick":

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  • ignore_hydrogens?:boolean

    Controls whether hydrogen atoms are drawn.

    Default: false

  Case type: "line":

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  • ignore_hydrogens?:boolean

    Controls whether hydrogen atoms are drawn.

    Default: false

  Case type: "spacefill":

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  • ignore_hydrogens?:boolean

    Controls whether hydrogen atoms are drawn.

    Default: false

  Case type: "carbohydrate":

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  Case type: "surface":

  • surface_type?:"molecular" | "gaussian"

    Type of surface representation. (Default is ‘molecular’)

    Default: "molecular"

  • size_factor?:number

    Scales the corresponding visuals.

    Default: 1

  • ignore_hydrogens?:boolean

    Controls whether hydrogen atoms are drawn.

    Default: false

volume

This node instructs to create a volume from a parsed data resource. “Volume” refers to an internal representation of volumetric data without any visual representation.

Parent: parse

Params:

• channel_id?:string | null

  Channel identifier (only applies when the input data contain multiple channels).

  Default: null

volume_representation

This node instructs to create a visual representation of a volume.

Parent: volume

Params:

• type:isosurface | grid_slice

  Representation type

  [This parameter determines the rest of parameters]

  Case type: "isosurface":

  • relative_isovalue?:number | null

    Relative isovalue.

    Default: null

  • absolute_isovalue?:number | null

    Absolute isovalue. Overrides relative_isovalue.

    Default: null

  • show_wireframe?:boolean

    Show mesh wireframe. Defaults to false.

    Default: false

  • show_faces?:boolean

    Show mesh faces. Defaults to true.

    Default: true

  Case type: "grid_slice":

  • dimension:"x" | "y" | "z"

    Dimension of the grid slice, i.e. ‘x’, ‘y’, or ‘z’.

  • absolute_index?:Integer | null

    Index of the grid slice in the specified dimension. 0-based index, i.e. 0 is the first slice.

    Default: null

  • relative_index?:number | null

    Relative index of the grid slice in the specified dimension. 0.0 is the first slice, 1.0 is the last slice. Overrides absolute_index.

    Default: null

  • relative_isovalue?:number | null

    Relative isovalue.

    Default: null

  • absolute_isovalue?:number | null

    Absolute isovalue. Overrides relative_isovalue.

    Default: null

color

This node instructs to apply color to a visual representation.

Parent: representation or volume_representation

Params:

• color?:ColorName | HexColor

  Color to apply to the representation. Can be either an X11 color name (e.g. "red") or a hexadecimal code (e.g. "#FF0011").

  Default: "white"

• selector?:("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water" | "coarse") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>

  Defines to what part of the representation this color should be applied.

  Default: "all"

color_from_uri

This node instructs to apply colors to a visual representation. The colors are defined by an external annotation resource.

Parent: representation

Params:

• uri:string

  URL of the annotation resource.

• format:"cif" | "bcif" | "json"

  Format of the annotation resource.

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the color.

  Default: "color"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

• palette?:{ kind: "categorical", colors?: (("Reds" | "Oranges" | "Greens" | "Blues" | "Purples" | "Greys" | "OrRd" | "BuGn" | "PuBuGn" | "GnBu" | "PuBu" | "BuPu" | "RdPu" | "PuRd" | "YlOrRd" | "YlOrBr" | "YlGn" | "YlGnBu" | "Magma" | "Inferno" | "Plasma" | "Viridis" | "Cividis" | "Turbo" | "Warm" | "Cool" | "CubehelixDefault" | "Rainbow" | "Sinebow" | "RdBu" | "RdGy" | "PiYG" | "BrBG" | "PRGn" | "PuOr" | "RdYlGn" | "RdYlBu" | "Spectral" | "Category10" | "Observable10" | "Tableau10" | "Set1" | "Set2" | "Set3" | "Pastel1" | "Pastel2" | "Dark2" | "Paired" | "Accent" | "Chainbow") | ("ElementSymbol" | "ResidueName" | "ResidueProperties" | "SecondaryStructure") | Array<(ColorName | HexColor)> | { [K in string]: (ColorName | HexColor) }), repeat_color_list?: boolean, sort?: ("none" | "lexical" | "numeric"), sort_direction?: ("ascending" | "descending"), case_insensitive?: boolean, missing_color?: (ColorName | HexColor | null) } | { kind: "discrete", colors?: (("Reds" | "Oranges" | "Greens" | "Blues" | "Purples" | "Greys" | "OrRd" | "BuGn" | "PuBuGn" | "GnBu" | "PuBu" | "BuPu" | "RdPu" | "PuRd" | "YlOrRd" | "YlOrBr" | "YlGn" | "YlGnBu" | "Magma" | "Inferno" | "Plasma" | "Viridis" | "Cividis" | "Turbo" | "Warm" | "Cool" | "CubehelixDefault" | "Rainbow" | "Sinebow" | "RdBu" | "RdGy" | "PiYG" | "BrBG" | "PRGn" | "PuOr" | "RdYlGn" | "RdYlBu" | "Spectral" | "Category10" | "Observable10" | "Tableau10" | "Set1" | "Set2" | "Set3" | "Pastel1" | "Pastel2" | "Dark2" | "Paired" | "Accent" | "Chainbow") | Array<(ColorName | HexColor)> | Array<[(ColorName | HexColor), number]> | Array<[(ColorName | HexColor | null), (number | null), (number | null)]>), reverse?: boolean, mode?: ("normalized" | "absolute"), value_domain?: [(number | null), (number | null)] } | { kind: "continuous", colors?: (("Reds" | "Oranges" | "Greens" | "Blues" | "Purples" | "Greys" | "OrRd" | "BuGn" | "PuBuGn" | "GnBu" | "PuBu" | "BuPu" | "RdPu" | "PuRd" | "YlOrRd" | "YlOrBr" | "YlGn" | "YlGnBu" | "Magma" | "Inferno" | "Plasma" | "Viridis" | "Cividis" | "Turbo" | "Warm" | "Cool" | "CubehelixDefault" | "Rainbow" | "Sinebow" | "RdBu" | "RdGy" | "PiYG" | "BrBG" | "PRGn" | "PuOr" | "RdYlGn" | "RdYlBu" | "Spectral" | "Category10" | "Observable10" | "Tableau10" | "Set1" | "Set2" | "Set3" | "Pastel1" | "Pastel2" | "Dark2" | "Paired" | "Accent" | "Chainbow") | Array<(ColorName | HexColor)> | Array<[(ColorName | HexColor), number]>), reverse?: boolean, mode?: ("normalized" | "absolute"), value_domain?: [(number | null), (number | null)], underflow_color?: ("auto" | ColorName | HexColor | null), overflow_color?: ("auto" | ColorName | HexColor | null) } | null

  Customize mapping of annotation values to colors.

  Default: null

• selector?:("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water" | "coarse") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>

  Defines to what part of the representation this coloring should be applied.

  Default: "all"

color_from_source

This node instructs to apply colors to a visual representation. The colors are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: representation

Params:

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from. If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from. If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the color.

  Default: "color"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

• palette?:{ kind: "categorical", colors?: (("Reds" | "Oranges" | "Greens" | "Blues" | "Purples" | "Greys" | "OrRd" | "BuGn" | "PuBuGn" | "GnBu" | "PuBu" | "BuPu" | "RdPu" | "PuRd" | "YlOrRd" | "YlOrBr" | "YlGn" | "YlGnBu" | "Magma" | "Inferno" | "Plasma" | "Viridis" | "Cividis" | "Turbo" | "Warm" | "Cool" | "CubehelixDefault" | "Rainbow" | "Sinebow" | "RdBu" | "RdGy" | "PiYG" | "BrBG" | "PRGn" | "PuOr" | "RdYlGn" | "RdYlBu" | "Spectral" | "Category10" | "Observable10" | "Tableau10" | "Set1" | "Set2" | "Set3" | "Pastel1" | "Pastel2" | "Dark2" | "Paired" | "Accent" | "Chainbow") | ("ElementSymbol" | "ResidueName" | "ResidueProperties" | "SecondaryStructure") | Array<(ColorName | HexColor)> | { [K in string]: (ColorName | HexColor) }), repeat_color_list?: boolean, sort?: ("none" | "lexical" | "numeric"), sort_direction?: ("ascending" | "descending"), case_insensitive?: boolean, missing_color?: (ColorName | HexColor | null) } | { kind: "discrete", colors?: (("Reds" | "Oranges" | "Greens" | "Blues" | "Purples" | "Greys" | "OrRd" | "BuGn" | "PuBuGn" | "GnBu" | "PuBu" | "BuPu" | "RdPu" | "PuRd" | "YlOrRd" | "YlOrBr" | "YlGn" | "YlGnBu" | "Magma" | "Inferno" | "Plasma" | "Viridis" | "Cividis" | "Turbo" | "Warm" | "Cool" | "CubehelixDefault" | "Rainbow" | "Sinebow" | "RdBu" | "RdGy" | "PiYG" | "BrBG" | "PRGn" | "PuOr" | "RdYlGn" | "RdYlBu" | "Spectral" | "Category10" | "Observable10" | "Tableau10" | "Set1" | "Set2" | "Set3" | "Pastel1" | "Pastel2" | "Dark2" | "Paired" | "Accent" | "Chainbow") | Array<(ColorName | HexColor)> | Array<[(ColorName | HexColor), number]> | Array<[(ColorName | HexColor | null), (number | null), (number | null)]>), reverse?: boolean, mode?: ("normalized" | "absolute"), value_domain?: [(number | null), (number | null)] } | { kind: "continuous", colors?: (("Reds" | "Oranges" | "Greens" | "Blues" | "Purples" | "Greys" | "OrRd" | "BuGn" | "PuBuGn" | "GnBu" | "PuBu" | "BuPu" | "RdPu" | "PuRd" | "YlOrRd" | "YlOrBr" | "YlGn" | "YlGnBu" | "Magma" | "Inferno" | "Plasma" | "Viridis" | "Cividis" | "Turbo" | "Warm" | "Cool" | "CubehelixDefault" | "Rainbow" | "Sinebow" | "RdBu" | "RdGy" | "PiYG" | "BrBG" | "PRGn" | "PuOr" | "RdYlGn" | "RdYlBu" | "Spectral" | "Category10" | "Observable10" | "Tableau10" | "Set1" | "Set2" | "Set3" | "Pastel1" | "Pastel2" | "Dark2" | "Paired" | "Accent" | "Chainbow") | Array<(ColorName | HexColor)> | Array<[(ColorName | HexColor), number]>), reverse?: boolean, mode?: ("normalized" | "absolute"), value_domain?: [(number | null), (number | null)], underflow_color?: ("auto" | ColorName | HexColor | null), overflow_color?: ("auto" | ColorName | HexColor | null) } | null

  Customize mapping of annotation values to colors.

  Default: null

• selector?:("all" | "polymer" | "protein" | "nucleic" | "branched" | "ligand" | "ion" | "water" | "coarse") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>

  Defines to what part of the representation this coloring should be applied.

  Default: "all"

clip

This node instructs to apply clipping to a visual representation.

Parent: representation or volume_representation or primitives or primitives_from_uri

Params:

• type:plane | sphere | box

  Clip type

  [This parameter determines the rest of parameters]

  Case type: "plane":

  • check_transform?:Array<number> | null

    Transformation matrix to applied to each point before clipping. For example, can be used to clip volumes in the grid/fractional space. Default is null.

    Default: null

  • invert?:boolean

    Inverts the clipping region. Default is false

    Default: false

  • variant?:"object" | "pixel"

    Variant of the clip node, either “object” or “pixel”

    Default: "pixel"

  • normal:[number, number, number]

    Normal vector of the clipping plane.

  • point:[number, number, number]

    Point on the clipping plane.

  Case type: "sphere":

  • check_transform?:Array<number> | null

    Transformation matrix to applied to each point before clipping. For example, can be used to clip volumes in the grid/fractional space. Default is null.

    Default: null

  • invert?:boolean

    Inverts the clipping region. Default is false

    Default: false

  • variant?:"object" | "pixel"

    Variant of the clip node, either “object” or “pixel”

    Default: "pixel"

  • center:[number, number, number]

    Center of the clipping sphere.

  • radius?:number

    Radius of the clipping sphere.

    Default: 1

  Case type: "box":

  • check_transform?:Array<number> | null

    Transformation matrix to applied to each point before clipping. For example, can be used to clip volumes in the grid/fractional space. Default is null.

    Default: null

  • invert?:boolean

    Inverts the clipping region. Default is false

    Default: false

  • variant?:"object" | "pixel"

    Variant of the clip node, either “object” or “pixel”

    Default: "pixel"

  • center:[number, number, number]

    Center of the clipping box.

  • size?:[number, number, number]

    Size of the clipping box.

    Default: [1, 1, 1]

  • rotation?:Array<number>

    Rotation matrix (3x3 matrix flattened in column major format (j*3+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. The default value is the identity matrix (corresponds to no rotation).

    Default: [1, 0, 0, 0, 1, 0, 0, 0, 1]

opacity

This node instructs to apply opacity/transparency to a visual representation.

Parent: representation or volume_representation

Params:

• opacity:number

  Opacity of a representation. 0.0: fully transparent, 1.0: fully opaque.

label

This node instructs to add a label (textual visual representation) to a component.

Parent: component or component_from_uri or component_from_source

Params:

• text:string

  Content of the shown label.

label_from_uri

This node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an external annotation resource.

Parent: structure

Params:

• uri:string

  URL of the annotation resource.

• format:"cif" | "bcif" | "json"

  Format of the annotation resource.

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the label text.

  Default: "label"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

label_from_source

This node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: structure

Params:

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from. If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from. If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the label text.

  Default: "label"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

tooltip

This node instructs to add a tooltip to a component. “Tooltip” is a text which is not a part of the visualization but should be presented to the users when they interact with the component (typically, the tooltip will be shown somewhere on the screen when the user hovers over a visual representation of the component).

Parent: component or component_from_uri or component_from_source

Params:

• text:string

  Content of the shown tooltip.

tooltip_from_uri

This node instructs to add tooltips to parts of a structure. The tooltips are defined by an external annotation resource.

Parent: structure

Params:

• uri:string

  URL of the annotation resource.

• format:"cif" | "bcif" | "json"

  Format of the annotation resource.

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from (only applies when format is "cif" or "bcif"). If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when format is "cif" or "bcif" and block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from (only applies when format is "cif" or "bcif"). If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the tooltip text.

  Default: "tooltip"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

tooltip_from_source

This node instructs to add tooltips to parts of a structure. The tooltips are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file.

Parent: structure

Params:

• schema:"whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"

  Annotation schema defines what fields in the annotation will be taken into account.

• block_header?:string | null

  Header of the CIF block to read annotation from. If null, block is selected based on block_index.

  Default: null

• block_index?:Integer

  0-based index of the CIF block to read annotation from (only applies when block_header is null).

  Default: 0

• category_name?:string | null

  Name of the CIF category to read annotation from. If null, the first category in the block is used.

  Default: null

• field_name?:string

  Name of the column in CIF or field name (key) in JSON that contains the tooltip text.

  Default: "tooltip"

• field_remapping?:{ [K in string]: (string | null) }

  Optional remapping of annotation field names { standardName1: actualName1, ... }. Use { "label_asym_id": "X" } to load actual field “X” as “label_asym_id”. Use { "label_asym_id": null } to ignore actual field “label_asym_id”. Fields not mentioned here are mapped implicitely (i.e. actual name = standard name).

  Default: {}

focus

This node instructs to set the camera focus to a component (zoom in).

Parent: root or component or component_from_uri or component_from_source or primitives or primitives_from_uri or volume or volume_representation

Params:

• direction?:[number, number, number]

  Vector describing the direction of the view (camera position -> focused target).

  Default: [0, 0, -1]

• up?:[number, number, number]

  Vector which will be aligned with the screen Y axis.

  Default: [0, 1, 0]

• radius?:number | null

  Radius of the focused sphere (overrides radius_factor and radius_extra).

  Default: null

• radius_factor?:number

  Radius of the focused sphere relative to the radius of parent component (default: 1). Focused radius = component_radius * radius_factor + radius_extent.

  Default: 1

• radius_extent?:number

  Addition to the radius of the focused sphere, if computed from the radius of parent component (default: 0). Focused radius = component_radius * radius_factor + radius_extent.

  Default: 0

camera

This node instructs to set the camera position and orientation.

Parent: root

Params:

• target:[number, number, number]

  Coordinates of the point in space at which the camera is pointing.

• position:[number, number, number]

  Coordinates of the camera.

• up?:[number, number, number]

  Vector which will be aligned with the screen Y axis.

  Default: [0, 1, 0]

• near?:number | null

  Near clipping plane distance from the position.

  Default: null

canvas

This node sets canvas properties.

Parent: root

Params:

• background_color?:ColorName | HexColor

  Color of the canvas background. Can be either an X11 color name (e.g. "red") or a hexadecimal code (e.g. "#FF0011"). Defaults to white.

  Default: "white"

primitives

This node groups a list of geometrical primitives

Parent: structure or root

Params:

• color?:ColorName | HexColor

  Default color for primitives in this group.

  Default: "white"

• label_color?:ColorName | HexColor

  Default label color for primitives in this group.

  Default: "white"

• tooltip?:string | null

  Default tooltip for primitives in this group.

  Default: null

• opacity?:number

  Opacity of primitive geometry in this group.

  Default: 1

• label_opacity?:number

  Opacity of primitive labels in this group.

  Default: 1

• label_show_tether?:boolean

  Whether to show a tether line between the label and the target. Defaults to false.

  Default: false

• label_tether_length?:number

  Length of the tether line between the label and the target. Defaults to 1 (Angstrom).

  Default: 1

• label_attachment?:"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right"

  How to attach the label to the target. Defaults to “middle-center”.

  Default: "middle-center"

• label_background_color?:ColorName | HexColor | null

  Background color of the label. Defaults to none/transparent.

  Default: null

• snapshot_key?:string | null

  Load snapshot with the provided key when interacting with this primitives group.

  Default: null

• instances?:Array<Array<number>> | null

  Instances of this primitive group defined as 4x4 column major (j * 4 + i indexing) transformation matrices.

  Default: null

primitives_from_uri

This node loads a list of primitives from URI

Parent: structure or root

Params:

• uri:string

  Location of the resource.

• format:"mvs-node-json"

  Format of the data.

• references?:Array<string>

  List of nodes the data are referencing.

  Default: []

primitive

This node represents a geometrical primitive

Parent: primitives

Params:

• kind:mesh | lines | tube | arrow | distance_measurement | angle_measurement | label | ellipse | ellipsoid | box

  Kind of geometrical primitive

  [This parameter determines the rest of parameters]

  Case kind: "mesh":

  • vertices:Array<number>

    3*n_vertices length array of floats with vertex position (x1, y1, z1, …).

  • indices:Array<Integer>

    3*n_triangles length array of indices into vertices that form triangles (t1_1, t1_2, t1_3, …).

  • triangle_groups?:Array<Integer> | null

    Assign a number to each triangle to group them. If not specified, each triangle is considered a separate group (triangle i = group i).

    Default: null

  • group_colors?:{ [K in Integer]: (ColorName | HexColor) }

    Assign a color to each group. Where not assigned, uses color.

    Default: {}

  • group_tooltips?:{ [K in Integer]: string }

    Assign a tooltip to each group. Where not assigned, uses tooltip.

    Default: {}

  • color?:ColorName | HexColor | null

    Color of the triangles and wireframe. Can be overwritten by group_colors. If not specified, uses the parent primitives group color.

    Default: null

  • tooltip?:string | null

    Tooltip shown when hovering over the mesh. Can be overwritten by group_tooltips. If not specified, uses the parent primitives group tooltip.

    Default: null

  • show_triangles?:boolean

    Determine whether to render triangles of the mesh.

    Default: true

  • show_wireframe?:boolean

    Determine whether to render wireframe of the mesh.

    Default: false

  • wireframe_width?:number

    Wireframe line width (in screen-space units).

    Default: 1

  • wireframe_color?:ColorName | HexColor | null

    Wireframe color. If not specified, uses group_colors.

    Default: null

  Case kind: "lines":

  • vertices:Array<number>

    3*n_vertices length array of floats with vertex position (x1, y1, z1, …).

  • indices:Array<Integer>

    2*n_lines length array of indices into vertices that form lines (l1_1, l1_2, …).

  • line_groups?:Array<Integer> | null

    Assign a number to each triangle to group them. If not specified, each line is considered a separate group (line i = group i).

    Default: null

  • group_colors?:{ [K in Integer]: (ColorName | HexColor) }

    Assign a color to each group. Where not assigned, uses color.

    Default: {}

  • group_tooltips?:{ [K in Integer]: string }

    Assign a tooltip to each group. Where not assigned, uses tooltip.

    Default: {}

  • group_widths?:{ [K in Integer]: number }

    Assign a line width to each group. Where not assigned, uses width.

    Default: {}

  • color?:ColorName | HexColor | null

    Color of the lines. Can be overwritten by group_colors. If not specified, uses the parent primitives group color.

    Default: null

  • tooltip?:string | null

    Tooltip shown when hovering over the lines. Can be overwritten by group_tooltips. If not specified, uses the parent primitives group tooltip.

    Default: null

  • width?:number

    Line width (in screen-space units). Can be overwritten by group_widths.

    Default: 1

  Case kind: "tube":

  • start:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Start point of the tube.

  • end:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    End point of the tube.

  • radius?:number

    Tube radius (in Angstroms).

    Default: 0.05

  • dash_length?:number | null

    Length of each dash and gap between dashes. If not specified (null), draw full line.

    Default: null

  • color?:ColorName | HexColor | null

    Color of the tube. If not specified, uses the parent primitives group color.

    Default: null

  • tooltip?:string | null

    Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

    Default: null

  Case kind: "arrow":

  • start:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Start point of the arrow.

  • end?:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> } | null

    End point of the arrow.

    Default: null

  • direction?:[number, number, number] | null

    If specified, the endpoint is computed as start + direction.

    Default: null

  • length?:number | null

    Length of the arrow. If unset, the distance between start and end is used.

    Default: null

  • show_start_cap?:boolean

    Draw a cap at the start of the arrow.

    Default: false

  • start_cap_length?:number | null

    Length of the start cap. If not provided, will be 2 * start_cap_radius.

    Default: null

  • start_cap_radius?:number | null

    Radius of the start cap. If not provided, will be 2 * tube_radius.

    Default: null

  • show_end_cap?:boolean

    Draw a cap at the end of the arrow.

    Default: false

  • end_cap_length?:number | null

    Length of the end cap. If not provided, will be 2 * end_cap_radius.

    Default: null

  • end_cap_radius?:number | null

    Radius of the end cap. If not provided, will be 2 * tube_radius.

    Default: null

  • show_tube?:boolean

    Draw a tube connecting the start and end points.

    Default: true

  • tube_radius?:number

    Tube radius (in Angstroms).

    Default: 0.05

  • tube_dash_length?:number | null

    Length of each dash and gap between dashes. If not specified (null), draw full line.

    Default: null

  • color?:ColorName | HexColor | null

    Color of the tube. If not specified, uses the parent primitives group color.

    Default: null

  • tooltip?:string | null

    Tooltip to show when hovering over the arrow. If not specified, uses the parent primitives group tooltip.

    Default: null

  Case kind: "distance_measurement":

  • start:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Start point of the tube.

  • end:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    End point of the tube.

  • radius?:number

    Tube radius (in Angstroms).

    Default: 0.05

  • dash_length?:number | null

    Length of each dash and gap between dashes. If not specified (null), draw full line.

    Default: null

  • color?:ColorName | HexColor | null

    Color of the tube. If not specified, uses the parent primitives group color.

    Default: null

  • label_template?:string

    Template used to construct the label. Use {{distance}} as placeholder for the distance.

    Default: "{{distance}}"

  • label_size?:number | null

    Size of the label (text height in Angstroms). If not specified, size will be relative to the distance (see label_auto_size_scale, label_auto_size_min).

    Default: null

  • label_auto_size_scale?:number

    Scaling factor for relative size.

    Default: 0.1

  • label_auto_size_min?:number

    Minimum size for relative size.

    Default: 0

  • label_color?:ColorName | HexColor | null

    Color of the label. If not specified, uses the parent primitives group label_color.

    Default: null

  Case kind: "angle_measurement":

  • a:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Point A.

  • b:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Point B.

  • c:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Point C.

  • label_template?:string

    Template used to construct the label. Use {{angle}} as placeholder for the angle in radians.

    Default: "{{angle}}"

  • label_size?:number | null

    Size of the label (text height in Angstroms). If not specified, size will be relative to the distance (see label_auto_size_scale, label_auto_size_min).

    Default: null

  • label_auto_size_scale?:number

    Scaling factor for relative size.

    Default: 0.33

  • label_auto_size_min?:number

    Minimum size for relative size.

    Default: 0

  • label_color?:ColorName | HexColor | null

    Color of the label. If not specified, uses the parent primitives group label_color.

    Default: null

  • show_vector?:boolean

    Draw vectors between (a, b) and (b, c).

    Default: true

  • vector_color?:ColorName | HexColor | null

    Color of the vectors.

    Default: null

  • vector_radius?:number

    Radius of the vectors.

    Default: 0.05

  • show_section?:boolean

    Draw a filled circle section representing the angle.

    Default: true

  • section_color?:ColorName | HexColor | null

    Color of the angle section. If not specified, the primitives group color is used.

    Default: null

  • section_radius?:number | null

    Radius of the angle section. In angstroms.

    Default: null

  • section_radius_scale?:number

    Factor to scale the radius of the angle section. Ignored if section_radius is set.

    Default: 0.33

  Case kind: "label":

  • position:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    Position of this label.

  • text:string

    The label.

  • label_size?:number

    Size of the label (text height in Angstroms).

    Default: 1

  • label_color?:ColorName | HexColor | null

    Color of the label. If not specified, uses the parent primitives group label_color.

    Default: null

  • label_offset?:number

    Camera-facing offset to prevent overlap with geometry.

    Default: 0

  Case kind: "ellipse":

  • color?:ColorName | HexColor | null

    Color of the ellipse. If not specified, uses the parent primitives group color.

    Default: null

  • as_circle?:boolean

    If true, ignores radius_minor/magnitude of the minor axis.

    Default: false

  • center:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    The center of the ellipse.

  • major_axis?:[number, number, number] | null

    Major axis of this ellipse.

    Default: null

  • minor_axis?:[number, number, number] | null

    Minor axis of this ellipse.

    Default: null

  • major_axis_endpoint?:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> } | null

    Major axis endpoint. If specified, overrides major axis to be major_axis_endpoint - center.

    Default: null

  • minor_axis_endpoint?:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> } | null

    Minor axis endpoint. If specified, overrides minor axis to be minor_axis_endpoint - center.

    Default: null

  • radius_major?:number | null

    Radius of the major axis. If unset, the length of the major axis is used.

    Default: null

  • radius_minor?:number | null

    Radius of the minor axis. If unset, the length of the minor axis is used.

    Default: null

  • theta_start?:number

    Start of the arc. In radians

    Default: 0

  • theta_end?:number

    End of the arc. In radians

    Default: 6.283185307179586

  • tooltip?:string | null

    Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

    Default: null

  Case kind: "ellipsoid":

  • color?:ColorName | HexColor | null

    Color of the ellipsoid. If not specified, uses the parent primitives group color.

    Default: null

  • center:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    The center of the ellipsoid.

  • major_axis?:[number, number, number] | null

    Major axis of this ellipsoid.

    Default: null

  • minor_axis?:[number, number, number] | null

    Minor axis of this ellipsoid.

    Default: null

  • major_axis_endpoint?:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> } | null

    Major axis endpoint. If specified, overrides major axis to be major_axis_endpoint - center.

    Default: null

  • minor_axis_endpoint?:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> } | null

    Minor axis endpoint. If specified, overrides minor axis to be minor_axis_endpoint - center.

    Default: null

  • radius?:[number, number, number] | number | null

    Radii of the ellipsoid along each axis.

    Default: null

  • radius_extent?:[number, number, number] | number | null

    Added to the radii of the ellipsoid along each axis.

    Default: null

  • tooltip?:string | null

    Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

    Default: null

  Case kind: "box":

  • center:[number, number, number] | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | { structure_ref?: string, expression_schema?: ("whole_structure" | "entity" | "chain" | "auth_chain" | "residue" | "auth_residue" | "residue_range" | "auth_residue_range" | "atom" | "auth_atom" | "all_atomic"), expressions?: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }> }

    The center of the box.

  • extent?:[number, number, number] | null

    The width, the height, and the depth of the box. Added to the bounding box determined by the center.

    Default: null

  • show_faces?:boolean

    Determine whether to render the faces of the box.

    Default: true

  • face_color?:ColorName | HexColor | null

    Color of the box faces.

    Default: null

  • show_edges?:boolean

    Determine whether to render the edges of the box.

    Default: false

  • edge_radius?:number

    Radius of the box edges. In angstroms.

    Default: 0.1

  • edge_color?:ColorName | HexColor | null

    Color of the edges.

    Default: null

  • tooltip?:string | null

    Tooltip to show when hovering over the tube. If not specified, uses the parent primitives group tooltip.

    Default: null