TmMolStar/docs/state/transforms.md

Mol* Plugin State Transformer Reference

• build-in.root
• ms-plugin.download
• ms-plugin.read-file
• ms-plugin.parse-cif
• ms-plugin.parse-ccp4
• ms-plugin.parse-dsn6
• ms-plugin.trajectory-from-mmcif
• ms-plugin.trajectory-from-pdb
• ms-plugin.model-from-trajectory
• ms-plugin.structure-from-model
• ms-plugin.structure-assembly-from-model
• ms-plugin.structure-symmetry-from-model
• ms-plugin.structure-selection
• ms-plugin.structure-complex-element
• ms-plugin.custom-model-properties
• ms-plugin.volume-from-ccp4
• ms-plugin.volume-from-dsn6
• ms-plugin.representation-highlight-loci
• ms-plugin.representation-select-loci
• ms-plugin.default-loci-label-provider
• ms-plugin.structure-representation-3d
• ms-plugin.explode-structure-representation-3d
• ms-plugin.volume-representation-3d
• ms-plugin.focus-loci-on-select
• ms-plugin.pdbe-structure-quality-report-prop
• ms-plugin.rcsb-assembly-symmetry-prop
• ms-plugin.structure-animation
• ms-plugin.scene-labels

---

build-in.root :: () -> ()

For internal use.

---

ms-plugin.download :: Root -> String | Binary

Download string or binary data from the specified URL

Parameters

• url: String (Resource URL. Must be the same domain or support CORS.)
• label?: String
• isBinary?: true/false (If true, download data as binary (string otherwise))

Default Parameters

{
  "url": "https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif"
}

---

ms-plugin.read-file :: Root -> String | Binary

Read string or binary data from the specified file

Parameters

• file: JavaScript File Handle
• label?: String
• isBinary?: true/false (If true, open file as as binary (string otherwise))

Default Parameters

{}

---

ms-plugin.parse-cif :: String | Binary -> Cif

Parse CIF from String or Binary data

---

ms-plugin.parse-ccp4 :: Binary -> Ccp4

Parse CCP4/MRC/MAP from Binary data

---

ms-plugin.parse-dsn6 :: Binary -> Dsn6

Parse CCP4/BRIX from Binary data

---

ms-plugin.trajectory-from-mmcif :: Cif -> Trajectory

Identify and create all separate models in the specified CIF data block

Parameters

• blockHeader?: String (Header of the block to parse. If none is specifed, the 1st data block in the file is used.)

Default Parameters

{}

---

ms-plugin.trajectory-from-pdb :: String -> Trajectory

---

ms-plugin.model-from-trajectory :: Trajectory -> Model

Create a molecular structure from the specified model.

Parameters

• modelIndex: Numeric value (Zero-based index of the model)

Default Parameters

{
  "modelIndex": 0
}

---

ms-plugin.structure-from-model :: Model -> Structure

Create a molecular structure from the specified model.

---

ms-plugin.structure-assembly-from-model :: Model -> Structure

Create a molecular structure assembly.

Parameters

• id?: String (Assembly Id. Value 'deposited' can be used to specify deposited asymmetric unit.)

Default Parameters

{}

---

ms-plugin.structure-symmetry-from-model :: Model -> Structure

Create a molecular structure symmetry.

Parameters

• ijkMin: 3D vector [x, y, z]
• ijkMax: 3D vector [x, y, z]

Default Parameters

{
  "ijkMin": [
    -1,
    -1,
    -1
  ],
  "ijkMax": [
    1,
    1,
    1
  ]
}

---

ms-plugin.structure-selection :: Structure -> Structure

Create a molecular structure from the specified query expression.

Parameters

• query: Value
• label?: String

Default Parameters

{}

---

ms-plugin.structure-complex-element :: Structure -> Structure

Create a molecular structure from the specified model.

Parameters

• type: One of 'atomic-sequence', 'water', 'atomic-het', 'spheres'

Default Parameters

{
  "type": "atomic-sequence"
}

---

ms-plugin.custom-model-properties :: Model -> Model

Parameters

• properties: Array of (A list of property descriptor ids.)

Default Parameters

{
  "properties": []
}

---

ms-plugin.volume-from-ccp4 :: Ccp4 -> Data

Create Volume from CCP4/MRC/MAP data

Parameters

• voxelSize: 3D vector [x, y, z]

Default Parameters

{
  "voxelSize": [
    1,
    1,
    1
  ]
}

---

ms-plugin.volume-from-dsn6 :: Dsn6 -> Data

Create Volume from DSN6/BRIX data

Parameters

• voxelSize: 3D vector [x, y, z]

Default Parameters

{
  "voxelSize": [
    1,
    1,
    1
  ]
}

---

ms-plugin.representation-highlight-loci :: Root -> Behavior

---

ms-plugin.representation-select-loci :: Root -> Behavior

---

ms-plugin.default-loci-label-provider :: Root -> Behavior

---

ms-plugin.structure-representation-3d :: Structure -> Representation3D

Parameters

• type: Object { name: string, params: object } where name+params are:

  • cartoon: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • sizeFactor: Numeric value
    • linearSegments: Numeric value
    • radialSegments: Numeric value
    • aspectRatio: Numeric value
    • arrowFactor: Numeric value
    • visuals: Array of 'polymer-trace', 'polymer-gap', 'nucleotide-block', 'direction-wedge'

  • ball-and-stick: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • sizeFactor: Numeric value
    • detail: Numeric value
    • linkScale: Numeric value
    • linkSpacing: Numeric value
    • radialSegments: Numeric value
    • sizeAspectRatio: Numeric value
    • visuals: Array of 'element-sphere', 'intra-link', 'inter-link'

  • carbohydrate: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • detail: Numeric value
    • sizeFactor: Numeric value
    • linkScale: Numeric value
    • linkSpacing: Numeric value
    • radialSegments: Numeric value
    • linkSizeFactor: Numeric value
    • visuals: Array of 'carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'

  • distance-restraint: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • linkScale: Numeric value
    • linkSpacing: Numeric value
    • radialSegments: Numeric value
    • sizeFactor: Numeric value

  • molecular-surface: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • resolution: Numeric value
    • radiusOffset: Numeric value
    • smoothness: Numeric value
    • useGpu: true/false
    • ignoreCache: true/false
    • sizeFactor: Numeric value
    • lineSizeAttenuation: true/false
    • visuals: Array of 'gaussian-surface', 'gaussian-wireframe'

  • molecular-volume: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • isoValueNorm: Numeric value (Normalized Isolevel Value)
    • renderMode: One of 'isosurface', 'volume'
    • controlPoints: A list of 2d vectors [xi, yi][]
    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • resolution: Numeric value
    • radiusOffset: Numeric value
    • smoothness: Numeric value

  • point: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • sizeFactor: Numeric value
    • pointSizeAttenuation: true/false
    • pointFilledCircle: true/false
    • pointEdgeBleach: Numeric value
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'

  • spacefill: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • unitKinds: Array of 'atomic', 'spheres', 'gaussians'
    • sizeFactor: Numeric value
    • detail: Numeric value

• colorTheme: Object { name: string, params: object } where name+params are:

  • carbohydrate-symbol: Object with:

  • chain-id: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • cross-link: Object with:

    • domain: Interval [min, max]
    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • element-index: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • element-symbol: Object with:

  • molecule-type: Object with:

  • polymer-id: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • polymer-index: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • residue-name: Object with:

  • secondary-structure: Object with:

  • sequence-id: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • shape-group: Object with:

  • unit-index: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • uniform: Object with:

    • value: Color as 0xrrggbb

• sizeTheme: Object { name: string, params: object } where name+params are:

  • physical: Object with:

  • shape-group: Object with:

  • uniform: Object with:

    • value: Numeric value

Default Parameters

{
  "type": {
    "name": "cartoon",
    "params": {
      "alpha": 1,
      "useFog": true,
      "highlightColor": 16737945,
      "selectColor": 3407641,
      "quality": "auto",
      "doubleSided": false,
      "flipSided": false,
      "flatShaded": false,
      "unitKinds": [
        "atomic",
        "spheres"
      ],
      "sizeFactor": 0.2,
      "linearSegments": 8,
      "radialSegments": 16,
      "aspectRatio": 5,
      "arrowFactor": 1.5,
      "visuals": [
        "polymer-trace"
      ]
    }
  },
  "colorTheme": {
    "name": "polymer-id",
    "params": {
      "list": "RedYellowBlue"
    }
  },
  "sizeTheme": {
    "name": "uniform",
    "params": {
      "value": 1
    }
  }
}

---

ms-plugin.explode-structure-representation-3d :: Representation3D -> Obj

Parameters

• t: Numeric value

Default Parameters

{
  "t": 0
}

---

ms-plugin.volume-representation-3d :: Data -> Representation3D

Parameters

• type: Object { name: string, params: object } where name+params are:

  • isosurface: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • doubleSided: true/false
    • flipSided: true/false
    • flatShaded: true/false
    • isoValue: - absolute: Numeric value

    • relative: Numeric value

    • sizeFactor: Numeric value

    • lineSizeAttenuation: true/false

    • visuals: Array of 'solid', 'wireframe'

  • direct-volume: Object with:

    • alpha: Numeric value
    • useFog: true/false
    • highlightColor: Color as 0xrrggbb
    • selectColor: Color as 0xrrggbb
    • quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
    • isoValueNorm: Numeric value (Normalized Isolevel Value)
    • renderMode: One of 'isosurface', 'volume'
    • controlPoints: A list of 2d vectors [xi, yi][]
    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

• colorTheme: Object { name: string, params: object } where name+params are:

  • carbohydrate-symbol: Object with:

  • chain-id: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • cross-link: Object with:

    • domain: Interval [min, max]
    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • element-index: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • element-symbol: Object with:

  • molecule-type: Object with:

  • polymer-id: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • polymer-index: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • residue-name: Object with:

  • secondary-structure: Object with:

  • sequence-id: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • shape-group: Object with:

  • unit-index: Object with:

    • list: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'

  • uniform: Object with:

    • value: Color as 0xrrggbb

• sizeTheme: Object { name: string, params: object } where name+params are:

  • physical: Object with:

  • shape-group: Object with:

  • uniform: Object with:

    • value: Numeric value

Default Parameters

{
  "type": {
    "name": "isosurface",
    "params": {
      "alpha": 1,
      "useFog": true,
      "highlightColor": 16737945,
      "selectColor": 3407641,
      "quality": "auto",
      "doubleSided": false,
      "flipSided": false,
      "flatShaded": false,
      "isoValue": {
        "kind": "relative",
        "stats": {
          "min": 0,
          "max": 0,
          "mean": 0,
          "sigma": 0
        },
        "relativeValue": 2
      },
      "sizeFactor": 1,
      "lineSizeAttenuation": false,
      "visuals": [
        "solid"
      ]
    }
  },
  "colorTheme": {
    "name": "uniform",
    "params": {
      "value": 13421772
    }
  },
  "sizeTheme": {
    "name": "uniform",
    "params": {
      "value": 1
    }
  }
}

---

ms-plugin.focus-loci-on-select :: Root -> Behavior

Parameters

• minRadius: Numeric value
• extraRadius: Numeric value (Value added to the boundning sphere radius of the Loci.)

Default Parameters

{
  "minRadius": 10,
  "extraRadius": 4
}

---

ms-plugin.pdbe-structure-quality-report-prop :: Root -> Behavior

Parameters

• autoAttach: true/false

Default Parameters

{
  "autoAttach": false
}

---

ms-plugin.rcsb-assembly-symmetry-prop :: Root -> Behavior

Parameters

• autoAttach: true/false

Default Parameters

{
  "autoAttach": false
}

---

ms-plugin.structure-animation :: Root -> Behavior

Parameters

• rotate: true/false
• rotateValue: Numeric value
• explode: true/false
• explodeValue: Numeric value

Default Parameters

{
  "rotate": false,
  "rotateValue": 0,
  "explode": false,
  "explodeValue": 0
}

---

ms-plugin.scene-labels :: Root -> Behavior

Parameters

• alpha: Numeric value
• useFog: true/false
• highlightColor: Color as 0xrrggbb
• selectColor: Color as 0xrrggbb
• quality: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
• fontFamily: One of 'sans-serif', 'monospace', 'serif', 'cursive'
• fontQuality: One of '0', '1', '2', '3', '4'
• fontStyle: One of 'normal', 'italic', 'oblique'
• fontVariant: One of 'normal', 'small-caps'
• fontWeight: One of 'normal', 'bold'
• sizeFactor: Numeric value
• borderWidth: Numeric value
• borderColor: Color as 0xrrggbb
• offsetX: Numeric value
• offsetY: Numeric value
• offsetZ: Numeric value
• background: true/false
• backgroundMargin: Numeric value
• backgroundColor: Color as 0xrrggbb
• backgroundOpacity: Numeric value
• attachment: One of 'bottom-left', 'bottom-center', 'bottom-right', 'middle-left', 'middle-center', 'middle-right', 'top-left', 'top-center', 'top-right'
• levels: Array of 'structure', 'polymer', 'ligand'

Default Parameters

{
  "alpha": 1,
  "useFog": true,
  "highlightColor": 16737945,
  "selectColor": 3407641,
  "quality": "auto",
  "fontFamily": "sans-serif",
  "fontQuality": 3,
  "fontStyle": "normal",
  "fontVariant": "normal",
  "fontWeight": "normal",
  "sizeFactor": 1,
  "borderWidth": 0,
  "borderColor": 8421504,
  "offsetX": 0,
  "offsetY": 0,
  "offsetZ": 0,
  "background": true,
  "backgroundMargin": 0.2,
  "backgroundColor": 16775930,
  "backgroundOpacity": 0.9,
  "attachment": "middle-center",
  "levels": []
}

---