MarvinSpace Parameters and Events

Version 5.9.4

Contents

  1. Scene parameters
  2. Action parameters
  3. Ligand parameters
  4. MacroMolecule parameters
  5. Water parameters
  6. Ion parameters
  7. Pharmacophore parameters
  8. Surface parameters
  9. Secondary Structure parameters
 

Parameters

Parameters of the MarvinSpace applications can be set using the -p command line option, for applets they can be set using the <param> HTML tag.

  1. Scene parameters

    2. ParameterMeaningPossible valuesDefault
    Quality Rendering quality of the components "High", "Medium", "Low" Medium
    Background.Color Color of the scene, the same color applies to all cells java.awt.Color value as String #000000
    Background.Transparent Transparent background affects image saving, i.e. save image with or without background color true, false true
    Background.Smooth Smooth backgound means that the background color will be a linearly interpolated to a brighter color true, false false
    Depthcue Enable/disable depth cue (fog) effect true, false false
    Depthcue.Near Start position of fog relative to the view point Integer value as String 0
    Depthcue.Far End position of fog relative to the view point Integer value as String 40
    Clipping.Near Position of the near clipping plane Float value as String -59.9
    Clipping.Far Position of the far clipping plane Float value as String 450
    SynchronousMode Synchronous navigation (rotate, zoom, shift) in all cells true, false false

  2. Action parameters

    3. ParameterMeaningPossible valuesDefault
    ShowSurface Generates molecular surface on all visible components "van der Waals", "Solvent-accessible", "Connolly", "Blobby" Connolly
    ShowSecondaryStructure Generates secondary structure to all visible macromolecules Trace, Tube, Ribbon, Cartoon Cartoon

  3. Ligand parameters

    4. ParameterMeaningPossible valuesDefault
    Ligand.DrawType Draw type of all ligands/small molecules on the scene "Wire", "Stick", "Ball", "BallAndStick", "StickAndBall", "BallAndWire", "WireAndBall", "Spacefill" BallAndStick
    Ligand.ColorType Color type of all ligands/small molecules on the scene "Constant", "CPK" CPK
    Ligand.Quality Quality of all ligands/small molecules on the scene "High", "Medium", "Low" Medium
    Ligand.Hydrogens Hydrogens of ligands are displayed or not. Note that hydrogens are always calculated whether they are described in the input or not. true, false false
    Ligand.LonePairs Lone pairs of ligands are displayed or not. true, false false
    Ligand.BallRadius Radius of displayed balls in angstroms Double 0.4
    Ligand.BondRadius Radius of bond cylinders in ball&stick mode in angstroms Double 0.1
    Ligand.StickRadius Radius of bond cylinders in stick mode in angstroms Double 0.3
    Ligand.LineWidth Width of displayed lines in wire mode in pixels Double 2
    Ligand.BondDistance Gap between two lines/sticks representing a double bond. It is determined as a percentage of Bond radius. Integer 100
    Ligand.BondWidth Thickness of line/stick representing a double bond. It is expressed relative to the thickness of a single bond. Integer 50
    Ligand.SmoothStickStyle Smooth, shaded display of two colored bonds true, false false
    Ligand.ScaledBalls Are balls scaled according to vdW radius or have uniform size in ball mode or not true, false false
    Ligand.DisplayBondOrder Double, aromatic bonds are displayed differently from single bonds or not true, false true
    Ligand.Color The color used in constant color mode java.awt.Color #fff050

  4. MacroMolecule parameters

    5. ParameterMeaningPossible valuesDefault
    MacroMolecule.DrawType Draw type of all macromolecules on the scene "Wire", "Stick", "Ball", "BallAndStick", "StickAndBall", "BallAndWire", "WireAndBall", "Spacefill" Wire
    MacroMolecule.ColorType Color type of all macromolecules on the scene "Constant", "CPK", "Residue", "Chain", "Rainbow", "B-factor", "Secondary Structure" CPK
    MacroMolecule.Quality Quality of all macromolecules on the scene "High", "Medium", "Low" Medium
    MacroMolecule.Hydrogens Hydrogens of macromolecules are displayed or not. Note that hydrogens are not calculated for macromolecules. true, false false
    MacroMolecule.LonePairs Lone pairs of macromolecules are displayed or not. true, false false
    MacroMolecule.BallRadius Radius of displayed balls in angstroms Double 0.4
    MacroMolecule.BondRadius Radius of bond cylinders in ball&stick mode in angstroms Double 0.1
    MacroMolecule.StickRadius Radius of bond cylinders in stick mode in angstroms Double 0.15
    MacroMolecule.LineWidth Width of displayed lines in wire mode in pixels Double 2
    MacroMolecule.BondDistance Gap between two lines/sticks representing a double bond. It is determined as a percentage of Bond radius. Integer 100
    MacroMolecule.BondWidth Thickness of line/stick representing a double bond. It is expressed relative to the thickness of a single bond. Integer 50
    MacroMolecule.SmoothStickStyle Smooth, shaded display of two colored bonds true, false false
    MacroMolecule.ScaledBalls Are balls scaled according to vdW radius or have uniform size in ball mode or not true, false false
    MacroMolecule.DisplayBondOrder Double, aromatic bonds are displayed differently from single bonds or not true, false true
    MacroMolecule.Color The color used in constant color mode java.awt.Color #bebebe

  5. Water parameters

    6. ParameterMeaningPossible valuesDefault
    Water.DrawType Draw type of all water molecules on the scene "Wire", "Ball", "Spacefill" Wire
    Water.Quality Quality of all water molecules on the scene "High", "Medium", "Low" Medium
    Water.BallRadius Radius of displayed balls in angstroms Double 0.4
    Water.LineWidth Width of displayed lines in wire mode in pixels Double 2
    Water.Color The color used in constant color mode java.awt.Color #ff0000

  6. Ion parameters

    7. ParameterMeaningPossible valuesDefault
    Ion.DrawType Draw type of all ions on the scene "Dotted", "Wire", "Ball", "Spacefill" Spacefill
    Ion.ColorType Color type of all ions on the scene "Constant", "CPK" CPK
    Ion.Quality Quality of all ions on the scene "High", "Medium", "Low" Medium
    Ion.Color The color used in constant color mode java.awt.Color #871ece

  7. Pharmacophore parameters

    8. ParameterMeaningPossible valuesDefault
    PharmacophorePoint.DrawType Draw type of all pharmacophore points on the scene "Dotted", "Mesh", "Solid", "Transparent" Transparent
    PharmacophorePoint.Quality Quality of all pharmacophore points on the scene "High", "Medium", "Low" Medium
    PharmacophoreArrow.DrawType Draw type of all pharmacophore arrows on the scene "Dotted", "Mesh", "Solid", "Transparent" Solid
    PharmacophoreArrow.Quality Quality of all pharmacophore arrows on the scene "High", "Medium", "Low" Medium

  8. Surface parameters

    9. ParameterMeaningPossible valuesDefault
    Surface.DrawType Draw type of all molecular surfaces on the scene "Dot", "Mesh", "Solid", "Transparent" Solid
    Surface.ColorType Color type of all molecular surfaces on the scene
    • "Constant",
    • "AtomType/CPK",
    • "ResidueType",
    • "ChainType",
    • "ElectrostaticPotential",
    • "SecondaryStructureType",
    • "B-factor"
    		 Constant
    Surface.Quality Quality of all molecular surfaces on the scene "High", "Medium", "Low" Medium
    Surface.Palette Palette identifier used when coloring surface
    • "Red to Blue",
    • "Blue to Red",
    • "Rainbow",
    • "Reverse Rainbow",
    • "Blue to Green",
    • "Green to Blue",
    • "Fire",
    • "Blue",
    • "Green",
    • "Yellow"
    		 "Blue to Red"
    Surface.Color The color used in constant color mode java.awt.Color #cccccc

  9. Secondary Structure parameters

    10. ParameterMeaningPossible valuesDefault
    SecondaryStructure.DrawType Draw type of all secondary structure components of the scene
    • Trace,
    • Tube,
    • PipeAndPlank,
    • RibbonLines,
    • Ribbon,
    • CartoonSquare,
    • Cartoon
    		 Cartoon
    SecondaryStructure.ColorType Color type of all secondary structure components of the scene "Constant", "Residue", "Chain", "Rainbow", "B-factor", "SecondaryStructure" SecondaryStructure
    SecondaryStructure.Quality Quality of all secondary structure components of the scene "High", "Medium", "Low" Medium
    SecondaryStructure.Color The color used in constant color mode java.awt.Color #ffffff
    SecondaryStructure.HelixWidth . Float 1.2
    SecondaryStructure.HelixDepth . Float 0.3
    SecondaryStructure.HelixShift . Float 2.5
    SecondaryStructure.HelixArrow . true, false true
    SecondaryStructure.HelixArrowWidth . Float 3.8
    SecondaryStructure.SheetWidth . Float 1.2
    SecondaryStructure.SheetDepth . Float 0.4
    SecondaryStructure.SheetArrow . true, false true
    SecondaryStructure.SheetArrowWidth . Float 3.8
    SecondaryStructure.CoilWidth . Float 0.3
    SecondaryStructure.CoilDepth . Float 0.3
    SecondaryStructure.CoilUniform . true, false true
    SecondaryStructure.Threads . Integer 6

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