MSMS (Molecular Surface) Model Attributes

Once a model has been chosen in the left side of the Model Panel, clicking the attributes... button in the right side of the panel brings up a window that lists model attributes and allows them to be changed. Molecular surface models are of class MSMSModel and can be generated using the Surface section of the Actions menu or the command surface.

The list includes the attributes of the molecular surface model and selected attributes of its component atom surfaces.

MSMSModel Attributes

• active - whether the model is activated for motion
  • false
  • true
• color source - whether the surface color reflects the color at the model or atom level (see coloring hierarchy). When surface color is set independent of these levels, unknown is reported. This occurs when the surface is custom-colored, for example, when it is colored by electrostatic potential using DelPhiViewer.
  • model
  • atoms
  • unknown
• displayed - whether surface display is enabled at the model level (see display hierarchy)
  • false
  • true
• dot size - pixel size of dots used in the dot surface representation
• line width - pixel width of lines used in the mesh surface representation
• probe radius - radius in angstroms of the probe sphere used to compute the surface. A larger probe decreases surface bumpiness because it fits into fewer crevices. A probe radius of 1.4 angstroms is commonly used to approximate the size of a water molecule.
• representation - which type of surface representation is being used
  • solid
  • mesh
  • dots
• vertex density - number of vertices per square angstrom used to compute the surface. Greater density results in a smoother surface but increases computational demands for calculating and moving the surface.

Component Atom Attributes

Attributes of individual atom surfaces within a molecular surface model can be set independently. When different per-atom surfaces within the molecular surface model have different attribute values, the value is reported to be -- multiple --. If one of the other options is chosen, all per-atom surfaces in the molecular surface model will be changed accordingly.

• surface color (a color well) - atom-level surface color; see coloring hierarchy
• surface displayed - whether surface display is enabled at the atom level (see display hierarchy)
  • -- multiple --
  • false
  • true
• surface opacity - atom-level surface opacity, ranging from 0 (completely transparent) to 1 (completely opaque); a negative value indicates that the opacity included in the definition of the atom-level surface color(s) should be used instead