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 are usually created with the surface command.

• active - whether the model is activated for motion
  • false
  • true
• model-level display - whether surface display is enabled at the model level (see display hierarchy)
  • false
  • true
• atom-level display - whether surface display is enabled at the atom level (see display hierarchy). If the surfaces of some but not all atoms are displayed, the value is reported to be -- multiple --.
  • -- multiple --
  • false
  • true
• surface representation - which type of surface representation is being used
  • solid
  • mesh
  • dots
• surface color source - whether the surface color reflects the color at the model, residue, 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 the extension DelPhiViewer.
  • molecule
  • residues
  • atoms
  • unknown
• 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.
• density (vertices/sq. A) - number of surface vertices per square angstrom used to compute the surface. Greater density results in a smoother surface but increased computational demands for calculating and moving the surface.