Model Attributes: MSMSModel (Molecular Surface)
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 shows and allows changes in model attribute values.
models are of class MSMSModel
(a specialized subtype of SurfaceModel).
They 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
- active - whether the model is
activated for motion
- 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 has been custom-colored, for example with
- displayed - whether surface
display is enabled at the model level
(see display hierarchy)
- dot size - pixel size of dots used in the dot
- line width - pixel width of lines used in the mesh
- one transparent layer
- whether to show only the topmost layer when the surface is transparent
- number of surface pieces
(independently selectable subparts) in the model.
Surface piece attributes
are shown in the Selection Inspector.
- probe radius
- radius in Å of the probe sphere used to compute the surface.
A larger probe decreases surface bumpiness because it fits into fewer crevices.
A radius of 1.4 Å is commonly used to approximate a water molecule.
- representation - which type of
is being used
- selectable with mouse
- whether the surface piece(s)
comprising the model can be
picked with the mouse
- show disjoint surfaces - whether to check
for multiple disjoint surfaces rather than assuming there is only one
(increases calculation time)
- triangles - number of triangles in the surface model
- vertex density - vertices per Å2
used to compute the surface.
Greater density results in a smoother surface but
increases computational demands for calculating and moving the surface.
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.
Model Attributes: Molecule
- surface color (a color well)
- atom-level surface color; see
- surface displayed - whether surface
display is enabled at the atom level
(see display hierarchy)
- -- multiple --
- 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
Model Attributes: SurfaceModel
Model Attributes: VRMLModel
UCSF Computer Graphics Laboratory / February 2009