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.
Molecular surface
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
atom surfaces.
- 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
Surface
Color.
- displayed - whether surface
display is enabled at the model level
(see display hierarchy)
- dot size - pixel size of dots used in the dot
surface representation
- line width - pixel width of lines used in the mesh
surface representation
- pieces
- 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
surface representation
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)
- silhouette
- per-model setting for silhouettes, outlines that emphasize borders and
discontinuities; the silhouettes will only be shown when the
global setting is also true
- 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.
- 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
Model Attributes: Molecule
Model Attributes: SurfaceModel
and Volume
Model Attributes: VRMLModel
and Volume_Model
UCSF Computer Graphics Laboratory / January 2012