Pick Surface Pieces

Pick Surface Pieces enables coloring and measuring disconnected parts of a surface (less formally, blobs). When a blob is picked with the mouse, it is changed to the specified color, and its surface area and enclosed volume are measured.

Pick Surface Pieces acts on Surface_Model surfaces (see list; includes those from Volume Viewer and Multiscale Models), but not on standard molecular surfaces or VRML surfaces. For measurements on molecular surfaces, see Measure Volume and Area and Area/Volume from Web.

There are several ways to start Pick Surface Pieces, a tool in the Volume Data category (including from the Volume Viewer Tools menu). The dialog includes the options:

Use mouse [button] to pick blobs - which mouse button (1, 2, 3, Ctrl-1, Ctrl-2, or Ctrl-3) will be used to pick surface blobs from the screen. The icon representing this mouse mode in the Mouse preferences is shown at right.
Color blob [color well] - color to apply to subsequently picked blobs

Surfaces are composed of triangles. When a blob is picked from the screen, the exact area of its triangulated surface and the volume enclosed are reported in the Pick Surface Pieces dialog, the status line, and the Reply Log. Values reflect the physical units of the data, usually Å³ for volume and Å² for area.

Anything that alters the positions of vertices in a surface, such as smoothing the surface or changing its contour level in Volume Viewer, will change its area and enclosed volume.

The volume enclosed by a surface with holes is calculated by assuming each hole has a planar cap. These caps are not displayed or included in the surface area determination. The number of holes is reported, as planar caps may not represent missing data very well. Multiscale Models surfaces should never have holes. Holes in a contour surface from Volume Viewer may occur at the boundary of the data, but by default these will already be covered with planar caps. Such boundary caps will be included in the surface area calculation and will not be reported as holes.

While Pick Surface Pieces acts on a single disconnected blob at a time, Measure Volume and Area reports the total area and enclosed volume for a surface model even if comprised of multiple disconnected blobs.

LIMITATIONS

Colors applied with Pick Surface Pieces are lost when the surface contour level is changed.

Any mouse buttons assigned to pick blobs are not automatically reassigned to their previous functions; the Mouse preferences must be used to reassign them.

UCSF Computer Graphics Laboratory / November 2007