Measure and Color Blobs

Measure and Color Blobs enables measuring individual disconnected parts, or blobs, within a surface model. Quantities reported for a blob include:

the area of its triangulated surface
the volume enclosed
the size (dimensions from longest to shortest) of its bounding box

The surface area and enclosed volume are computed from surface triangles rather than analytically. To measure the total surface area and enclosed volume of a surface model (possibly containing multiple blobs), Measure Volume and Area or the command measure should be used instead. See also: Segger, Surfnet

Note that when a molecular surface is generated, the analytical solvent-accessible and solvent-excluded areas (total and for each disconnected component) are automatically reported in the Reply Log, and the values per atom and residue are assigned as attributes named areaSAS and areaSES. See also: CASTp Data

There are several ways to start Measure and Color Blobs, a tool in the Surface/Binding Analysis and Volume Data categories (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 use for the next picked blob
Change color automatically - whether to set a new color (randomly) each time a blob is picked
Show principal axes box [color well] - whether to show a bounding box in the specified color (default green) for each subsequently picked blob. A blob's bounding box is aligned with its principal axes of inertia, calculated assuming a constant mass per unit surface area. Box outlines are placed in a surface model named Principal axes box. Clicking Erase closes the box model. Even if the box is not shown, its size will be reported along with the other measurements described below.

Surfaces are composed of triangles. 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.

When a blob is picked from the screen, the area of its triangulated surface, the volume enclosed, and its bounding box size (dimensions from longest to shortest) are reported in the Measure and Color Blobs dialog, the status line, and the Reply Log. Values reflect the physical units of the data, usually Å³ for volume, Å² for area, Å for length.

Blob surface area and volume are not affected by clipping (the clipped-away parts will still be included), but the planar cap can itself be measured. In that case, the volume will be near-zero, and the boundary (circumference) will also be reported.

Circumferences of any holes in the blob surface are also reported. 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.

LIMITATIONS

Colors applied with Measure and Color Blobs are lost when the surface contour level is changed.

After the tool is closed, it may be necessary to use the Mouse preferences to reassign mouse buttons to their previous functions.

UCSF Computer Graphics Laboratory / October 2013