Measure and Color Blobs Measure and Color Blobs icon

Measure and Color Blobs enables coloring and measuring individual disconnected parts, or blobs, within a surface model. Clicking a blob with the mouse changes it to the specified color and reports its surface area and enclosed volume. To measure the model's total surface area and enclosed volume, use Measure Volume and Area or the command measure instead. These tools compute surface area and enclosed volume from surface triangles rather than analytically.

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.

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:

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 Measure and Color Blobs 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 Measure and Color Blobs 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.


Colors applied with Measure and Color Blobs 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 / February 2009