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Tool: Measure and Color Blobs

Measure and Color Blobs measures individual disconnected parts or blobs within a surface model. It is also implemented as the command measure blob.

The related commands measure area and measure volume report the total surface area and enclosed volume, respectively, of a surface model (possibly comprising multiple blobs), as does Measure Volume and Area. To measure the solvent-accessible surface area of an atomic structure, the command measure sasa should be used instead. See also: Volume Viewer, Segment Map, measure buriedarea, marker connected, measurements

Measure and Color Blobs can be started from the Volume Data section of the Tools menu or by clicking the pick blobs icon in the Right Mouse toolbar. The tool window can be moved, resized, etc.

Clicking a blob using the button assigned to the pick blobs mouse mode reports the following in the tool window and in the Log:

Values reflect the physical units of the data, usually Å3 for volume, Å2 for area, Å for length.


The surface area and enclosed volume are computed from surface triangles. Anything that alters the positions of vertices, such as changing the surface threshold level in Volume Viewer, will change the enclosed volume and surface area, and lose any colors previously applied with Measure and Color Blobs.

Blob surface area and volume are not affected by clipping (the clipped-away parts will still be included), but the surface cap where the clipping plane intersects the blob 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. Holes in an isosurface 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 of the overall blob and will not be reported as holes.

UCSF Resource for Biocomputing, Visualization, and Informatics / March 2021