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