Measure Volume reports the volume enclosed in a surface. Surfaces handled are:
There are several ways to start Measure Volume, a tool in the Volume Data category.
The surface of interest should be chosen from the Volume for surface menu. Clicking Compute Volume calculates the volume and reports it in the physical units appropriate for the data, e.g., cubic angstroms or nanometers. The value is shown in the Measure Volume interface and written to the Reply Log.
The volume enclosed by a surface is sensitive to the positions and spacing of vertices within the surface. For example, the volume enclosed by a molecular surface will change if its vertex density attribute is changed, and the volume enclosed by a contour surface will change if the contour surface is smoothed.
Close closes the Measure Volume interface. Help opens this manual page in a browser window.
Clipping and hiding are ignored. The volume calculation uses the full surface, even if part of it is hidden by clipping planes or zoning (with Surface Zone or zoning in Volume Viewer).
Surface holes. If the surface has holes, the volume will not be computed because it is not known what is inside and what is outside the surface. Molecular surfaces and surfaces from Multiscale Models should never have holes. A contour surface from Volume Viewer will only have holes if it reaches the boundary of the volume data set. Several methods can eliminate such holes:
Multiple enclosed volumes. If a surface encloses disjoint regions of space, the total volume of all regions will be reported. There is no way to select a particular enclosure to calculate its volume. For contour surfaces from Volume Viewer, subregion selection or Volume Eraser can be used to limit the calculation to the region of interest.
Speed. The volume calculation is implemented entirely in Python and is about 100 times slower than what is possible. Example times are 4 seconds to calculate the volume of a molecular surface of a 350-residue protein (one chain of 1bvp), and 4 seconds to compute the volume of a contour surface of a 50 x 50 x 50 portion of a density map (emd 1080 at threshold 1) on a 2 GHz PC (circa 2005).