Measure Volume and Area

Measure Volume and Area reports total surface areas and surface-enclosed volumes. Surfaces handled are:

molecular surfaces (MSMS models)
surface models from Volume Viewer and Multiscale Models
GRASP surfaces
surface models from Intersurf

Surfaces in VRML models such as from Surfnet are not handled.

The related tool Area/Volume from Web uses the StrucTools server to calculate surface areas and Voronoi volumes from molecular coordinates and assigns the per-atom values as atom attributes (see the summary of differences).

There are several ways to start Measure Volume and Area, a tool in the Surface/Binding Analysis and Volume Data categories (including from the Volume Viewer Tools menu).

The surface of interest should be chosen from the Surface menu. The surface area and enclosed volume are reported in the dialog and written to the Reply Log. Values reflect the physical units of the data, usually Å³ for volume and Å² for area.

Surfaces are composed of triangles. Anything that changes the positions of the vertices in a surface will change its area and enclosed volume, for example:

adjusting the contour level of an isosurface shown with Volume Viewer
smoothing a Multiscale Models surface
changing the probe radius or vertex density attribute of a molecular surface

Update automatically (on by default) indicates volume and area should be recomputed automatically whenever such a change occurs. Otherwise, a new calculation can be triggered by clicking Update. A current limitation is that changes in molecular surfaces are not detected automatically (the Update button must always be used).

TECHNICAL NOTES

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. 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.

Multiple enclosed volumes. If a surface encloses disjoint regions of space, the total volume of all regions will be reported. To calculate the surface area and volume for a single disjoint region, use Pick Surface Pieces instead.

UCSF Computer Graphics Laboratory / October 2007