Usage:
measure property arguments

The measure command performs various calculations and sends results to the Reply Log. Possible values of property:

• area - calculate total area of an existing surface
• buriedArea - calculate surface area buried between two sets of atoms
• correlation - report correlation of two maps
• inertia - calculate inertia ellipsoid
• rotation - report transformation of one model relative to another
• spine - calculate a path along the center line of a segmentation region
• volume - calculate volume enclosed by an existing surface

See also: distance, angle, Structure Measurements

Calculate the total area of an existing surface model by summing over its triangles (same calculation as performed by Measure Volume and Area). Note that the solvent-excluded and solvent-accessible surface areas of a molecular surface are reported in the Reply Log when the surface is first shown. See also: surface, volume

Calculate the surface area buried between two specified sets of atoms. A surface is calculated for each set of atoms separately (surfA, surfB) and for their combination (surfAB). The surfaces are not created or displayed, but calculated internally. The difference in total area between the separate and combined states is reported for each set, as well as the average over the two sets. Buried areas are reported for both solvent-excluded and solvent-accessible surfaces. Only the averages are sent to the status line, but full results can be viewed in the Reply Log.

The atoms are grouped as specified regardless of surface category, and a set may span multiple models. Be careful to specify only the intended atoms, which could mean excluding or deleting beforehand any solvent, ligands, ions, and/or alternate location atoms. New Surfaces preference settings are not used; disjoint surfaces are always included, and the default probe radius and vertex density are 1.4 Šand 2.0/Ų, respectively.

Atoms are assigned the attributes buriedSESArea (buried solvent-excluded surface area) and buriedSASArea (buried solvent-accessible surface area) with their individual contributions to the specified interface. These can be summed over selected atoms with Attribute Calculator, for example to determine the contribution from carbons only.

See also: surface, intersurf, Area/Volume from Web

Calculate the correlation between two volume data sets (maps):

	<u,v>
correlation =
	|u||v|

	<u–uave,v–vave>
correlation about mean =
	|u–uave||v–vave|

where vector u contains the values of the first map (map-model1) and u_ave is a vector with all components equal to the average of the components of u. Vectors v and v_ave are defined analogously for the second map (map-model2), except that the values are sampled at the grid point locations of the first map using trilinear interpolation.

• If aboveThreshold is true (default), the calculation will include only the grid points in the first map with values above its lowest contour level in Volume Viewer. Otherwise, all nonzero-valued grid points will be included.
• Specifying rotationAxis allows calculating the correlation multiple times for different orientations of the first map about an axis, described by an atom-spec of exactly two atoms (not necessarily bonded or in the same model) or one bond. If two atoms, the order of specification defines a handedness, and right-handed rotations are positive. If a bond, the handedness is not under user control. A bond can only be specified by selecting it and using the word selected, sel, or picked; any atoms also selected at the time will be ignored. The calculations are performed internally, without moving the map in the display.
• The angleRange arguments control how many correlation calculations should be performed and at what angles of the first map relative to its current position. By default, start = 0°, end = 360°, and step = 2°.
• If plot is true (default), the correlation values will be graphed in a separate window in addition to being tabulated in the Reply Log. Clicking and dragging in the plot window will show a vertical line and rotate the first map to the indicated angle.

See also: volume, molmap, Fit in Map, Fit to Segments

Calculate the inertia ellipsoid for atom-spec, which could include atoms or surface pieces. Atoms are mass-weighted; surface pieces are treated as thin shells with mass proportional to surface area. If both atoms and surfaces are specified, two separate ellipsoids are calculated (a combined calculation cannot be performed). Principal axes, lengths, moments, and center are reported for each ellipsoid. The vectors v1, v2, and v3 are the principal axes (longest to shortest). The lengths a, b, c are half-diameters along axes v1, v2, and v3, respectively. The moments r1, r2, and r3 are calculated as (inertia/mass)^½ about axes v1, v2, and v3, respectively. They can be considered effective radii; placing all of the mass at that distance from the center would reproduce the moment of inertia calculated for the structure around that axis.

The perChain option indicates whether to calculate a separate ellipsoid for each chain in atom-spec. If showEllipsoid is true (default), the ellipsoid(s) will be opened as a surface model. The ellipsoid-color can be any color name that specifies a single color. Otherwise, an ellipsoid will be colored to match the first atom or surface piece in its calculation.

See also: define axis, aniso, shape ellipsoid, Measure and Color Blobs

Report the transformation of model2 relative to model1 as:

• a matrix in which the first three columns describe a rotation and the fourth describes a translation (performed after the rotation)
• an axis of rotation (a unit vector), point on the axis, rotation angle, and shift parallel to the axis, expressed in the coordinate system of model1

If showAxis is true (default), a marker set showing the axis as a rod will be opened as a separate model. The rod length equals the largest dimension of the bounding box of model1, and its diameter is set to 5% of the length. If showSlabs is true (default false), two rectangular slabs showing the rotation axis and angle and the shift will be opened as a surface model. The axis and/or slab color can be any color name that specifies a single color. See also: superimposing structures, Fit in Map

Calculate and display a path along the center line of each specified segmentation region. The length of the path (spine) and orthogonal diameters at its midpoint are reported. Regions can be specified as a selection (e.g., sel) or with model number(s) (e.g., #1). The longest principal axis of inertia of a region is determined using equal weighting of the enclosed volume grid points. The region is then divided into slices along that axis, with end slices tipLength t thick and interior slices at least spacing s thick. Both distances are specified in physical units (typically Å). The spacing is increased as needed to make the interior slices of equal width. A marker is placed at the geometric center of the grid points within each slice. The markers are linked, and the markers and links together form a path. The path color can be any color name that specifies a single color. See also: Segment Map

Calculate the total volume enclosed by an existing surface model, not including any interior bubbles (same calculation as performed by Measure Volume and Area). See also: surface, volume