Chimera Commands Index

measure property arguments

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

Each property keyword has different arguments, described below. Property keywords and their sub-keywords can be truncated to unique strings, and their case does not matter. Models are specified by model number preceded by #. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.

See also: distance, angle, Structure Measurements

measure area surf-model
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
measure buriedArea  atom-specA  atom-specBprobeRadius radius ] [ vertexDensity density ]
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 Å and 2.02, 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

measure correlation map-model1 map-model2aboveThreshold true|false ] [ rotationAxis axis ] [ angleRange start,end,step ] [ plot true|false ]
Calculate the correlation between two volume data sets (maps):
correlation =  
where vector u contains the values of the first map (map-model1) and uave is a vector with all components equal to the average of the components of u. Vectors v and vave 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. See also: volume, molmap, Fit in Map

measure inertia atom-specperChain true|false ] [ showEllipsoid true|false ] [ color ellipsoid-color ]
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, and moments are reported for each ellipsoid. The vectors v1, v2, and v3 are the principle 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, aniso, shape, Axes/Planes

measure rotation model1 model2showAxis true|false ] [ showSlabs true|false ] [ color color ]
Report the transformation of model2 relative to model1 as: 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
measure volume surf-model
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