The define command calculates and displays geometric objects based on atomic coordinates:
The objects can be used in distance and angle measurements. See also: measure inertia, shape, 3D object formats, measurements• define centroid atom-spec [ massWeighting true | false ] general-options
Define the centroid of the specified atoms with or without mass-weighting (default without). The centroid is added as a marker. The related command measure center can also calculate center of mass for density maps.• define plane atom-spec [ thickness d ] [ padding offset ] general-options
Define a plane for the specified atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane). The plane is added as a surface model shaped like a disk. The default thickness is 0.1 Å. The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms (default). An extra margin (padding, default 0.0 Å) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied.
Object color (default the most prevalent color among the specified atoms, if at least 30% share that color, otherwise #909090
Object radius in Å. Defaults:
- for centroids, 2.0 Å
- for planes, to enclose the projections of the atoms (an additional margin can be specified with the padding option)
Object name (default centroid for a centroid, plane for a plane). A user-specified name for a centroid object will also be assigned as its atom name.