The define command calculates and displays geometric objects based on atomic coordinates:
The objects are listed in the Axes/Planes/Centroids tool (which can also be used to define them) and can be used in distance and angle measurements. See also: measure inertia, shape, cartoon style, 3D object formats, measurements• define axis atom-spec [ perHelix true | false ] [ padding offset ] [ length d ] [ primary true | false ] [ secondary true | false ] [ tertiary true | false ] [ massWeighting true | false ] general-options
Axes can be defined:• define centroid atom-spec [ massWeighting true | false ] general-options
Axes are displayed as cylindrical rods (surface models). The default length d is the minimum needed to span the projections of the specified atoms or points, or if the axis is defined from a plane object, equal to the plane's disk radius. An extra margin (padding, default 0.0 Å) can be added to both ends when the default length is used, but will be ignored if the length is specified. To produce a specified length, the center will stay the same, but the ends will be adjusted symmetrically.
- by a set of at least two specified atoms (perHelix false), where markers such as from define centroid are equivalent to atoms
- for each protein helix in models containing the specified atoms (perHelix true)
- by two points given with the fromPoint and toPoint options
- normal to a specified plane
Setting perHelix to true indicates defining an axis for each peptide/protein helix in the entire atomic model(s) containing the specified atoms, even if only parts were specified. Peptide/protein helix assignments are taken from the input structure file or generated with dssp. Only the backbone atoms N, CA, C are used to define the axes. Sometimes two helices are adjacent in sequence (not separated by any other residues), and the integer-valued residue attribute ss_id is automatically used to distinguish them. To force combining adjacent helices or breaking a longer helix into shorter ones, ss_id can be changed “manually” with setattr.
Eigenvectors/values are calculated from the coordinates of the set of atoms or points after subtracting the position of their collective centroid. Axes are anchored at the corresponding collective centroid and aligned with the first (if primary is true, default), second (secondary true), and/or third (tertiary true) eigenvector of the corresponding coordinates. If massWeighting is true (default false), the specification must contain either only “real” atoms or only markers (which could include centroid objects). The radius of a marker (Å) is used as its “mass.”
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. To simply add a marker at a specified point, see the marker command.• 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 axes defined by three or more atoms, the average axis-atom/centroid distance; for axes defined by two atoms, half of the smaller atom's radius; for axes defined by points, 1.0 Å; or for an axis normal to a plane, 5% of the plane radius
- 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 model name (default centroid for a centroid, plane for a plane). A user-specified name for a centroid model is also assigned as its atom name. Default axis model names:
- axis when the command defines only one axis for a set of atoms or points
- normal when the axis is defined by a plane model
- when perHelix is true, a grouping model named helix axes with submodels named helix N (or chain ID helix N if the model has multiple chains), where N is the value of the residue attribute ss_id; a user-specified name replaces the grouping-model name only
- when axes are generated for more than one eigenvector of a single set of atoms, a grouping model named axes with submodels named primary, secondary, tertiary as appropriate; a user-specified name replaces the grouping-model name only
- if perHelix is true and axes are generated for more than eigenvector per helix, a grouping model named helix axes with submodels helix N (or chain ID helix N), in turn containing submodels primary, secondary, tertiary as appropriate
showTool true | false
Whether to show the Axes/Planes/Centroids tool, which lists the objects and allows modifying (name, color, etc.), deleting, or using them for measurements.