Chimera Commands Index

define ( axis | plane | centroid )  options  atom-spec

define  axis  options  plane-ID

~defineID-list | axes | planes | centroids ]

The define command calculates and displays geometric objects based on atomic coordinates. It is the command-line implementation of Axes/Planes/Centroids. The type of object to define can be:

Axes can also be calculated from centroids, some combination of atoms and centroids, or normal to a plane. Each object is created as a surface model (hidden from the Model Panel) in the coordinate system of the lowest-numbered model involved in its calculation. The objects are listed in the Axes/Planes/Centroids table and can be used in distance and angle measurements. See also: distance, angle, align, aniso, pipes, measure center, measure inertia, shape, geometric objects

The ~define command removes objects, either those specified as a space-separated list of IDs (for example, p1 a3), or all axes, all planes, all centroids, or all of the preceding if ~define is given without arguments.

Some options of define are specific to a given type of object, while others are general. Keywords and their sub-keywords can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar “|” designates mutually exclusive options, and default settings are indicated with bold.

define axisperHelix true | false ] [ helicalCorrection true | false ] [ massWeighting true | false ] general-options  atom-spec
define axis  general-options  plane-ID
Axes can be defined: If perHelix is false, a set of atoms and/or centroids can be specified by including space-separated object IDs (for example, c1 c2) with the atom specification string, or by selection and using the word sel or one of its equivalents. Eigenvectors/values are calculated from the coordinates of each set of atoms/centroids after subtracting the position of their collective centroid. Each axis is anchored at the corresponding collective centroid and aligned with the first eigenvector of the corresponding coordinates (prior to any helical correction). Helical correction (by default, on if perHelix is true, off otherwise) adjusts the orientation to reduce the spread of atom-axis distances. Mass-weighting (off by default) cannot be combined with helical correction or the perHelix option. For mass-weighting, the radius of a centroid (Å) is used as its “mass” (daltons). Axes are displayed as rods. Axis radius is reported in the Reply Log.

Setting perHelix to true indicates defining an axis for each peptide/protein helix in the entire molecule 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 ksdssp. 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 ssId is used to distinguish them. Although such cases are detected automatically, ssId can also be set manually with setattr.

An axis defined from a plane is shown as a rod with length 50% of the plane radius.

define planethickness d ] [ padding offset ] general-options  atom-spec
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). Planes are displayed as disks. 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. Plane radius is reported in the Reply Log.
define centroidmassWeighting true | false ] general-options  atom-spec
Define a centroid for the specified atoms. Centroids are displayed as spheres. The default radius is 2.0 Å. Centroids can be purely geometric or calculated with atomic mass-weighting. Centroid coordinates are reported in the Reply Log.

General Options

color colorname
Set the object color to colorname, which can be any color name that specifies a single color, or none (default), meaning to match the structure as much as possible.
radius r
Set object radius to a fixed value r. If this option is not used, radius will be set automatically to:
name name
Assign the object a name (default axis for an axis, plane for a plane, centroid for a centroid).
number N
Assign the object the integer part of its ID. The ID will be aN for an axis, pN for a plane, cN for a centroid. The default is the next available number for that type of object. If the ID is already in use, the new object will replace the pre-existing object.
raiseTool true | false
Whether to raise the Axes/Planes/Centroids table of objects.