Chimera Commands Index

define  object  options  atom-spec

~defineID-list | axes | planes ]

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

The objects are listed in the Axes/Planes table for use in distance and angle measurements. See also: measure inertia, shape, Structure Measurements, PipesAndPlanks

The ~define command removes objects, either those specified as a space-separated list of IDs (for example, p1 a3), or all axes, all planes, 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 axishelicalCorrection true | false ] [ massWeighting true | false ] [ perHelix true | false ] general-options  atom-spec
Define an axis for the specified atoms. Axes are displayed as rods. An axis is anchored at the the geometric center (centroid) of the atomic coordinates and is initially aligned with the principal component of the coordinates. Helical correction (on by default) adjusts the orientation to reduce the spread of atom-axis distances. Mass-weighting (off by default) should not be combined with helical correction or the perHelix option.

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.

define planethickness d ] [ padding offset ] general-options  atom-spec
Define a plane for the specified atoms. 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.

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:
name name
Assign the object a name (default axis for an axis, plane for a plane).
number N
Assign the object the integer part of its ID. The ID will be aN for an axis, pN for a plane. The default is the lowest unused number for that type of object. If the ID is already in use, the new object will replace the pre-existing object.