Chimera Commands Index

Usage:
nucleotides sidechain representation [ sidechain-options ] atom-spec

Usage:
nucleotides ndbcolor atom-spec

The nucleotides command generates special representations of nucleotide bases and sugars; it is the command-line implementation of the Nucleotides tool. The nucleotides command does not control ribbon display, as that can be done separately (for example, with the command ribbon). See also: aromatic, fillring, represent

The command keywords and their sub-keywords can be truncated to unique strings, and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.

The sidechain keyword indicates the base/sugar representation (for which there may be further options):

The ndbcolor keyword specifies coloring residues by the convention used in the Nucleic Acid Database (NDB) Atlas: A red, T blue, C yellow, G green, and U cyan.

Sidechain Representations and Sub-Options

atoms
Include all currently displayed nucleic acid sidechain atoms/bonds. Atom/bond representations can be controlled separately (for example, with the command represent).
fill/fillorient true|false ]
Show the sugar (ribose) and base moieties as filled rings. The orient option controls whether the positive faces of bases are shown with bumps. The positive faces point towards the 3' end of a strand in right-handed A- and B-DNA (the positive Z direction in the standard reference frame). By default, ring fill thickness will track the thickness of the surrounding bonds: only a thin layer for a ring in the wire representation, but thick when surrounded by stick bonds (like what is obtained with fillring thick). Regardless of the orient setting, orientation bumps will not be shown where the fill is thin.
fill/slabshape box | tube | ellipsoid ] [ style big | fat | long | skinny | custom-style ] [ thickness d ] [ hide true|false ] [ orient true|false ]
Fill sugar rings and show bases as slabs of the specified shape (box, elliptical tube, or ellipsoid) and style. Custom styles can be used. The default slab thickness is 0.5 Å. The hide option indicates whether to hide base atoms/bonds. The orient option controls whether the positive faces of bases are shown with bumps.
tube/slabshape box | tube | ellipsoid ] [ style big | fat | long | skinny | custom-style ] [ thickness d ] [ hide true|false ] [ orient true|false ] [ glycosidic true|false ]
Show sugars as tubes connecting the bases to the backbone, and show bases as slabs of the specified shape (box, elliptical tube, or ellipsoid) and style. Custom styles can be used. The default slab thickness is 0.5 Å. The hide option indicates whether to hide base atoms/bonds. The orient option controls whether the positive faces of bases are shown with bumps. The glycosidic option applies only to base-anchored slab styles (long, skinny) and controls whether the sugar tubes should each consist of a single straight segment (default) or two segments, one along the glycosidic (sugar-base) bond.
ladderignore true|false ] [ stubs true|false ] [ radius r ]
Show H-bonded residue pairs as rods or ladder rungs. The ignore option indicates whether to ignore non-base atoms when identifying H-bonds; otherwise, all nucleic acid atoms will be considered (default). The stubs option sets whether to show bases without H-bonds to other bases as half-rungs (default) or not at all. The radius (default 0.45 Å) is used for ladder rungs showing H-bonds between bases, and for stubs representing bases that lack H-bonds to other bases. When ignore is true, any H-bonds involving non-base atoms (on either or both ends) will be shown with a smaller radius corresponding to the smallest ribbon dimension, or if the backbone is not shown as a ribbon, the model stick size.

Custom Slab Styles

Usage:
nucleotides add custom-style anchor sugar|base purine x1 y1 x2 y2 pyrimidine x1 y1 x2 y2

Usage:
nucleotides delete custom-style

A slab style refers to the slab dimensions and location relative to the atoms in purine and pyrimidine bases. The settings define a virtual rectangle in the plane of the base, as shown in the schematic diagrams in the Slab Style section of the Nucleotides dialog. Ellipsoid slab shapes are drawn to enclose the the virtual rectangle.

The add keyword of the nucleotides command allows defining a new custom slab style or modifying one that already exists, where custom-style is the name of the style. Custom slab styles are saved in the Chimera preferences file. The delete keyword allows removing a style from the preferences file. All arguments are mandatory for adding or modifying a style, but anchor, purine, and pyrimidine can be given in any order. Example:
nuc add square pur 0 -3.5 3.5 0 pyr 0 -2.5 2.5 0 anchor base
nuc side tube/slab style square orient false
Details:
anchor sugar | base
Indicate whether the point of reference for the virtual rectangle should be at the sugar end of the glycosidic bond (atom C1') or at the base end.
purine x1 y1 x2 y2
For purine bases, indicate virtual rectangle position (x1 and y1 specify the lower-left corner, x2 and y2 specify the upper right corner) in Å from the anchor; positive values are rightward along the X-axis and upward along the Y-axis in the standard reference frame.
pyrimidine x1 y1 x2 y2
For pyrimidine and pseudopyrimidine bases, indicate virtual rectangle position (x1 and y1 specify the lower-left corner, x2 and y2 specify the upper right corner) in Å from the anchor; positive values are rightward along the X-axis and upward along the Y-axis in the standard reference frame.